Starting phenix.real_space_refine on Mon Sep 30 02:29:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/09_2024/5wsg_6684.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/09_2024/5wsg_6684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/09_2024/5wsg_6684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/09_2024/5wsg_6684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/09_2024/5wsg_6684.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/09_2024/5wsg_6684.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 379 5.49 5 Mg 6 5.21 5 S 236 5.16 5 C 47113 2.51 5 N 13437 2.21 5 O 15553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76730 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 15939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1931, 15939 Classifications: {'peptide': 1931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 99, 'TRANS': 1830} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7019 Classifications: {'peptide': 878} Link IDs: {'PTRANS': 49, 'TRANS': 828} Chain breaks: 2 Chain: "J" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 190 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "O" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2646 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 323} Chain: "P" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1583 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1472 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain breaks: 3 Chain: "R" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2089 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "S" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 560 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1291 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "Z" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3651 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 6} Chain: "N" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 5, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 10} Chain: "D" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2465 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 10, 'rna3p_pur': 39, 'rna3p_pyr': 56} Link IDs: {'rna2p': 22, 'rna3p': 94} Chain breaks: 2 Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2192 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 46, 'rna3p_pyr': 36} Link IDs: {'rna2p': 21, 'rna3p': 81} Chain: "L" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1909 Classifications: {'RNA': 91} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 17, 'rna3p_pur': 29, 'rna3p_pyr': 39} Link IDs: {'rna2p': 23, 'rna3p': 67} Chain breaks: 2 Chain: "M" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 486 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 19} Chain: "c" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1754 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 1 Chain: "c" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1217 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 6 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 5, 'UNK:plan-1': 118, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 288 Chain: "d" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 2055 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "d" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 1451 Classifications: {'peptide': 292} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 283} Link IDs: {'TRANS': 291} Chain breaks: 19 Unresolved non-hydrogen bonds: 593 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'UNK:plan-1': 292} Unresolved non-hydrogen planarities: 292 Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 822 Classifications: {'peptide': 102} Link IDs: {'CIS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "v" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 3183 Classifications: {'peptide': 593} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 458} Link IDs: {'PTRANS': 6, 'TRANS': 586} Chain breaks: 32 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1166 Unresolved non-hydrogen angles: 1721 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 2, 'TYR:plan': 2, 'UNK:plan-1': 460, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 4, 'PHE:plan': 4, 'GLU:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 595 Chain: "n" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 1870 Classifications: {'peptide': 296} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 26} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 277} Chain breaks: 11 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 767 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 336 Chain: "o" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 830 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "p" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 843 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "q" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2345 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain breaks: 14 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 778 Unresolved non-hydrogen angles: 1052 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 22, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 420 Chain: "r" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 823 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "t" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 926 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 258 Chain: "k" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "i" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "h" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 554 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "m" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "g" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 554 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "V" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 528 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "X" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 513 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 841 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 167 Chain: "b" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 208 Classifications: {'DNA': 1, 'RNA': 13} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna3p': 13} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' A:plan': 1, ' A%rna3p_pur:plan2': 1, ' U%rna3p_pyr:plan': 6, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 85 Chain: "e" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 3360 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 604} Link IDs: {'PTRANS': 27, 'TRANS': 651} Chain breaks: 2 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 2129 Unresolved non-hydrogen angles: 2722 Unresolved non-hydrogen dihedrals: 1756 Unresolved non-hydrogen chiralities: 222 Planarities with less than four sites: {'GLN:plan1': 31, 'ARG:plan': 30, 'TYR:plan': 24, 'ASN:plan1': 26, 'TRP:plan': 5, 'HIS:plan': 12, 'PHE:plan': 31, 'GLU:plan': 32, 'ASP:plan': 42} Unresolved non-hydrogen planarities: 1065 Chain: "f" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1202 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27462 SG CYS Q 13 71.706 143.566 123.380 1.00 0.00 S ATOM 27920 SG CYS Q 71 75.010 142.431 124.896 1.00 0.00 S ATOM 27935 SG CYS Q 73 73.056 145.072 126.419 1.00 0.00 S ATOM 27941 SG CYS Q 74 71.662 141.512 126.440 1.00 0.00 S ATOM 27620 SG CYS Q 34 85.492 145.909 132.214 1.00 0.00 S ATOM 27643 SG CYS Q 37 88.856 145.639 133.508 1.00 0.00 S ATOM 27842 SG CYS Q 61 88.123 146.171 129.869 1.00 0.00 S ATOM 27866 SG CYS Q 64 87.591 142.784 131.635 1.00 0.00 S ATOM 29431 SG CYS R 73 60.098 157.767 144.124 1.00 0.00 S ATOM 29493 SG CYS R 81 59.017 161.214 144.854 1.00 0.00 S ATOM 29533 SG CYS R 87 59.052 159.801 141.327 1.00 0.00 S ATOM 32386 SG CYS T 104 59.573 177.754 124.490 1.00 0.00 S ATOM 32392 SG CYS T 105 62.432 180.185 125.431 1.00 0.00 S ATOM 32417 SG CYS T 108 63.270 176.761 123.657 1.00 0.00 S ATOM 32731 SG CYS T 148 62.723 177.510 126.930 1.00 0.00 S ATOM 32386 SG CYS T 104 59.573 177.754 124.490 1.00 0.00 S ATOM 32520 SG CYS T 122 60.447 174.868 122.707 1.00 0.00 S ATOM 32741 SG CYS T 150 56.979 175.153 123.776 1.00 0.00 S ATOM 32762 SG CYS T 153 58.059 177.665 121.171 1.00 0.00 S ATOM 32417 SG CYS T 108 63.270 176.761 123.657 1.00 0.00 S ATOM 32506 SG CYS T 120 64.333 173.386 122.600 1.00 0.00 S ATOM 32520 SG CYS T 122 60.447 174.868 122.707 1.00 0.00 S ATOM 32708 SG CYS T 145 62.677 173.476 125.566 1.00 0.00 S Time building chain proxies: 32.88, per 1000 atoms: 0.43 Number of scatterers: 76730 At special positions: 0 Unit cell: (232.468, 304.298, 282.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 236 16.00 P 379 15.00 Mg 6 11.99 O 15553 8.00 N 13437 7.00 C 47113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.95 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 400 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 73 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 13 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 71 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 74 " pdb=" ZN Q 401 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 37 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 34 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 64 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 61 " pdb=" ZN R 400 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 81 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 73 " pdb="ZN ZN R 400 " - pdb=" NE2 HIS R 91 " pdb=" ZN T1000 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 148 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 105 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 104 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 104 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 150 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 153 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 145 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 120 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 122 " Number of angles added : 33 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18150 Finding SS restraints... Secondary structure from input PDB file: 346 helices and 74 sheets defined 53.0% alpha, 13.4% beta 88 base pairs and 156 stacking pairs defined. Time for finding SS restraints: 21.18 Creating SS restraints... Processing helix chain 'A' and resid 135 through 147 removed outlier: 4.266A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 165 removed outlier: 3.962A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 removed outlier: 3.568A pdb=" N ALA A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.964A pdb=" N ASN A 257 " --> pdb=" O HIS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.513A pdb=" N THR A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.834A pdb=" N LYS A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.739A pdb=" N TYR A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 472 through 480 Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.933A pdb=" N PHE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 535 removed outlier: 3.769A pdb=" N LYS A 519 " --> pdb=" O PRO A 515 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 removed outlier: 3.720A pdb=" N ASN A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 606 through 612 Processing helix chain 'A' and resid 616 through 641 Processing helix chain 'A' and resid 645 through 664 removed outlier: 5.931A pdb=" N GLY A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLN A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 673 through 690 removed outlier: 3.502A pdb=" N ILE A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 678 " --> pdb=" O MET A 674 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 684 " --> pdb=" O CYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 718 removed outlier: 3.647A pdb=" N THR A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 736 Processing helix chain 'A' and resid 749 through 770 removed outlier: 3.672A pdb=" N TYR A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 796 Processing helix chain 'A' and resid 805 through 835 Processing helix chain 'A' and resid 842 through 870 removed outlier: 3.823A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 894 Processing helix chain 'A' and resid 907 through 925 removed outlier: 3.686A pdb=" N ILE A 911 " --> pdb=" O ASN A 907 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 960 Processing helix chain 'A' and resid 985 through 1006 Processing helix chain 'A' and resid 1020 through 1035 Processing helix chain 'A' and resid 1057 through 1061 removed outlier: 3.548A pdb=" N LYS A1060 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1074 removed outlier: 3.704A pdb=" N ARG A1068 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1087 removed outlier: 4.002A pdb=" N ASN A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1127 removed outlier: 3.889A pdb=" N ILE A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1136 Processing helix chain 'A' and resid 1149 through 1155 removed outlier: 3.689A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 Processing helix chain 'A' and resid 1216 through 1233 Processing helix chain 'A' and resid 1242 through 1246 Processing helix chain 'A' and resid 1273 through 1276 Processing helix chain 'A' and resid 1305 through 1323 Processing helix chain 'A' and resid 1328 through 1346 removed outlier: 3.682A pdb=" N SER A1341 " --> pdb=" O THR A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1352 Processing helix chain 'A' and resid 1353 through 1374 removed outlier: 3.670A pdb=" N LEU A1357 " --> pdb=" O THR A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1390 removed outlier: 4.129A pdb=" N PHE A1388 " --> pdb=" O PRO A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1416 removed outlier: 3.716A pdb=" N SER A1415 " --> pdb=" O ASP A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1443 Processing helix chain 'A' and resid 1446 through 1471 Processing helix chain 'A' and resid 1480 through 1484 Processing helix chain 'A' and resid 1490 through 1496 Processing helix chain 'A' and resid 1498 through 1503 Processing helix chain 'A' and resid 1507 through 1519 removed outlier: 4.060A pdb=" N ARG A1511 " --> pdb=" O GLY A1507 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1550 Processing helix chain 'A' and resid 1551 through 1557 removed outlier: 3.943A pdb=" N THR A1555 " --> pdb=" O GLY A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1560 No H-bonds generated for 'chain 'A' and resid 1558 through 1560' Processing helix chain 'A' and resid 1579 through 1583 removed outlier: 3.692A pdb=" N ASP A1583 " --> pdb=" O GLY A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1598 Processing helix chain 'A' and resid 1600 through 1610 removed outlier: 3.769A pdb=" N ARG A1604 " --> pdb=" O GLN A1600 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A1606 " --> pdb=" O PRO A1602 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A1608 " --> pdb=" O ARG A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1649 Processing helix chain 'A' and resid 1652 through 1669 Processing helix chain 'A' and resid 1673 through 1676 removed outlier: 3.604A pdb=" N LEU A1676 " --> pdb=" O LEU A1673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1673 through 1676' Processing helix chain 'A' and resid 1723 through 1726 removed outlier: 3.943A pdb=" N GLY A1726 " --> pdb=" O SER A1723 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1723 through 1726' Processing helix chain 'A' and resid 1747 through 1761 removed outlier: 4.185A pdb=" N TYR A1751 " --> pdb=" O ASP A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1809 removed outlier: 4.609A pdb=" N LEU A1797 " --> pdb=" O GLY A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1824 removed outlier: 4.172A pdb=" N TYR A1813 " --> pdb=" O ASN A1809 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1840 through 1845 Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1905 through 1924 Processing helix chain 'A' and resid 1937 through 1939 No H-bonds generated for 'chain 'A' and resid 1937 through 1939' Processing helix chain 'A' and resid 1940 through 1949 Processing helix chain 'A' and resid 1967 through 1970 Processing helix chain 'A' and resid 1971 through 1979 removed outlier: 4.126A pdb=" N SER A1975 " --> pdb=" O ILE A1971 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2017 removed outlier: 3.657A pdb=" N ALA A2004 " --> pdb=" O SER A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2028 Processing helix chain 'A' and resid 2044 through 2067 removed outlier: 4.231A pdb=" N ILE A2059 " --> pdb=" O MET A2055 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A2060 " --> pdb=" O ARG A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2085 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.581A pdb=" N MET C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 removed outlier: 5.712A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 131' Processing helix chain 'C' and resid 145 through 158 Processing helix chain 'C' and resid 165 through 171 removed outlier: 3.701A pdb=" N LEU C 170 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 221 through 232 removed outlier: 4.146A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.683A pdb=" N SER C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 323 through 331 removed outlier: 3.609A pdb=" N PHE C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 331 " --> pdb=" O PHE C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 335 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 340 through 347 removed outlier: 3.570A pdb=" N THR C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 377 Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 392 through 402 removed outlier: 3.881A pdb=" N ARG C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.792A pdb=" N LEU C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 through 414' Processing helix chain 'C' and resid 417 through 429 Processing helix chain 'C' and resid 433 through 441 Processing helix chain 'C' and resid 444 through 447 removed outlier: 3.669A pdb=" N GLU C 447 " --> pdb=" O GLN C 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 444 through 447' Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 505 through 510 removed outlier: 3.696A pdb=" N GLU C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 571 removed outlier: 3.989A pdb=" N TYR C 571 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.647A pdb=" N GLN C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 613 No H-bonds generated for 'chain 'C' and resid 611 through 613' Processing helix chain 'C' and resid 614 through 629 removed outlier: 3.658A pdb=" N LEU C 618 " --> pdb=" O GLU C 614 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 661 Processing helix chain 'C' and resid 716 through 724 Processing helix chain 'C' and resid 743 through 756 removed outlier: 3.697A pdb=" N GLY C 756 " --> pdb=" O ARG C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 765 Processing helix chain 'C' and resid 778 through 784 removed outlier: 3.855A pdb=" N GLU C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 805 removed outlier: 3.848A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 852 removed outlier: 4.203A pdb=" N LYS C 835 " --> pdb=" O ILE C 831 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix removed outlier: 4.008A pdb=" N THR C 852 " --> pdb=" O VAL C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 884 removed outlier: 3.985A pdb=" N VAL C 876 " --> pdb=" O LEU C 872 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 878 " --> pdb=" O PRO C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 912 removed outlier: 4.121A pdb=" N ALA C 912 " --> pdb=" O ILE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 922 Processing helix chain 'C' and resid 958 through 961 Processing helix chain 'C' and resid 962 through 975 removed outlier: 3.767A pdb=" N ARG C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 118 removed outlier: 3.508A pdb=" N LEU O 118 " --> pdb=" O ARG O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 396 through 400 Processing helix chain 'P' and resid 31 through 35 removed outlier: 4.416A pdb=" N ALA P 35 " --> pdb=" O THR P 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 31 through 35' Processing helix chain 'P' and resid 39 through 43 Processing helix chain 'P' and resid 62 through 85 removed outlier: 3.542A pdb=" N CYS P 66 " --> pdb=" O GLU P 62 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA P 68 " --> pdb=" O GLN P 64 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER P 85 " --> pdb=" O LYS P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 94 removed outlier: 3.670A pdb=" N VAL P 94 " --> pdb=" O SER P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 163 removed outlier: 4.107A pdb=" N GLU P 162 " --> pdb=" O ALA P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 186 removed outlier: 3.943A pdb=" N ARG P 185 " --> pdb=" O ALA P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 243 Processing helix chain 'Q' and resid 63 through 68 removed outlier: 3.650A pdb=" N ARG Q 68 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 94 removed outlier: 4.148A pdb=" N HIS Q 89 " --> pdb=" O GLN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 116 removed outlier: 3.977A pdb=" N LEU Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS Q 116 " --> pdb=" O PHE Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 4.094A pdb=" N ILE Q 125 " --> pdb=" O GLY Q 121 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR Q 126 " --> pdb=" O GLY Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 227 Processing helix chain 'Q' and resid 256 through 264 Processing helix chain 'R' and resid 62 through 68 Processing helix chain 'R' and resid 73 through 78 Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'R' and resid 95 through 103 removed outlier: 4.017A pdb=" N ILE R 99 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 146 Processing helix chain 'R' and resid 152 through 166 removed outlier: 4.089A pdb=" N ARG R 166 " --> pdb=" O PHE R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 removed outlier: 3.562A pdb=" N SER R 200 " --> pdb=" O LYS R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 218 removed outlier: 4.240A pdb=" N ARG R 216 " --> pdb=" O ASP R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 261 removed outlier: 3.942A pdb=" N GLN R 235 " --> pdb=" O ASP R 231 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS R 252 " --> pdb=" O ASN R 248 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 19 removed outlier: 3.942A pdb=" N ALA S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 130 removed outlier: 3.939A pdb=" N LYS S 129 " --> pdb=" O SER S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 173 removed outlier: 3.676A pdb=" N GLN S 167 " --> pdb=" O SER S 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 34 removed outlier: 3.896A pdb=" N ILE T 19 " --> pdb=" O GLY T 15 " (cutoff:3.500A) Proline residue: T 21 - end of helix removed outlier: 3.663A pdb=" N PHE T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN T 29 " --> pdb=" O ASP T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 68 removed outlier: 3.690A pdb=" N ILE T 52 " --> pdb=" O GLN T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 84 Processing helix chain 'T' and resid 88 through 97 removed outlier: 3.639A pdb=" N LYS T 97 " --> pdb=" O ALA T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 136 removed outlier: 3.767A pdb=" N LEU T 129 " --> pdb=" O PRO T 125 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU T 131 " --> pdb=" O ALA T 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 14 Processing helix chain 'Z' and resid 14 through 23 Processing helix chain 'Z' and resid 25 through 31 Processing helix chain 'Z' and resid 36 through 44 Processing helix chain 'Z' and resid 49 through 51 No H-bonds generated for 'chain 'Z' and resid 49 through 51' Processing helix chain 'Z' and resid 52 through 66 Processing helix chain 'Z' and resid 71 through 85 removed outlier: 3.889A pdb=" N ALA Z 75 " --> pdb=" O ARG Z 71 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER Z 77 " --> pdb=" O ILE Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 108 Processing helix chain 'Z' and resid 110 through 127 removed outlier: 3.753A pdb=" N TYR Z 127 " --> pdb=" O ILE Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 145 removed outlier: 4.092A pdb=" N ILE Z 135 " --> pdb=" O HIS Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 166 removed outlier: 5.704A pdb=" N TRP Z 160 " --> pdb=" O LYS Z 156 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS Z 161 " --> pdb=" O ILE Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 184 removed outlier: 3.739A pdb=" N LEU Z 181 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 203 removed outlier: 3.945A pdb=" N SER Z 193 " --> pdb=" O THR Z 189 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE Z 198 " --> pdb=" O LEU Z 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 Processing helix chain 'Z' and resid 305 through 316 removed outlier: 3.837A pdb=" N ALA Z 309 " --> pdb=" O GLY Z 305 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS Z 310 " --> pdb=" O ASP Z 306 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS Z 316 " --> pdb=" O LEU Z 312 " (cutoff:3.500A) Processing helix chain 'Z' and resid 323 through 336 Processing helix chain 'Z' and resid 340 through 352 removed outlier: 3.855A pdb=" N SER Z 344 " --> pdb=" O SER Z 340 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 371 removed outlier: 3.846A pdb=" N GLN Z 358 " --> pdb=" O HIS Z 354 " (cutoff:3.500A) Processing helix chain 'Z' and resid 372 through 376 Processing helix chain 'Z' and resid 380 through 394 removed outlier: 4.384A pdb=" N LYS Z 386 " --> pdb=" O ARG Z 382 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU Z 391 " --> pdb=" O PHE Z 387 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR Z 394 " --> pdb=" O HIS Z 390 " (cutoff:3.500A) Processing helix chain 'Z' and resid 398 through 405 removed outlier: 3.751A pdb=" N ILE Z 404 " --> pdb=" O CYS Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 432 removed outlier: 4.254A pdb=" N ASN Z 429 " --> pdb=" O GLN Z 425 " (cutoff:3.500A) Processing helix chain 'Z' and resid 434 through 442 Processing helix chain 'Z' and resid 454 through 468 Processing helix chain 'Z' and resid 474 through 485 removed outlier: 4.212A pdb=" N GLN Z 485 " --> pdb=" O LEU Z 481 " (cutoff:3.500A) Processing helix chain 'c' and resid 14 through 29 Processing helix chain 'c' and resid 32 through 40 removed outlier: 3.884A pdb=" N VAL c 36 " --> pdb=" O GLN c 32 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER c 38 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU c 39 " --> pdb=" O LYS c 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU c 40 " --> pdb=" O VAL c 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 66 through 80 Processing helix chain 'c' and resid 83 through 91 Processing helix chain 'c' and resid 94 through 106 Processing helix chain 'c' and resid 146 through 159 Processing helix chain 'c' and resid 164 through 193 removed outlier: 3.504A pdb=" N THR c 168 " --> pdb=" O GLY c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 252 removed outlier: 3.504A pdb=" N GLN c 236 " --> pdb=" O THR c 232 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG c 250 " --> pdb=" O ARG c 246 " (cutoff:3.500A) Processing helix chain 'c' and resid 337 through 356 removed outlier: 3.785A pdb=" N UNK c 355 " --> pdb=" O UNK c 351 " (cutoff:3.500A) Processing helix chain 'c' and resid 358 through 364 Processing helix chain 'c' and resid 373 through 382 Processing helix chain 'c' and resid 385 through 401 removed outlier: 3.637A pdb=" N UNK c 390 " --> pdb=" O UNK c 386 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N UNK c 401 " --> pdb=" O UNK c 397 " (cutoff:3.500A) Processing helix chain 'c' and resid 423 through 438 removed outlier: 3.595A pdb=" N UNK c 427 " --> pdb=" O UNK c 423 " (cutoff:3.500A) Processing helix chain 'c' and resid 445 through 469 removed outlier: 3.505A pdb=" N UNK c 450 " --> pdb=" O UNK c 446 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N UNK c 468 " --> pdb=" O UNK c 464 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK c 469 " --> pdb=" O UNK c 465 " (cutoff:3.500A) Processing helix chain 'c' and resid 483 through 582 removed outlier: 3.597A pdb=" N HIS c 487 " --> pdb=" O SER c 483 " (cutoff:3.500A) Proline residue: c 504 - end of helix removed outlier: 4.515A pdb=" N SER c 515 " --> pdb=" O GLU c 511 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS c 516 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS c 526 " --> pdb=" O GLN c 522 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU c 527 " --> pdb=" O LEU c 523 " (cutoff:3.500A) Proline residue: c 532 - end of helix removed outlier: 3.688A pdb=" N GLN c 536 " --> pdb=" O PRO c 532 " (cutoff:3.500A) Proline residue: c 550 - end of helix removed outlier: 3.965A pdb=" N ILE c 553 " --> pdb=" O LEU c 549 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU c 554 " --> pdb=" O PRO c 550 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN c 556 " --> pdb=" O LEU c 552 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG c 557 " --> pdb=" O ILE c 553 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER c 572 " --> pdb=" O GLN c 568 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG c 577 " --> pdb=" O LEU c 573 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS c 578 " --> pdb=" O GLU c 574 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG c 579 " --> pdb=" O GLY c 575 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU c 580 " --> pdb=" O ARG c 576 " (cutoff:3.500A) Processing helix chain 'c' and resid 582 through 587 removed outlier: 3.704A pdb=" N SER c 586 " --> pdb=" O ALA c 582 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER c 587 " --> pdb=" O MET c 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 582 through 587' Processing helix chain 'd' and resid 39 through 61 removed outlier: 3.609A pdb=" N LYS d 50 " --> pdb=" O TYR d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 78 removed outlier: 3.662A pdb=" N TRP d 68 " --> pdb=" O ASP d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 95 removed outlier: 3.920A pdb=" N ALA d 84 " --> pdb=" O ASP d 80 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 111 removed outlier: 3.916A pdb=" N TRP d 102 " --> pdb=" O PHE d 98 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU d 109 " --> pdb=" O TYR d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 115 through 129 removed outlier: 4.073A pdb=" N MET d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 145 removed outlier: 4.323A pdb=" N TRP d 136 " --> pdb=" O VAL d 132 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 162 removed outlier: 4.053A pdb=" N VAL d 152 " --> pdb=" O ASN d 148 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 177 removed outlier: 3.802A pdb=" N TRP d 169 " --> pdb=" O GLY d 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 196 removed outlier: 3.909A pdb=" N ARG d 186 " --> pdb=" O TRP d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 213 Processing helix chain 'd' and resid 214 through 232 removed outlier: 3.811A pdb=" N THR d 228 " --> pdb=" O LEU d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 236 Processing helix chain 'd' and resid 239 through 256 Processing helix chain 'd' and resid 259 through 274 Processing helix chain 'd' and resid 297 through 311 removed outlier: 3.800A pdb=" N UNK d 301 " --> pdb=" O UNK d 297 " (cutoff:3.500A) Processing helix chain 'd' and resid 316 through 333 Processing helix chain 'd' and resid 341 through 354 Processing helix chain 'd' and resid 360 through 368 removed outlier: 3.812A pdb=" N UNK d 366 " --> pdb=" O UNK d 362 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK d 367 " --> pdb=" O UNK d 363 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N UNK d 368 " --> pdb=" O UNK d 364 " (cutoff:3.500A) Processing helix chain 'd' and resid 369 through 375 Processing helix chain 'd' and resid 380 through 390 Processing helix chain 'd' and resid 394 through 401 Processing helix chain 'd' and resid 413 through 425 removed outlier: 3.950A pdb=" N UNK d 418 " --> pdb=" O UNK d 414 " (cutoff:3.500A) Processing helix chain 'd' and resid 429 through 444 removed outlier: 3.501A pdb=" N UNK d 443 " --> pdb=" O UNK d 439 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK d 444 " --> pdb=" O UNK d 440 " (cutoff:3.500A) Processing helix chain 'd' and resid 453 through 463 removed outlier: 3.606A pdb=" N UNK d 457 " --> pdb=" O UNK d 453 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N UNK d 463 " --> pdb=" O UNK d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 469 through 480 removed outlier: 3.676A pdb=" N UNK d 473 " --> pdb=" O UNK d 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK d 479 " --> pdb=" O UNK d 475 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N UNK d 480 " --> pdb=" O UNK d 476 " (cutoff:3.500A) Processing helix chain 'd' and resid 487 through 499 removed outlier: 3.568A pdb=" N UNK d 491 " --> pdb=" O UNK d 487 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK d 494 " --> pdb=" O UNK d 490 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N UNK d 498 " --> pdb=" O UNK d 494 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N UNK d 499 " --> pdb=" O UNK d 495 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 516 Processing helix chain 'd' and resid 520 through 528 Processing helix chain 'd' and resid 539 through 551 Processing helix chain 'd' and resid 560 through 576 removed outlier: 3.696A pdb=" N UNK d 564 " --> pdb=" O UNK d 560 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N UNK d 575 " --> pdb=" O UNK d 571 " (cutoff:3.500A) Processing helix chain 'd' and resid 584 through 595 Processing helix chain 'd' and resid 601 through 620 Processing helix chain 'I' and resid 96 through 122 removed outlier: 3.751A pdb=" N ALA I 101 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 190 removed outlier: 4.200A pdb=" N TYR I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 211 removed outlier: 4.440A pdb=" N SER I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'v' and resid 157 through 169 Processing helix chain 'v' and resid 172 through 183 Processing helix chain 'v' and resid 187 through 201 Processing helix chain 'v' and resid 205 through 218 Processing helix chain 'v' and resid 221 through 233 Processing helix chain 'v' and resid 237 through 250 removed outlier: 3.728A pdb=" N UNK v 250 " --> pdb=" O UNK v 246 " (cutoff:3.500A) Processing helix chain 'v' and resid 255 through 267 Processing helix chain 'v' and resid 270 through 283 removed outlier: 3.608A pdb=" N UNK v 276 " --> pdb=" O UNK v 272 " (cutoff:3.500A) Processing helix chain 'v' and resid 286 through 299 Processing helix chain 'v' and resid 302 through 315 Processing helix chain 'v' and resid 320 through 334 Processing helix chain 'v' and resid 338 through 351 Processing helix chain 'v' and resid 356 through 363 removed outlier: 3.574A pdb=" N UNK v 363 " --> pdb=" O UNK v 359 " (cutoff:3.500A) Processing helix chain 'v' and resid 364 through 366 No H-bonds generated for 'chain 'v' and resid 364 through 366' Processing helix chain 'v' and resid 369 through 383 Processing helix chain 'v' and resid 388 through 400 Processing helix chain 'v' and resid 404 through 415 Processing helix chain 'v' and resid 420 through 437 Processing helix chain 'v' and resid 440 through 459 removed outlier: 4.253A pdb=" N UNK v 457 " --> pdb=" O UNK v 453 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK v 458 " --> pdb=" O UNK v 454 " (cutoff:3.500A) Processing helix chain 'v' and resid 463 through 483 Processing helix chain 'v' and resid 488 through 501 Processing helix chain 'v' and resid 505 through 524 Processing helix chain 'v' and resid 528 through 542 removed outlier: 3.537A pdb=" N UNK v 534 " --> pdb=" O UNK v 530 " (cutoff:3.500A) Processing helix chain 'v' and resid 547 through 560 removed outlier: 4.127A pdb=" N UNK v 551 " --> pdb=" O UNK v 547 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N UNK v 557 " --> pdb=" O UNK v 553 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N UNK v 558 " --> pdb=" O UNK v 554 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK v 560 " --> pdb=" O UNK v 556 " (cutoff:3.500A) Processing helix chain 'v' and resid 570 through 579 removed outlier: 4.380A pdb=" N VAL v 577 " --> pdb=" O ALA v 573 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE v 578 " --> pdb=" O TYR v 574 " (cutoff:3.500A) Processing helix chain 'v' and resid 585 through 598 Processing helix chain 'v' and resid 601 through 612 Processing helix chain 'v' and resid 615 through 636 removed outlier: 4.277A pdb=" N ILE v 619 " --> pdb=" O PHE v 615 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR v 621 " --> pdb=" O PRO v 617 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU v 622 " --> pdb=" O GLU v 618 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU v 626 " --> pdb=" O GLU v 622 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN v 635 " --> pdb=" O ALA v 631 " (cutoff:3.500A) Processing helix chain 'v' and resid 641 through 653 removed outlier: 4.281A pdb=" N LYS v 653 " --> pdb=" O GLU v 649 " (cutoff:3.500A) Processing helix chain 'v' and resid 664 through 676 removed outlier: 4.047A pdb=" N ARG v 675 " --> pdb=" O VAL v 671 " (cutoff:3.500A) Processing helix chain 'v' and resid 680 through 689 Processing helix chain 'v' and resid 707 through 720 Processing helix chain 'v' and resid 722 through 734 removed outlier: 4.016A pdb=" N ARG v 726 " --> pdb=" O PRO v 722 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU v 727 " --> pdb=" O SER v 723 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN v 730 " --> pdb=" O ARG v 726 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU v 731 " --> pdb=" O GLU v 727 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN v 734 " --> pdb=" O GLN v 730 " (cutoff:3.500A) Processing helix chain 'v' and resid 741 through 756 removed outlier: 4.292A pdb=" N UNK v 751 " --> pdb=" O UNK v 747 " (cutoff:3.500A) Processing helix chain 'v' and resid 759 through 773 removed outlier: 3.865A pdb=" N UNK v 763 " --> pdb=" O UNK v 759 " (cutoff:3.500A) Processing helix chain 'v' and resid 779 through 792 Processing helix chain 'v' and resid 797 through 818 Processing helix chain 'n' and resid 52 through 61 removed outlier: 4.060A pdb=" N LYS n 61 " --> pdb=" O LYS n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 423 through 427 removed outlier: 3.755A pdb=" N LYS n 427 " --> pdb=" O PRO n 424 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 35 removed outlier: 3.725A pdb=" N GLN o 30 " --> pdb=" O SER o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 78 through 140 removed outlier: 3.723A pdb=" N LEU o 93 " --> pdb=" O ASP o 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE o 96 " --> pdb=" O MET o 92 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU o 98 " --> pdb=" O GLU o 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR o 101 " --> pdb=" O LYS o 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER o 104 " --> pdb=" O SER o 100 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS o 107 " --> pdb=" O ASP o 103 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU o 121 " --> pdb=" O ASP o 117 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL o 122 " --> pdb=" O ALA o 118 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN o 131 " --> pdb=" O LEU o 127 " (cutoff:3.500A) Proline residue: o 138 - end of helix Processing helix chain 'p' and resid 25 through 35 removed outlier: 3.590A pdb=" N LYS p 33 " --> pdb=" O GLU p 29 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 141 removed outlier: 3.594A pdb=" N GLU p 94 " --> pdb=" O ALA p 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET p 128 " --> pdb=" O ALA p 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN p 131 " --> pdb=" O LEU p 127 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU p 132 " --> pdb=" O MET p 128 " (cutoff:3.500A) Proline residue: p 138 - end of helix removed outlier: 3.648A pdb=" N SER p 141 " --> pdb=" O LEU p 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 35 Processing helix chain 'q' and resid 77 through 143 removed outlier: 3.652A pdb=" N LEU q 81 " --> pdb=" O ILE q 77 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA q 90 " --> pdb=" O ASN q 86 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS q 97 " --> pdb=" O LEU q 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR q 101 " --> pdb=" O LYS q 97 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS q 108 " --> pdb=" O SER q 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL q 122 " --> pdb=" O ALA q 118 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA q 123 " --> pdb=" O ALA q 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET q 128 " --> pdb=" O ALA q 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS q 135 " --> pdb=" O ASN q 131 " (cutoff:3.500A) Proline residue: q 138 - end of helix removed outlier: 3.709A pdb=" N GLN q 143 " --> pdb=" O LYS q 139 " (cutoff:3.500A) Processing helix chain 'q' and resid 473 through 476 Processing helix chain 'r' and resid 25 through 35 Processing helix chain 'r' and resid 78 through 137 removed outlier: 3.717A pdb=" N THR r 82 " --> pdb=" O PRO r 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU r 93 " --> pdb=" O ASP r 89 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU r 98 " --> pdb=" O GLU r 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG r 99 " --> pdb=" O ASN r 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR r 101 " --> pdb=" O LYS r 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU r 102 " --> pdb=" O LEU r 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU r 115 " --> pdb=" O THR r 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS r 120 " --> pdb=" O ARG r 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU r 121 " --> pdb=" O ASP r 117 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN r 125 " --> pdb=" O LEU r 121 " (cutoff:3.500A) Processing helix chain 't' and resid 13 through 32 Processing helix chain 't' and resid 52 through 65 removed outlier: 4.244A pdb=" N THR t 56 " --> pdb=" O ASN t 52 " (cutoff:3.500A) Processing helix chain 't' and resid 82 through 103 removed outlier: 3.579A pdb=" N LYS t 94 " --> pdb=" O GLU t 90 " (cutoff:3.500A) Proline residue: t 96 - end of helix Processing helix chain 't' and resid 103 through 110 removed outlier: 4.054A pdb=" N SER t 109 " --> pdb=" O PRO t 105 " (cutoff:3.500A) Processing helix chain 't' and resid 111 through 175 removed outlier: 3.654A pdb=" N VAL t 117 " --> pdb=" O LEU t 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR t 120 " --> pdb=" O ILE t 116 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL t 127 " --> pdb=" O HIS t 123 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU t 128 " --> pdb=" O GLN t 124 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP t 129 " --> pdb=" O GLU t 125 " (cutoff:3.500A) Proline residue: t 133 - end of helix removed outlier: 3.741A pdb=" N ARG t 148 " --> pdb=" O ASN t 144 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU t 155 " --> pdb=" O CYS t 151 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG t 172 " --> pdb=" O LEU t 168 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 16 Processing helix chain 'i' and resid 12 through 24 Processing helix chain 'i' and resid 84 through 87 Processing helix chain 'h' and resid 14 through 22 removed outlier: 3.667A pdb=" N PHE h 18 " --> pdb=" O ASN h 14 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 15 Processing helix chain 'l' and resid 65 through 67 No H-bonds generated for 'chain 'l' and resid 65 through 67' Processing helix chain 'l' and resid 75 through 80 Processing helix chain 'm' and resid 2 through 10 removed outlier: 3.879A pdb=" N PHE m 6 " --> pdb=" O LYS m 2 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 108 Processing helix chain 'g' and resid 16 through 29 Processing helix chain 'g' and resid 31 through 41 removed outlier: 3.781A pdb=" N ASN g 35 " --> pdb=" O MET g 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 16 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 84 through 87 Processing helix chain 'H' and resid 14 through 22 removed outlier: 3.667A pdb=" N PHE H 18 " --> pdb=" O ASN H 14 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 15 Processing helix chain 'U' and resid 65 through 67 No H-bonds generated for 'chain 'U' and resid 65 through 67' Processing helix chain 'U' and resid 75 through 80 Processing helix chain 'V' and resid 2 through 10 removed outlier: 3.877A pdb=" N PHE V 6 " --> pdb=" O LYS V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 108 Processing helix chain 'X' and resid 40 through 54 removed outlier: 4.195A pdb=" N THR X 54 " --> pdb=" O LEU X 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 89 removed outlier: 3.517A pdb=" N ALA X 82 " --> pdb=" O THR X 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 10 removed outlier: 3.511A pdb=" N ASP Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 51 removed outlier: 3.907A pdb=" N HIS Y 49 " --> pdb=" O SER Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 120 removed outlier: 4.608A pdb=" N ARG Y 116 " --> pdb=" O ASP Y 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG Y 119 " --> pdb=" O ARG Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 137 Processing helix chain 'Y' and resid 139 through 148 Processing helix chain 'e' and resid 310 through 314 removed outlier: 4.456A pdb=" N LEU e 313 " --> pdb=" O GLY e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 322 through 332 Processing helix chain 'e' and resid 337 through 349 Processing helix chain 'e' and resid 350 through 354 Processing helix chain 'e' and resid 355 through 366 Processing helix chain 'e' and resid 378 through 387 removed outlier: 3.779A pdb=" N ALA e 384 " --> pdb=" O THR e 380 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN e 385 " --> pdb=" O THR e 381 " (cutoff:3.500A) Processing helix chain 'e' and resid 392 through 397 Processing helix chain 'e' and resid 406 through 422 Processing helix chain 'e' and resid 451 through 461 Processing helix chain 'e' and resid 479 through 496 removed outlier: 3.676A pdb=" N ALA e 494 " --> pdb=" O LYS e 490 " (cutoff:3.500A) Processing helix chain 'e' and resid 510 through 517 Processing helix chain 'e' and resid 543 through 558 Processing helix chain 'e' and resid 559 through 562 Processing helix chain 'e' and resid 572 through 594 removed outlier: 3.666A pdb=" N SER e 592 " --> pdb=" O LEU e 588 " (cutoff:3.500A) Processing helix chain 'e' and resid 616 through 623 removed outlier: 3.576A pdb=" N ILE e 623 " --> pdb=" O LEU e 619 " (cutoff:3.500A) Processing helix chain 'e' and resid 639 through 644 removed outlier: 3.935A pdb=" N THR e 643 " --> pdb=" O ASN e 639 " (cutoff:3.500A) Processing helix chain 'e' and resid 679 through 689 Processing helix chain 'e' and resid 690 through 692 No H-bonds generated for 'chain 'e' and resid 690 through 692' Processing helix chain 'e' and resid 703 through 709 Processing helix chain 'e' and resid 724 through 734 Processing helix chain 'e' and resid 750 through 765 Processing helix chain 'e' and resid 774 through 781 Processing helix chain 'e' and resid 786 through 796 Processing helix chain 'e' and resid 801 through 811 Processing helix chain 'e' and resid 824 through 834 Processing helix chain 'e' and resid 840 through 853 Processing helix chain 'e' and resid 857 through 865 Processing helix chain 'e' and resid 868 through 889 Processing helix chain 'e' and resid 898 through 912 Processing helix chain 'e' and resid 971 through 979 Processing helix chain 'f' and resid 81 through 86 Processing helix chain 'f' and resid 96 through 100 Processing helix chain 'f' and resid 105 through 127 Processing helix chain 'f' and resid 128 through 131 Processing helix chain 'f' and resid 135 through 153 Proline residue: f 145 - end of helix Processing helix chain 'f' and resid 156 through 171 Processing helix chain 'f' and resid 172 through 174 No H-bonds generated for 'chain 'f' and resid 172 through 174' Processing helix chain 'f' and resid 175 through 188 Processing helix chain 'f' and resid 223 through 246 removed outlier: 3.555A pdb=" N SER f 232 " --> pdb=" O LEU f 228 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS f 234 " --> pdb=" O ILE f 230 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG f 235 " --> pdb=" O THR f 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.921A pdb=" N VAL A 494 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 593 Processing sheet with id=AA5, first strand: chain 'A' and resid 970 through 973 Processing sheet with id=AA6, first strand: chain 'A' and resid 1158 through 1163 removed outlier: 5.431A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A1160 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id=AA8, first strand: chain 'A' and resid 1258 through 1262 removed outlier: 3.863A pdb=" N ALA A1298 " --> pdb=" O LEU A1288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1407 through 1408 removed outlier: 3.567A pdb=" N PHE A1425 " --> pdb=" O GLN J 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id=AB2, first strand: chain 'A' and resid 1678 through 1683 removed outlier: 3.756A pdb=" N SER A1680 " --> pdb=" O GLU A1704 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A1704 " --> pdb=" O SER A1680 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id=AB4, first strand: chain 'A' and resid 1715 through 1716 removed outlier: 6.327A pdb=" N ASP A1735 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A1777 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN A1737 " --> pdb=" O ILE A1777 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1955 through 1956 removed outlier: 3.889A pdb=" N ILE A1933 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A1850 " --> pdb=" O ILE A1934 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A1880 " --> pdb=" O ASP A1853 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1859 through 1860 removed outlier: 3.989A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1863 through 1864 Processing sheet with id=AB8, first strand: chain 'C' and resid 75 through 77 removed outlier: 5.629A pdb=" N GLU C 75 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE O 425 " --> pdb=" O SER O 132 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL O 134 " --> pdb=" O ILE O 423 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE O 423 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY O 417 " --> pdb=" O CYS O 404 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS O 404 " --> pdb=" O GLY O 417 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 194 through 201 removed outlier: 6.673A pdb=" N ILE C 134 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU C 213 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 136 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 235 " --> pdb=" O CYS C 264 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL C 266 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE C 237 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASN C 268 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 239 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 537 through 538 removed outlier: 6.784A pdb=" N TRP C 469 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 485 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N THR C 475 " --> pdb=" O TRP C 483 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TRP C 483 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AC3, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC4, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.501A pdb=" N LYS C 604 " --> pdb=" O LEU C 674 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 679 through 681 Processing sheet with id=AC6, first strand: chain 'C' and resid 710 through 714 removed outlier: 3.530A pdb=" N VAL C 773 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 767 " --> pdb=" O LEU C 774 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 887 through 893 removed outlier: 5.690A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 164 through 167 Processing sheet with id=AC9, first strand: chain 'O' and resid 185 through 190 removed outlier: 3.703A pdb=" N LEU O 197 " --> pdb=" O TRP O 209 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER O 199 " --> pdb=" O LYS O 207 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER O 201 " --> pdb=" O THR O 205 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR O 205 " --> pdb=" O SER O 201 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG O 218 " --> pdb=" O CYS O 208 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP O 210 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE O 216 " --> pdb=" O ASP O 210 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 229 through 233 removed outlier: 4.520A pdb=" N LEU O 238 " --> pdb=" O HIS O 233 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY O 243 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL O 247 " --> pdb=" O GLY O 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 269 through 274 removed outlier: 3.766A pdb=" N GLN O 271 " --> pdb=" O SER O 284 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL O 281 " --> pdb=" O TRP O 293 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL O 290 " --> pdb=" O VAL O 303 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL O 303 " --> pdb=" O VAL O 290 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU O 292 " --> pdb=" O MET O 301 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 314 through 316 Processing sheet with id=AD4, first strand: chain 'O' and resid 353 through 357 removed outlier: 4.171A pdb=" N THR O 355 " --> pdb=" O GLY O 367 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL O 372 " --> pdb=" O GLY O 368 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN O 385 " --> pdb=" O PHE O 375 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 114 through 116 removed outlier: 6.179A pdb=" N MET Q 25 " --> pdb=" O VAL P 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'Q' and resid 241 through 243 Processing sheet with id=AD7, first strand: chain 'R' and resid 172 through 176 removed outlier: 3.853A pdb=" N CYS R 181 " --> pdb=" O VAL R 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 143 through 145 Processing sheet with id=AD9, first strand: chain 'n' and resid 153 through 158 removed outlier: 5.000A pdb=" N VAL n 154 " --> pdb=" O ASP n 455 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP n 455 " --> pdb=" O VAL n 154 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS n 450 " --> pdb=" O GLY n 446 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'n' and resid 168 through 170 Processing sheet with id=AE2, first strand: chain 'n' and resid 188 through 190 removed outlier: 6.558A pdb=" N ILE n 189 " --> pdb=" O LEU n 199 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'n' and resid 211 through 214 removed outlier: 4.514A pdb=" N THR n 242 " --> pdb=" O ILE n 232 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP n 234 " --> pdb=" O VAL n 240 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL n 240 " --> pdb=" O ASP n 234 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'n' and resid 253 through 255 removed outlier: 3.532A pdb=" N ILE n 272 " --> pdb=" O TYR n 289 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'n' and resid 296 through 301 removed outlier: 4.214A pdb=" N PHE n 308 " --> pdb=" O TRP n 320 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'n' and resid 342 through 344 Processing sheet with id=AE7, first strand: chain 'n' and resid 381 through 383 removed outlier: 3.749A pdb=" N TRP n 410 " --> pdb=" O SER n 400 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP n 402 " --> pdb=" O PHE n 408 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE n 408 " --> pdb=" O ASP n 402 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'o' and resid 13 through 15 Processing sheet with id=AE9, first strand: chain 'p' and resid 13 through 15 Processing sheet with id=AF1, first strand: chain 'q' and resid 13 through 15 Processing sheet with id=AF2, first strand: chain 'q' and resid 163 through 164 removed outlier: 3.609A pdb=" N GLN q 468 " --> pdb=" O CYS q 481 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'q' and resid 184 through 184 removed outlier: 3.952A pdb=" N GLU q 181 " --> pdb=" O GLN q 184 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'q' and resid 209 through 214 removed outlier: 6.494A pdb=" N ARG q 214 " --> pdb=" O LEU q 220 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU q 220 " --> pdb=" O ARG q 214 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'q' and resid 232 through 235 Processing sheet with id=AF6, first strand: chain 'q' and resid 292 through 295 removed outlier: 3.594A pdb=" N TYR q 292 " --> pdb=" O ALA q 305 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'q' and resid 335 through 338 removed outlier: 3.837A pdb=" N SER q 335 " --> pdb=" O TYR q 348 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN q 358 " --> pdb=" O GLN q 364 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLN q 364 " --> pdb=" O ASN q 358 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'q' and resid 379 through 382 removed outlier: 3.759A pdb=" N LEU q 409 " --> pdb=" O CYS q 399 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP q 401 " --> pdb=" O GLY q 407 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLY q 407 " --> pdb=" O ASP q 401 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'q' and resid 423 through 428 Processing sheet with id=AG1, first strand: chain 'r' and resid 21 through 24 removed outlier: 4.188A pdb=" N THR r 21 " --> pdb=" O SER r 16 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'l' and resid 56 through 64 removed outlier: 6.669A pdb=" N VAL l 56 " --> pdb=" O THR l 50 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR l 50 " --> pdb=" O VAL l 56 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS l 58 " --> pdb=" O ILE l 48 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE l 48 " --> pdb=" O HIS l 58 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP l 60 " --> pdb=" O ASP l 46 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN l 43 " --> pdb=" O VAL l 34 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL l 47 " --> pdb=" O ARG l 30 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG l 30 " --> pdb=" O VAL l 47 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE l 18 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL l 74 " --> pdb=" O ILE l 18 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER l 20 " --> pdb=" O ILE l 72 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE l 72 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU l 22 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU k 84 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS k 48 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU k 84 " --> pdb=" O ASN k 46 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN k 46 " --> pdb=" O LEU k 84 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE k 86 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL k 44 " --> pdb=" O ILE k 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA k 36 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN k 46 " --> pdb=" O LEU k 34 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU k 34 " --> pdb=" O ASN k 46 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS k 48 " --> pdb=" O GLY k 32 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY k 32 " --> pdb=" O CYS k 48 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU k 50 " --> pdb=" O TYR k 30 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR k 30 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL k 97 " --> pdb=" O TYR m 84 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR m 84 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER m 81 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS m 44 " --> pdb=" O SER m 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN m 83 " --> pdb=" O ASP m 42 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA m 38 " --> pdb=" O VAL m 32 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL m 32 " --> pdb=" O ALA m 38 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU m 40 " --> pdb=" O GLN m 30 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLN m 30 " --> pdb=" O LEU m 40 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP m 42 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR m 28 " --> pdb=" O ASP m 42 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU m 13 " --> pdb=" O LEU m 29 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'i' and resid 27 through 31 removed outlier: 4.260A pdb=" N LEU i 31 " --> pdb=" O ILE i 37 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE i 37 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS i 42 " --> pdb=" O GLU i 56 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU i 56 " --> pdb=" O LYS i 42 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL i 52 " --> pdb=" O LEU i 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU i 82 " --> pdb=" O VAL i 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU i 81 " --> pdb=" O ILE h 81 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS h 30 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE h 81 " --> pdb=" O GLY h 28 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY h 28 " --> pdb=" O ILE h 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL h 29 " --> pdb=" O TYR h 38 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU h 37 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLU h 58 " --> pdb=" O GLU h 37 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG h 39 " --> pdb=" O ALA h 56 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA h 56 " --> pdb=" O ARG h 39 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN h 52 " --> pdb=" O VAL h 43 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN h 52 " --> pdb=" O PHE h 72 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE h 72 " --> pdb=" O GLN h 52 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN h 54 " --> pdb=" O GLU h 70 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU h 70 " --> pdb=" O ASN h 54 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA h 56 " --> pdb=" O LEU h 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY h 66 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU h 70 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL g 103 " --> pdb=" O SER g 47 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS g 53 " --> pdb=" O GLU g 74 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU g 74 " --> pdb=" O LYS g 53 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE g 55 " --> pdb=" O VAL g 72 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL g 72 " --> pdb=" O ILE g 55 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER g 92 " --> pdb=" O ASN g 71 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS g 73 " --> pdb=" O PHE g 90 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE g 90 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU g 75 " --> pdb=" O GLU g 88 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLU g 88 " --> pdb=" O LEU g 75 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'i' and resid 89 through 90 removed outlier: 6.049A pdb=" N ASP j 41 " --> pdb=" O LEU j 29 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU j 29 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'j' and resid 23 through 25 Processing sheet with id=AG6, first strand: chain 'j' and resid 44 through 45 removed outlier: 3.605A pdb=" N GLU j 45 " --> pdb=" O HIS j 55 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS j 55 " --> pdb=" O GLU j 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'U' and resid 56 through 64 removed outlier: 6.667A pdb=" N VAL U 56 " --> pdb=" O THR U 50 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR U 50 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS U 58 " --> pdb=" O ILE U 48 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE U 48 " --> pdb=" O HIS U 58 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP U 60 " --> pdb=" O ASP U 46 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN U 43 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL U 47 " --> pdb=" O ARG U 30 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG U 30 " --> pdb=" O VAL U 47 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE U 18 " --> pdb=" O VAL U 74 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL U 74 " --> pdb=" O ILE U 18 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER U 20 " --> pdb=" O ILE U 72 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE U 72 " --> pdb=" O SER U 20 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU U 22 " --> pdb=" O LYS U 70 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU F 84 " --> pdb=" O VAL U 74 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS F 48 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 84 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN F 46 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE F 86 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F 44 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 36 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN F 46 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU F 34 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS F 48 " --> pdb=" O GLY F 32 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY F 32 " --> pdb=" O CYS F 48 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU F 50 " --> pdb=" O TYR F 30 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR F 30 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL F 97 " --> pdb=" O TYR V 84 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR V 84 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER V 81 " --> pdb=" O LYS V 44 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS V 44 " --> pdb=" O SER V 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN V 83 " --> pdb=" O ASP V 42 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA V 38 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL V 32 " --> pdb=" O ALA V 38 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU V 40 " --> pdb=" O GLN V 30 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN V 30 " --> pdb=" O LEU V 40 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP V 42 " --> pdb=" O THR V 28 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR V 28 " --> pdb=" O ASP V 42 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU V 13 " --> pdb=" O LEU V 29 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 27 through 31 removed outlier: 4.259A pdb=" N LEU G 31 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE G 37 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS G 42 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU G 56 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL G 52 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 82 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 81 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS H 30 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE H 81 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY H 28 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL H 29 " --> pdb=" O TYR H 38 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU H 37 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU H 58 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG H 39 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA H 56 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN H 52 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN H 52 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE H 72 " --> pdb=" O GLN H 52 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN H 54 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU H 70 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA H 56 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY H 66 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU H 70 " --> pdb=" O LYS W 106 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL W 103 " --> pdb=" O SER W 47 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS W 53 " --> pdb=" O GLU W 74 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU W 74 " --> pdb=" O LYS W 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE W 55 " --> pdb=" O VAL W 72 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL W 72 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER W 92 " --> pdb=" O ASN W 71 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS W 73 " --> pdb=" O PHE W 90 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE W 90 " --> pdb=" O LYS W 73 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU W 75 " --> pdb=" O GLU W 88 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU W 88 " --> pdb=" O LEU W 75 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 89 through 90 removed outlier: 6.049A pdb=" N ASP K 41 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU K 29 " --> pdb=" O ASP K 41 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 23 through 25 Processing sheet with id=AH2, first strand: chain 'K' and resid 44 through 45 removed outlier: 3.605A pdb=" N GLU K 45 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS K 55 " --> pdb=" O GLU K 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'X' and resid 72 through 74 Processing sheet with id=AH4, first strand: chain 'X' and resid 93 through 94 Processing sheet with id=AH5, first strand: chain 'Y' and resid 13 through 15 removed outlier: 6.180A pdb=" N LEU Y 34 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP Y 58 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU Y 36 " --> pdb=" O ASP Y 58 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU Y 79 " --> pdb=" O THR Y 102 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 66 through 67 Processing sheet with id=AH7, first strand: chain 'e' and resid 429 through 430 removed outlier: 6.249A pdb=" N ILE e 400 " --> pdb=" O LYS e 447 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL e 449 " --> pdb=" O ILE e 400 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL e 402 " --> pdb=" O VAL e 449 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER e 399 " --> pdb=" O CYS e 469 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE e 471 " --> pdb=" O SER e 399 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL e 401 " --> pdb=" O ILE e 471 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL e 369 " --> pdb=" O ILE e 503 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SER e 505 " --> pdb=" O VAL e 369 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE e 371 " --> pdb=" O SER e 505 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 534 through 535 removed outlier: 6.971A pdb=" N ASP e 565 " --> pdb=" O ARG e 651 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL e 653 " --> pdb=" O ASP e 565 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU e 567 " --> pdb=" O VAL e 653 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE e 566 " --> pdb=" O ILE e 635 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA e 637 " --> pdb=" O ILE e 566 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE e 568 " --> pdb=" O ALA e 637 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 658 through 665 Processing sheet with id=AI1, first strand: chain 'e' and resid 924 through 926 Processing sheet with id=AI2, first strand: chain 'e' and resid 934 through 935 removed outlier: 6.363A pdb=" N GLN e 934 " --> pdb=" O ILE e 964 " (cutoff:3.500A) 3581 hydrogen bonds defined for protein. 10179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 213 hydrogen bonds 386 hydrogen bond angles 0 basepair planarities 88 basepair parallelities 156 stacking parallelities Total time for adding SS restraints: 48.45 Time building geometry restraints manager: 18.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.56: 77409 1.56 - 1.92: 1189 1.92 - 2.27: 0 2.27 - 2.63: 0 2.63 - 2.99: 1 Bond restraints: 78599 Sorted by residual: bond pdb=" C ALA q 247 " pdb=" N ARG q 256 " ideal model delta sigma weight residual 1.335 2.990 -1.655 1.97e-02 2.58e+03 7.06e+03 bond pdb=" CB CYS n 399 " pdb=" SG CYS n 399 " ideal model delta sigma weight residual 1.808 1.408 0.400 3.30e-02 9.18e+02 1.47e+02 bond pdb=" CB CYS n 444 " pdb=" SG CYS n 444 " ideal model delta sigma weight residual 1.808 1.429 0.379 3.30e-02 9.18e+02 1.32e+02 bond pdb=" CA ASP Y 69 " pdb=" CB ASP Y 69 " ideal model delta sigma weight residual 1.532 1.381 0.151 1.42e-02 4.96e+03 1.13e+02 bond pdb=" CB CYS n 454 " pdb=" SG CYS n 454 " ideal model delta sigma weight residual 1.808 1.479 0.329 3.30e-02 9.18e+02 9.92e+01 ... (remaining 78594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.60: 107778 7.60 - 15.21: 330 15.21 - 22.81: 13 22.81 - 30.42: 0 30.42 - 38.02: 1 Bond angle restraints: 108122 Sorted by residual: angle pdb=" O ALA q 247 " pdb=" C ALA q 247 " pdb=" N ARG q 256 " ideal model delta sigma weight residual 122.59 84.57 38.02 1.33e+00 5.65e-01 8.17e+02 angle pdb=" N PRO Y 44 " pdb=" CA PRO Y 44 " pdb=" CB PRO Y 44 " ideal model delta sigma weight residual 103.23 113.92 -10.69 6.70e-01 2.23e+00 2.55e+02 angle pdb=" C ALA q 247 " pdb=" N ARG q 256 " pdb=" CA ARG q 256 " ideal model delta sigma weight residual 120.17 141.02 -20.85 1.54e+00 4.22e-01 1.83e+02 angle pdb=" C LEU Y 81 " pdb=" N GLY Y 82 " pdb=" CA GLY Y 82 " ideal model delta sigma weight residual 120.10 131.58 -11.48 9.50e-01 1.11e+00 1.46e+02 angle pdb=" N PHE e 595 " pdb=" CA PHE e 595 " pdb=" C PHE e 595 " ideal model delta sigma weight residual 108.60 123.45 -14.85 1.46e+00 4.69e-01 1.03e+02 ... (remaining 108117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 46772 35.94 - 71.88: 1333 71.88 - 107.83: 132 107.83 - 143.77: 34 143.77 - 179.71: 21 Dihedral angle restraints: 48292 sinusoidal: 20589 harmonic: 27703 Sorted by residual: dihedral pdb=" CA GLY n 67 " pdb=" C GLY n 67 " pdb=" N PRO n 68 " pdb=" CA PRO n 68 " ideal model delta harmonic sigma weight residual -180.00 -51.01 -128.99 0 5.00e+00 4.00e-02 6.66e+02 dihedral pdb=" CA ALA l 81 " pdb=" C ALA l 81 " pdb=" N PRO l 82 " pdb=" CA PRO l 82 " ideal model delta harmonic sigma weight residual -180.00 -52.74 -127.26 0 5.00e+00 4.00e-02 6.48e+02 dihedral pdb=" CA ALA U 81 " pdb=" C ALA U 81 " pdb=" N PRO U 82 " pdb=" CA PRO U 82 " ideal model delta harmonic sigma weight residual -180.00 -52.83 -127.17 0 5.00e+00 4.00e-02 6.47e+02 ... (remaining 48289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 12803 0.243 - 0.485: 145 0.485 - 0.728: 14 0.728 - 0.971: 5 0.971 - 1.214: 1 Chirality restraints: 12968 Sorted by residual: chirality pdb=" CA LYS e 631 " pdb=" N LYS e 631 " pdb=" C LYS e 631 " pdb=" CB LYS e 631 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA PHE e 595 " pdb=" N PHE e 595 " pdb=" C PHE e 595 " pdb=" CB PHE e 595 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA ASN e 923 " pdb=" N ASN e 923 " pdb=" C ASN e 923 " pdb=" CB ASN e 923 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.87e+01 ... (remaining 12965 not shown) Planarity restraints: 12497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA q 247 " 0.167 2.00e-02 2.50e+03 2.29e-01 5.23e+02 pdb=" C ALA q 247 " -0.387 2.00e-02 2.50e+03 pdb=" O ALA q 247 " 0.171 2.00e-02 2.50e+03 pdb=" N ARG q 256 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 81 " -0.033 2.00e-02 2.50e+03 6.89e-02 4.74e+01 pdb=" C ALA U 81 " 0.119 2.00e-02 2.50e+03 pdb=" O ALA U 81 " -0.045 2.00e-02 2.50e+03 pdb=" N PRO U 82 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA l 81 " 0.033 2.00e-02 2.50e+03 6.84e-02 4.68e+01 pdb=" C ALA l 81 " -0.118 2.00e-02 2.50e+03 pdb=" O ALA l 81 " 0.045 2.00e-02 2.50e+03 pdb=" N PRO l 82 " 0.040 2.00e-02 2.50e+03 ... (remaining 12494 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 249 2.24 - 2.91: 35506 2.91 - 3.57: 111661 3.57 - 4.24: 175364 4.24 - 4.90: 280939 Nonbonded interactions: 603719 Sorted by model distance: nonbonded pdb=" NZ LYS C 99 " pdb=" OP2 G D 43 " model vdw 1.580 3.120 nonbonded pdb=" P G N 100 " pdb=" O2' A M 501 " model vdw 1.599 3.400 nonbonded pdb=" OP2 U E 21 " pdb=" OG SER n 54 " model vdw 1.708 3.040 nonbonded pdb=" CB GLN c 193 " pdb=" CG PRO n 436 " model vdw 1.726 3.840 nonbonded pdb=" CE2 PHE R 75 " pdb=" C8 A E 35 " model vdw 1.741 3.560 ... (remaining 603714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'k' and (resid 6 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 102)) } ncs_group { reference = chain 'G' selection = chain 'i' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'K' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'l' } ncs_group { reference = chain 'V' selection = chain 'm' } ncs_group { reference = (chain 'o' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 through 6 \ 3 or (resid 64 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 139)) selection = (chain 'p' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 through 6 \ 3 or (resid 64 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 139)) selection = (chain 'r' and (resid 1 through 52 or resid 57 through 139)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 2.220 Check model and map are aligned: 0.450 Set scattering table: 0.560 Process input model: 178.050 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.655 78599 Z= 0.919 Angle : 1.474 38.022 108122 Z= 0.872 Chirality : 0.083 1.214 12968 Planarity : 0.008 0.229 12497 Dihedral : 16.802 179.710 30142 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 1.58 % Allowed : 12.54 % Favored : 85.88 % Rotamer: Outliers : 1.96 % Allowed : 3.85 % Favored : 94.19 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 3.29 % Twisted General : 1.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.07), residues: 8398 helix: -3.46 (0.06), residues: 3400 sheet: -2.42 (0.13), residues: 1164 loop : -3.20 (0.08), residues: 3834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP A 823 HIS 0.028 0.004 HIS A 675 PHE 0.050 0.004 PHE A1495 TYR 0.075 0.005 TYR f 168 ARG 0.034 0.002 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1301 time to evaluate : 5.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping revert: symmetry clash Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 196 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping REVERT: A 188 GLU cc_start: 0.6937 (tt0) cc_final: 0.6546 (tm-30) REVERT: A 210 GLU cc_start: 0.7460 (tt0) cc_final: 0.7158 (tm-30) REVERT: A 262 ASP cc_start: 0.8482 (m-30) cc_final: 0.8203 (p0) REVERT: A 275 TYR cc_start: 0.8418 (m-80) cc_final: 0.8168 (m-80) REVERT: A 289 ASP cc_start: 0.6929 (m-30) cc_final: 0.6496 (m-30) REVERT: A 308 MET cc_start: 0.7622 (tpt) cc_final: 0.7210 (tpt) REVERT: A 325 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8643 (mtmt) REVERT: A 458 PHE cc_start: 0.7713 (t80) cc_final: 0.7024 (t80) REVERT: A 775 ARG cc_start: 0.7449 (ttm170) cc_final: 0.6741 (tmm160) REVERT: A 788 GLU cc_start: 0.8682 (tp30) cc_final: 0.7778 (tm-30) REVERT: A 873 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8353 (mp0) REVERT: A 890 LEU cc_start: 0.9301 (mt) cc_final: 0.9036 (tp) REVERT: A 996 ASP cc_start: 0.8363 (t70) cc_final: 0.8153 (t70) REVERT: A 1180 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7928 (mm-30) REVERT: A 1217 ARG cc_start: 0.8298 (mmt-90) cc_final: 0.7167 (tmm-80) REVERT: A 1287 ASP cc_start: 0.9171 (m-30) cc_final: 0.8784 (m-30) REVERT: A 1455 GLN cc_start: 0.9297 (tt0) cc_final: 0.9064 (tm-30) REVERT: A 1521 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8266 (mmt180) REVERT: A 1533 ASP cc_start: 0.8238 (m-30) cc_final: 0.8026 (m-30) REVERT: A 1585 MET cc_start: 0.2028 (tpp) cc_final: 0.0529 (ptt) REVERT: A 1632 ILE cc_start: 0.8708 (mt) cc_final: 0.8330 (pt) REVERT: A 1713 LYS cc_start: 0.7437 (mttt) cc_final: 0.7034 (tptp) REVERT: A 1756 PHE cc_start: 0.7939 (t80) cc_final: 0.7710 (t80) REVERT: A 1783 MET cc_start: 0.8755 (mmm) cc_final: 0.8442 (mmm) REVERT: A 1806 MET cc_start: 0.8096 (mmm) cc_final: 0.7867 (ppp) REVERT: A 1945 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 1946 VAL cc_start: 0.9102 (t) cc_final: 0.8857 (p) REVERT: C 186 ASP cc_start: 0.7887 (m-30) cc_final: 0.7365 (t0) REVERT: C 208 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7344 (mtt90) REVERT: C 243 GLU cc_start: 0.8591 (tt0) cc_final: 0.8228 (mm-30) REVERT: C 306 PRO cc_start: 0.7554 (Cg_exo) cc_final: 0.7339 (Cg_endo) REVERT: C 347 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7930 (mmm160) REVERT: C 364 PHE cc_start: 0.7711 (p90) cc_final: 0.7450 (t80) REVERT: C 538 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8581 (tp30) REVERT: C 541 GLU cc_start: 0.8848 (tt0) cc_final: 0.8456 (tp30) REVERT: C 542 ILE cc_start: 0.8140 (mt) cc_final: 0.7710 (mm) REVERT: C 635 LYS cc_start: 0.8155 (mttt) cc_final: 0.7863 (mmmt) REVERT: C 741 MET cc_start: 0.4736 (mmm) cc_final: 0.3576 (ppp) REVERT: C 745 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7751 (tpp-160) REVERT: C 842 MET cc_start: 0.7715 (tpp) cc_final: 0.7501 (tpp) REVERT: C 863 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8059 (tm-30) REVERT: C 947 LYS cc_start: 0.7368 (mptt) cc_final: 0.6890 (tppt) REVERT: C 955 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8421 (mtmm) REVERT: O 286 THR cc_start: 0.8993 (p) cc_final: 0.8754 (m) REVERT: P 112 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7724 (mt) REVERT: Q 244 HIS cc_start: 0.6503 (m90) cc_final: 0.6222 (m90) REVERT: R 112 PHE cc_start: 0.7646 (m-80) cc_final: 0.7022 (m-10) REVERT: R 247 LEU cc_start: 0.8181 (tt) cc_final: 0.7834 (tp) REVERT: T 27 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6623 (tm-30) REVERT: Z 148 LEU cc_start: 0.7578 (mt) cc_final: 0.7280 (mt) REVERT: Z 160 TRP cc_start: 0.4963 (t60) cc_final: 0.4715 (t-100) REVERT: I 116 THR cc_start: 0.6768 (p) cc_final: 0.6567 (m) REVERT: v 725 THR cc_start: 0.2013 (OUTLIER) cc_final: 0.1642 (m) REVERT: n 57 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7547 (tptm) REVERT: n 59 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6402 (ttt90) REVERT: k 45 LEU cc_start: 0.7238 (mt) cc_final: 0.6958 (tt) REVERT: i 11 VAL cc_start: 0.4101 (t) cc_final: 0.2648 (p) REVERT: i 18 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: i 83 LYS cc_start: 0.6882 (tttt) cc_final: 0.6251 (pttt) REVERT: h 16 LYS cc_start: 0.7879 (pttt) cc_final: 0.7584 (tttm) REVERT: j 9 LYS cc_start: 0.7594 (mmmt) cc_final: 0.7327 (mmmt) REVERT: j 15 ILE cc_start: 0.7404 (mt) cc_final: 0.6972 (mm) REVERT: j 35 PHE cc_start: 0.7842 (m-80) cc_final: 0.7617 (m-80) REVERT: l 23 LEU cc_start: 0.6664 (mt) cc_final: 0.6448 (mt) REVERT: m 20 LYS cc_start: 0.3258 (OUTLIER) cc_final: 0.1977 (mmtt) REVERT: g 24 PHE cc_start: 0.2464 (OUTLIER) cc_final: 0.1970 (t80) REVERT: g 61 PHE cc_start: 0.4498 (t80) cc_final: 0.3602 (t80) REVERT: U 59 MET cc_start: 0.1423 (ptp) cc_final: 0.0873 (ptm) REVERT: V 77 ASP cc_start: 0.2477 (OUTLIER) cc_final: 0.1285 (p0) REVERT: f 168 TYR cc_start: 0.4891 (t80) cc_final: 0.4519 (t80) REVERT: f 242 TRP cc_start: 0.5962 (t60) cc_final: 0.5027 (t60) outliers start: 162 outliers final: 77 residues processed: 1441 average time/residue: 0.8222 time to fit residues: 2040.3429 Evaluate side-chains 860 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 775 time to evaluate : 5.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1326 THR Chi-restraints excluded: chain A residue 1988 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain R residue 169 ASP Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain T residue 120 CYS Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 506 THR Chi-restraints excluded: chain c residue 517 VAL Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 641 PRO Chi-restraints excluded: chain v residue 712 CYS Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain v residue 723 SER Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain n residue 62 THR Chi-restraints excluded: chain n residue 66 ASP Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 258 THR Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain q residue 61 SER Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 196 PRO Chi-restraints excluded: chain q residue 235 THR Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 93 LEU Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 100 THR Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain m residue 20 LYS Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 99 ASP Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain W residue 99 ASP Chi-restraints excluded: chain W residue 100 SER Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 44 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 747 optimal weight: 2.9990 chunk 670 optimal weight: 0.6980 chunk 372 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 452 optimal weight: 5.9990 chunk 358 optimal weight: 8.9990 chunk 693 optimal weight: 0.0980 chunk 268 optimal weight: 2.9990 chunk 421 optimal weight: 10.0000 chunk 516 optimal weight: 1.9990 chunk 803 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 265 ASN A 343 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 429 ASN A 528 ASN A 541 ASN A 584 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A 685 HIS A 705 GLN A 733 GLN A 760 ASN A 784 GLN A 785 HIS ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS A 848 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 ASN ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS A1449 ASN A1529 ASN A1626 GLN A1718 HIS A1856 ASN A1932 GLN C 82 ASN C 101 GLN C 143 HIS C 158 HIS ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN C 289 ASN ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN C 418 GLN C 642 HIS C 776 ASN C 794 GLN C 869 HIS C 929 GLN O 265 HIS O 270 ASN O 382 HIS O 428 GLN P 84 ASN P 198 ASN Q 72 GLN ** Q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 201 ASN R 202 GLN R 227 ASN ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 5 HIS S 34 HIS ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 HIS S 173 HIS ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 143 HIS Z 131 HIS ** Z 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 354 HIS Z 390 HIS Z 457 HIS d 67 GLN d 78 GLN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 85 GLN i 15 ASN i 86 ASN h 24 ASN j 18 ASN j 66 ASN ** l 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 HIS m 86 ASN m 94 GLN g 28 HIS g 52 HIS G 15 ASN G 34 GLN G 86 ASN H 24 ASN H 77 ASN K 66 ASN f 87 GLN f 149 GLN f 169 HIS f 171 GLN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 78599 Z= 0.229 Angle : 0.801 15.632 108122 Z= 0.414 Chirality : 0.046 0.356 12968 Planarity : 0.006 0.090 12497 Dihedral : 17.574 176.354 15750 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.38 % Favored : 93.17 % Rotamer: Outliers : 2.83 % Allowed : 10.56 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.64 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.08), residues: 8400 helix: -0.90 (0.08), residues: 3465 sheet: -1.90 (0.13), residues: 1206 loop : -2.29 (0.09), residues: 3729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Q 217 HIS 0.013 0.002 HIS Z 223 PHE 0.026 0.002 PHE d 172 TYR 0.030 0.002 TYR A 923 ARG 0.010 0.001 ARG A1442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1131 time to evaluate : 5.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping REVERT: A 174 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7889 (mtpt) REVERT: A 177 GLU cc_start: 0.8989 (pt0) cc_final: 0.8688 (tt0) REVERT: A 184 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7171 (mt-10) REVERT: A 188 GLU cc_start: 0.6734 (tt0) cc_final: 0.6180 (tm-30) REVERT: A 210 GLU cc_start: 0.7291 (tt0) cc_final: 0.6897 (tm-30) REVERT: A 235 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7608 (ptpt) REVERT: A 251 TYR cc_start: 0.6764 (t80) cc_final: 0.6406 (t80) REVERT: A 275 TYR cc_start: 0.8459 (m-80) cc_final: 0.8233 (m-80) REVERT: A 288 GLU cc_start: 0.8771 (pm20) cc_final: 0.8550 (pm20) REVERT: A 304 ASP cc_start: 0.7533 (t0) cc_final: 0.7224 (t0) REVERT: A 392 ASN cc_start: 0.7877 (t0) cc_final: 0.7668 (t0) REVERT: A 397 SER cc_start: 0.8912 (t) cc_final: 0.8512 (p) REVERT: A 458 PHE cc_start: 0.7975 (t80) cc_final: 0.7091 (t80) REVERT: A 653 ILE cc_start: 0.7615 (pt) cc_final: 0.7328 (mt) REVERT: A 667 TYR cc_start: 0.8251 (p90) cc_final: 0.7624 (p90) REVERT: A 682 ASP cc_start: 0.7523 (m-30) cc_final: 0.7299 (m-30) REVERT: A 757 GLU cc_start: 0.7238 (pt0) cc_final: 0.6572 (mm-30) REVERT: A 772 GLU cc_start: 0.7805 (pt0) cc_final: 0.7561 (pm20) REVERT: A 775 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6737 (tmt170) REVERT: A 788 GLU cc_start: 0.8599 (tp30) cc_final: 0.7639 (tm-30) REVERT: A 792 CYS cc_start: 0.9029 (m) cc_final: 0.8672 (m) REVERT: A 886 MET cc_start: 0.9078 (tpp) cc_final: 0.8825 (tpp) REVERT: A 890 LEU cc_start: 0.9055 (mt) cc_final: 0.8846 (mt) REVERT: A 971 MET cc_start: 0.8778 (mmm) cc_final: 0.8545 (mmt) REVERT: A 997 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: A 1095 MET cc_start: 0.9200 (mtt) cc_final: 0.8969 (mtt) REVERT: A 1145 MET cc_start: 0.8693 (mmp) cc_final: 0.8413 (mmm) REVERT: A 1180 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7701 (mm-30) REVERT: A 1183 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7569 (t) REVERT: A 1217 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7429 (ttp80) REVERT: A 1244 GLU cc_start: 0.8902 (mp0) cc_final: 0.8664 (tm-30) REVERT: A 1405 ILE cc_start: 0.8008 (mt) cc_final: 0.7782 (mt) REVERT: A 1455 GLN cc_start: 0.9164 (tt0) cc_final: 0.8833 (tm-30) REVERT: A 1465 ARG cc_start: 0.8256 (ttt180) cc_final: 0.7681 (tmm-80) REVERT: A 1521 ARG cc_start: 0.8606 (ptp90) cc_final: 0.8163 (mmt180) REVERT: A 1585 MET cc_start: 0.2634 (tpp) cc_final: 0.0899 (ptt) REVERT: A 1713 LYS cc_start: 0.7574 (mttt) cc_final: 0.7103 (tptm) REVERT: A 1732 MET cc_start: 0.4278 (tpt) cc_final: 0.3991 (tpp) REVERT: A 1740 TYR cc_start: 0.9122 (t80) cc_final: 0.8919 (t80) REVERT: A 1774 MET cc_start: 0.7577 (ttt) cc_final: 0.7275 (ttt) REVERT: A 1927 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7920 (pt0) REVERT: A 1946 VAL cc_start: 0.9046 (t) cc_final: 0.8778 (m) REVERT: C 151 ASP cc_start: 0.8401 (t70) cc_final: 0.8189 (t0) REVERT: C 186 ASP cc_start: 0.7765 (m-30) cc_final: 0.7427 (t0) REVERT: C 208 ARG cc_start: 0.7384 (mtt180) cc_final: 0.7120 (mtt90) REVERT: C 243 GLU cc_start: 0.8577 (tt0) cc_final: 0.8173 (mm-30) REVERT: C 347 ARG cc_start: 0.8313 (mmt180) cc_final: 0.8002 (mmm160) REVERT: C 431 GLN cc_start: 0.7385 (mp10) cc_final: 0.7164 (pm20) REVERT: C 538 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8584 (tp30) REVERT: C 541 GLU cc_start: 0.8515 (tt0) cc_final: 0.8308 (tp30) REVERT: C 542 ILE cc_start: 0.8367 (mt) cc_final: 0.8088 (mm) REVERT: C 741 MET cc_start: 0.4400 (mmm) cc_final: 0.3413 (ppp) REVERT: C 745 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7663 (mmt180) REVERT: C 800 TYR cc_start: 0.8848 (m-10) cc_final: 0.8543 (m-10) REVERT: C 832 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7392 (p0) REVERT: C 863 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8033 (tm-30) REVERT: C 947 LYS cc_start: 0.7233 (mptt) cc_final: 0.6861 (tppt) REVERT: C 955 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8260 (mtmm) REVERT: J 9 LYS cc_start: 0.7474 (mmtt) cc_final: 0.7248 (mmpt) REVERT: O 131 LEU cc_start: 0.8451 (tp) cc_final: 0.7856 (tp) REVERT: O 221 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7913 (t80) REVERT: O 225 SER cc_start: 0.8486 (t) cc_final: 0.7949 (m) REVERT: Q 102 GLU cc_start: 0.4990 (mp0) cc_final: 0.4770 (mm-30) REVERT: R 106 THR cc_start: 0.8377 (p) cc_final: 0.7875 (t) REVERT: R 110 ASP cc_start: 0.7650 (p0) cc_final: 0.6144 (m-30) REVERT: R 247 LEU cc_start: 0.7817 (tt) cc_final: 0.7155 (tp) REVERT: S 127 TRP cc_start: 0.6348 (p-90) cc_final: 0.6124 (p-90) REVERT: S 175 ARG cc_start: 0.6235 (mtp180) cc_final: 0.5947 (mmm160) REVERT: Z 200 ILE cc_start: 0.7521 (mt) cc_final: 0.7149 (mt) REVERT: d 58 LEU cc_start: 0.9221 (mt) cc_final: 0.8939 (mt) REVERT: d 132 VAL cc_start: 0.8691 (t) cc_final: 0.8436 (p) REVERT: d 159 TRP cc_start: 0.8049 (t-100) cc_final: 0.7697 (t-100) REVERT: I 200 ASN cc_start: 0.8933 (t0) cc_final: 0.7776 (t0) REVERT: v 669 TYR cc_start: 0.1825 (t80) cc_final: 0.1306 (t80) REVERT: o 1 MET cc_start: -0.0623 (mmm) cc_final: -0.2121 (mpp) REVERT: o 81 LEU cc_start: 0.3062 (mt) cc_final: 0.2246 (tt) REVERT: p 102 LEU cc_start: 0.1925 (OUTLIER) cc_final: 0.1413 (pt) REVERT: k 6 VAL cc_start: -0.0839 (p) cc_final: -0.1087 (t) REVERT: k 45 LEU cc_start: 0.7187 (mt) cc_final: 0.6944 (tt) REVERT: k 51 GLU cc_start: 0.2897 (mm-30) cc_final: 0.1929 (tp30) REVERT: i 50 MET cc_start: 0.2272 (tpp) cc_final: 0.2007 (tpp) REVERT: i 83 LYS cc_start: 0.6257 (tttt) cc_final: 0.5790 (pttt) REVERT: i 92 SER cc_start: -0.0349 (OUTLIER) cc_final: -0.0871 (t) REVERT: h 16 LYS cc_start: 0.7809 (pttt) cc_final: 0.7574 (tttm) REVERT: h 41 THR cc_start: 0.5633 (p) cc_final: 0.5262 (t) REVERT: h 72 PHE cc_start: 0.7013 (t80) cc_final: 0.6702 (t80) REVERT: h 77 ASN cc_start: 0.5245 (m-40) cc_final: 0.4924 (m-40) REVERT: j 69 ILE cc_start: 0.7302 (mm) cc_final: 0.6884 (mm) REVERT: l 70 LYS cc_start: 0.5218 (ttpt) cc_final: 0.4480 (ptmt) REVERT: l 71 PHE cc_start: 0.7820 (p90) cc_final: 0.7464 (p90) REVERT: m 6 PHE cc_start: 0.6681 (t80) cc_final: 0.6476 (t80) REVERT: m 36 MET cc_start: 0.4755 (mmt) cc_final: 0.4200 (ttm) REVERT: g 61 PHE cc_start: 0.4718 (t80) cc_final: 0.3767 (t80) REVERT: g 103 VAL cc_start: 0.7346 (t) cc_final: 0.7122 (t) REVERT: G 10 MET cc_start: 0.0107 (ttm) cc_final: -0.0967 (mtm) REVERT: V 1 MET cc_start: -0.0856 (tpp) cc_final: -0.1187 (tpp) REVERT: V 77 ASP cc_start: 0.2225 (OUTLIER) cc_final: 0.1268 (p0) REVERT: f 184 MET cc_start: 0.5487 (mmm) cc_final: 0.4964 (mmm) REVERT: f 242 TRP cc_start: 0.5922 (t60) cc_final: 0.5058 (t60) REVERT: f 247 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.5032 (t-90) outliers start: 215 outliers final: 121 residues processed: 1280 average time/residue: 0.7165 time to fit residues: 1597.3679 Evaluate side-chains 959 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 829 time to evaluate : 5.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 346 GLU Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 81 HIS Chi-restraints excluded: chain Q residue 211 ASP Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 481 LEU Chi-restraints excluded: chain c residue 16 VAL Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain c residue 184 GLU Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 517 VAL Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 76 ILE Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain v residue 577 VAL Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 641 PRO Chi-restraints excluded: chain v residue 649 GLU Chi-restraints excluded: chain v residue 684 ILE Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 295 SER Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 102 LEU Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain i residue 92 SER Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 69 ILE Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 52 HIS Chi-restraints excluded: chain g residue 99 ASP Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 176 ILE Chi-restraints excluded: chain f residue 236 LEU Chi-restraints excluded: chain f residue 247 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 446 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 668 optimal weight: 6.9990 chunk 547 optimal weight: 20.0000 chunk 221 optimal weight: 0.5980 chunk 805 optimal weight: 10.0000 chunk 869 optimal weight: 50.0000 chunk 717 optimal weight: 6.9990 chunk 798 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 645 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1086 ASN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 HIS A1115 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 ASN A1449 ASN A1799 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 608 GLN ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN O 270 ASN O 306 HIS P 37 ASN P 110 HIS Q 209 ASN ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 HIS T 46 ASN T 57 HIS ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN Z 131 HIS ** Z 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 358 GLN I 115 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 40 HIS i 23 GLN ** h 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 ASN ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 HIS F 40 HIS ** U 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 78599 Z= 0.382 Angle : 0.836 16.989 108122 Z= 0.426 Chirality : 0.048 0.290 12968 Planarity : 0.006 0.080 12497 Dihedral : 17.078 171.819 15698 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.04 % Favored : 91.58 % Rotamer: Outliers : 4.82 % Allowed : 14.12 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.64 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.09), residues: 8400 helix: -0.00 (0.09), residues: 3450 sheet: -1.69 (0.13), residues: 1251 loop : -2.11 (0.10), residues: 3699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP Q 217 HIS 0.047 0.002 HIS g 52 PHE 0.035 0.003 PHE A1562 TYR 0.030 0.003 TYR d 267 ARG 0.008 0.001 ARG W 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 873 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping REVERT: A 149 MET cc_start: 0.5491 (pmm) cc_final: 0.5159 (pmm) REVERT: A 161 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5909 (m-80) REVERT: A 174 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7576 (mtpt) REVERT: A 177 GLU cc_start: 0.8997 (pt0) cc_final: 0.8462 (tt0) REVERT: A 184 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6502 (mt-10) REVERT: A 210 GLU cc_start: 0.7530 (tt0) cc_final: 0.7094 (tm-30) REVERT: A 224 MET cc_start: 0.8478 (mmt) cc_final: 0.8237 (mtt) REVERT: A 235 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7304 (ptpt) REVERT: A 275 TYR cc_start: 0.8635 (m-80) cc_final: 0.8319 (m-80) REVERT: A 304 ASP cc_start: 0.7495 (t0) cc_final: 0.7199 (t0) REVERT: A 392 ASN cc_start: 0.7921 (t0) cc_final: 0.7612 (t0) REVERT: A 458 PHE cc_start: 0.8015 (t80) cc_final: 0.7336 (t80) REVERT: A 467 GLU cc_start: 0.6070 (pm20) cc_final: 0.5862 (pm20) REVERT: A 497 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: A 769 MET cc_start: 0.8784 (mmm) cc_final: 0.8127 (ttp) REVERT: A 775 ARG cc_start: 0.7256 (ttm170) cc_final: 0.6544 (tmm160) REVERT: A 788 GLU cc_start: 0.8470 (tp30) cc_final: 0.7488 (tm-30) REVERT: A 792 CYS cc_start: 0.8889 (m) cc_final: 0.8653 (m) REVERT: A 890 LEU cc_start: 0.9294 (mt) cc_final: 0.9047 (tp) REVERT: A 992 ASP cc_start: 0.8778 (m-30) cc_final: 0.8482 (m-30) REVERT: A 1020 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8479 (pt) REVERT: A 1056 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: A 1095 MET cc_start: 0.9272 (mtt) cc_final: 0.9053 (mtt) REVERT: A 1217 ARG cc_start: 0.8486 (mmt-90) cc_final: 0.7406 (ttp-170) REVERT: A 1244 GLU cc_start: 0.8926 (mp0) cc_final: 0.8633 (tm-30) REVERT: A 1307 GLU cc_start: 0.8999 (mp0) cc_final: 0.8747 (mp0) REVERT: A 1418 THR cc_start: 0.8152 (m) cc_final: 0.7747 (p) REVERT: A 1422 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8199 (mp) REVERT: A 1455 GLN cc_start: 0.9189 (tt0) cc_final: 0.8870 (tm-30) REVERT: A 1499 ARG cc_start: 0.8186 (ptt180) cc_final: 0.6704 (tpt-90) REVERT: A 1521 ARG cc_start: 0.8641 (ptp90) cc_final: 0.8136 (mmt180) REVERT: A 1585 MET cc_start: 0.2876 (tpp) cc_final: 0.1044 (ptt) REVERT: A 1659 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8314 (mm-30) REVERT: A 1774 MET cc_start: 0.7327 (ttt) cc_final: 0.7086 (ttt) REVERT: A 1916 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6954 (mm-30) REVERT: A 1927 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 1946 VAL cc_start: 0.9073 (t) cc_final: 0.8808 (m) REVERT: A 2024 MET cc_start: 0.7323 (mmt) cc_final: 0.6843 (ppp) REVERT: C 78 MET cc_start: 0.6631 (mmm) cc_final: 0.6400 (mmm) REVERT: C 126 MET cc_start: 0.7732 (mmt) cc_final: 0.7351 (tpp) REVERT: C 184 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7418 (tt0) REVERT: C 186 ASP cc_start: 0.7914 (m-30) cc_final: 0.7491 (t0) REVERT: C 208 ARG cc_start: 0.7280 (mtt180) cc_final: 0.7056 (mtt90) REVERT: C 229 LEU cc_start: 0.7991 (tp) cc_final: 0.7720 (tp) REVERT: C 243 GLU cc_start: 0.8723 (tt0) cc_final: 0.8260 (mm-30) REVERT: C 334 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.7293 (t70) REVERT: C 347 ARG cc_start: 0.8317 (mmt180) cc_final: 0.8040 (mmt180) REVERT: C 538 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8639 (tp30) REVERT: C 541 GLU cc_start: 0.8638 (tt0) cc_final: 0.8333 (tp30) REVERT: C 542 ILE cc_start: 0.8418 (mt) cc_final: 0.7995 (mp) REVERT: C 586 MET cc_start: 0.7505 (tpt) cc_final: 0.7016 (tpp) REVERT: C 635 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8028 (mtmm) REVERT: C 745 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7663 (mmt180) REVERT: C 775 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8294 (mm) REVERT: C 811 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8785 (mp0) REVERT: C 832 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7158 (p0) REVERT: C 863 GLU cc_start: 0.9114 (mt-10) cc_final: 0.7959 (tm-30) REVERT: C 947 LYS cc_start: 0.7227 (mptt) cc_final: 0.6757 (tppt) REVERT: C 955 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8328 (mtmm) REVERT: C 967 VAL cc_start: 0.8743 (t) cc_final: 0.8458 (m) REVERT: J 9 LYS cc_start: 0.7903 (mmpt) cc_final: 0.7645 (mmpt) REVERT: O 221 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7781 (t80) REVERT: O 256 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8081 (mtp85) REVERT: O 343 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8951 (m) REVERT: O 404 CYS cc_start: 0.7638 (p) cc_final: 0.7365 (p) REVERT: Q 102 GLU cc_start: 0.5164 (mp0) cc_final: 0.4671 (mm-30) REVERT: Q 252 ARG cc_start: 0.6266 (mmt90) cc_final: 0.5964 (mtt90) REVERT: R 106 THR cc_start: 0.8269 (p) cc_final: 0.7760 (t) REVERT: R 110 ASP cc_start: 0.7902 (p0) cc_final: 0.6714 (m-30) REVERT: S 127 TRP cc_start: 0.6710 (p-90) cc_final: 0.6085 (p-90) REVERT: T 92 ILE cc_start: 0.8364 (mm) cc_final: 0.8079 (mm) REVERT: Z 390 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.7880 (m-70) REVERT: c 217 ILE cc_start: 0.6623 (mm) cc_final: 0.6381 (mm) REVERT: d 235 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6360 (tp) REVERT: I 174 LYS cc_start: 0.8209 (mttp) cc_final: 0.8006 (ttmt) REVERT: I 200 ASN cc_start: 0.9281 (t0) cc_final: 0.8479 (t0) REVERT: v 687 LEU cc_start: 0.1445 (OUTLIER) cc_final: 0.1099 (tt) REVERT: n 231 LYS cc_start: 0.7185 (mttm) cc_final: 0.6890 (mttt) REVERT: o 1 MET cc_start: -0.0209 (mmm) cc_final: -0.2116 (mpp) REVERT: o 81 LEU cc_start: 0.2909 (mt) cc_final: 0.2133 (tt) REVERT: r 26 SER cc_start: 0.1754 (OUTLIER) cc_final: 0.1495 (m) REVERT: k 30 TYR cc_start: 0.7338 (m-80) cc_final: 0.6553 (m-10) REVERT: k 51 GLU cc_start: 0.3067 (mm-30) cc_final: 0.1505 (tm-30) REVERT: i 50 MET cc_start: 0.3020 (tpp) cc_final: 0.2753 (tpp) REVERT: i 83 LYS cc_start: 0.6298 (tttt) cc_final: 0.5666 (pttt) REVERT: i 90 ILE cc_start: 0.4291 (OUTLIER) cc_final: 0.4043 (mm) REVERT: h 16 LYS cc_start: 0.8091 (pttt) cc_final: 0.7713 (tttm) REVERT: h 41 THR cc_start: 0.5770 (p) cc_final: 0.5566 (t) REVERT: j 20 ASN cc_start: 0.7207 (t0) cc_final: 0.5380 (m110) REVERT: j 69 ILE cc_start: 0.7528 (mm) cc_final: 0.6689 (mm) REVERT: l 15 GLN cc_start: 0.6961 (tm-30) cc_final: 0.5980 (tt0) REVERT: l 63 PHE cc_start: 0.7247 (t80) cc_final: 0.7043 (t80) REVERT: l 70 LYS cc_start: 0.5758 (ttpt) cc_final: 0.4395 (ptmt) REVERT: g 61 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.4048 (t80) REVERT: F 35 MET cc_start: 0.0686 (mtp) cc_final: 0.0480 (mtp) REVERT: G 10 MET cc_start: 0.0190 (ttm) cc_final: -0.0917 (mtm) REVERT: f 114 ASN cc_start: 0.4303 (t0) cc_final: 0.4031 (t0) REVERT: f 184 MET cc_start: 0.6070 (mmm) cc_final: 0.5471 (mmm) REVERT: f 247 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.5211 (t-90) outliers start: 336 outliers final: 200 residues processed: 1131 average time/residue: 0.6825 time to fit residues: 1369.5479 Evaluate side-chains 970 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 751 time to evaluate : 5.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1529 ASN Chi-restraints excluded: chain A residue 1530 SER Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1961 LEU Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 256 ARG Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 328 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 346 GLU Chi-restraints excluded: chain O residue 355 THR Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain O residue 405 SER Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 79 ASN Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 149 MET Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 81 HIS Chi-restraints excluded: chain Q residue 211 ASP Chi-restraints excluded: chain Q residue 223 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 289 PHE Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 169 ASP Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 295 ILE Chi-restraints excluded: chain Z residue 351 ILE Chi-restraints excluded: chain Z residue 384 LEU Chi-restraints excluded: chain Z residue 390 HIS Chi-restraints excluded: chain Z residue 444 LYS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 517 VAL Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 235 LEU Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain v residue 577 VAL Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 641 PRO Chi-restraints excluded: chain v residue 649 GLU Chi-restraints excluded: chain v residue 687 LEU Chi-restraints excluded: chain v residue 706 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 258 THR Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 295 SER Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 27 LEU Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 46 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 101 THR Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 108 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain h residue 76 ASN Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 99 ASP Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 176 ILE Chi-restraints excluded: chain f residue 247 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 795 optimal weight: 20.0000 chunk 605 optimal weight: 9.9990 chunk 417 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 chunk 540 optimal weight: 20.0000 chunk 808 optimal weight: 8.9990 chunk 855 optimal weight: 40.0000 chunk 422 optimal weight: 0.0040 chunk 765 optimal weight: 20.0000 chunk 230 optimal weight: 0.6980 overall best weight: 2.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 977 ASN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1856 ASN A2054 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 209 ASN R 92 HIS ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 166 HIS T 46 ASN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 131 HIS Z 223 HIS ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN I 204 ASN l 17 HIS ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 HIS U 41 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 78599 Z= 0.245 Angle : 0.698 14.070 108122 Z= 0.357 Chirality : 0.044 0.308 12968 Planarity : 0.005 0.091 12497 Dihedral : 16.785 171.326 15693 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.70 % Favored : 93.00 % Rotamer: Outliers : 4.24 % Allowed : 16.03 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.09), residues: 8400 helix: 0.48 (0.09), residues: 3484 sheet: -1.40 (0.14), residues: 1272 loop : -1.96 (0.10), residues: 3644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP Q 217 HIS 0.010 0.001 HIS A1431 PHE 0.019 0.002 PHE A 506 TYR 0.025 0.002 TYR H 80 ARG 0.007 0.001 ARG d 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 861 time to evaluate : 5.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping revert: symmetry clash REVERT: A 177 GLU cc_start: 0.9135 (pt0) cc_final: 0.8506 (tt0) REVERT: A 210 GLU cc_start: 0.7408 (tt0) cc_final: 0.7003 (tm-30) REVERT: A 235 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7452 (ptpt) REVERT: A 275 TYR cc_start: 0.8738 (m-80) cc_final: 0.8341 (m-80) REVERT: A 304 ASP cc_start: 0.7600 (t0) cc_final: 0.7262 (t0) REVERT: A 308 MET cc_start: 0.7909 (tpt) cc_final: 0.7448 (tpt) REVERT: A 458 PHE cc_start: 0.8130 (t80) cc_final: 0.7185 (t80) REVERT: A 497 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: A 581 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 769 MET cc_start: 0.8719 (mmm) cc_final: 0.7835 (ttm) REVERT: A 775 ARG cc_start: 0.7225 (ttm170) cc_final: 0.6562 (tmm160) REVERT: A 788 GLU cc_start: 0.8699 (tp30) cc_final: 0.7499 (tm-30) REVERT: A 1001 TYR cc_start: 0.8350 (t80) cc_final: 0.7495 (t80) REVERT: A 1056 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: A 1183 THR cc_start: 0.7413 (OUTLIER) cc_final: 0.7049 (t) REVERT: A 1217 ARG cc_start: 0.8485 (mmt-90) cc_final: 0.7411 (ttp-170) REVERT: A 1244 GLU cc_start: 0.9018 (mp0) cc_final: 0.8702 (tm-30) REVERT: A 1422 ILE cc_start: 0.8492 (pp) cc_final: 0.8167 (mp) REVERT: A 1455 GLN cc_start: 0.9152 (tt0) cc_final: 0.8817 (tm-30) REVERT: A 1499 ARG cc_start: 0.8091 (ptt180) cc_final: 0.6493 (tpt-90) REVERT: A 1521 ARG cc_start: 0.8531 (ptp90) cc_final: 0.8047 (mmt180) REVERT: A 1586 GLN cc_start: 0.1889 (OUTLIER) cc_final: 0.1191 (mp10) REVERT: A 1659 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8267 (mm-30) REVERT: A 1774 MET cc_start: 0.7103 (ttt) cc_final: 0.6872 (ttt) REVERT: A 1946 VAL cc_start: 0.9000 (t) cc_final: 0.8778 (m) REVERT: A 2024 MET cc_start: 0.7295 (mmt) cc_final: 0.6822 (ppp) REVERT: C 126 MET cc_start: 0.7801 (mmt) cc_final: 0.7595 (tpp) REVERT: C 150 MET cc_start: 0.7881 (tpp) cc_final: 0.7477 (mtt) REVERT: C 208 ARG cc_start: 0.7335 (mtt180) cc_final: 0.7099 (mtt90) REVERT: C 229 LEU cc_start: 0.7865 (tp) cc_final: 0.7571 (tp) REVERT: C 243 GLU cc_start: 0.8599 (tt0) cc_final: 0.8072 (mm-30) REVERT: C 334 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.7207 (t70) REVERT: C 347 ARG cc_start: 0.8339 (mmt180) cc_final: 0.8046 (mmm160) REVERT: C 538 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8501 (tp30) REVERT: C 541 GLU cc_start: 0.8593 (tt0) cc_final: 0.8343 (tp30) REVERT: C 542 ILE cc_start: 0.8493 (mt) cc_final: 0.8056 (mp) REVERT: C 586 MET cc_start: 0.7503 (tpt) cc_final: 0.7008 (tpp) REVERT: C 635 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8033 (mtmm) REVERT: C 649 GLU cc_start: 0.9139 (mp0) cc_final: 0.8276 (mt-10) REVERT: C 741 MET cc_start: 0.4354 (mmm) cc_final: 0.3536 (ppp) REVERT: C 745 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7642 (mmt180) REVERT: C 811 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8731 (mp0) REVERT: C 832 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7243 (p0) REVERT: C 931 TYR cc_start: 0.8778 (p90) cc_final: 0.8069 (p90) REVERT: C 947 LYS cc_start: 0.7441 (mptt) cc_final: 0.6921 (tppt) REVERT: C 955 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8290 (mtmm) REVERT: O 131 LEU cc_start: 0.8494 (tp) cc_final: 0.8227 (tp) REVERT: O 221 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8034 (t80) REVERT: O 343 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8964 (m) REVERT: O 404 CYS cc_start: 0.7647 (p) cc_final: 0.7354 (p) REVERT: O 426 TRP cc_start: 0.8431 (m100) cc_final: 0.7974 (m100) REVERT: R 106 THR cc_start: 0.8387 (p) cc_final: 0.7720 (t) REVERT: R 109 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8209 (pp) REVERT: R 110 ASP cc_start: 0.7738 (p0) cc_final: 0.6525 (m-30) REVERT: S 127 TRP cc_start: 0.6937 (p-90) cc_final: 0.6216 (p-90) REVERT: S 175 ARG cc_start: 0.6406 (mtm180) cc_final: 0.5746 (mmm160) REVERT: T 92 ILE cc_start: 0.8321 (mm) cc_final: 0.8031 (mm) REVERT: Z 390 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7612 (m-70) REVERT: c 217 ILE cc_start: 0.6450 (mm) cc_final: 0.6233 (mm) REVERT: v 687 LEU cc_start: 0.1873 (OUTLIER) cc_final: 0.1437 (tt) REVERT: o 1 MET cc_start: -0.0241 (mmm) cc_final: -0.1469 (mpp) REVERT: o 81 LEU cc_start: 0.3012 (mt) cc_final: 0.2245 (tt) REVERT: q 10 PRO cc_start: 0.0283 (Cg_endo) cc_final: -0.0021 (Cg_exo) REVERT: r 26 SER cc_start: 0.1758 (p) cc_final: 0.1541 (m) REVERT: k 41 MET cc_start: 0.6897 (mtt) cc_final: 0.6568 (mtm) REVERT: k 51 GLU cc_start: 0.3457 (mm-30) cc_final: 0.1890 (tm-30) REVERT: i 83 LYS cc_start: 0.6233 (tttt) cc_final: 0.5646 (pttt) REVERT: i 89 LEU cc_start: 0.4568 (mp) cc_final: 0.4225 (mp) REVERT: i 90 ILE cc_start: 0.4563 (OUTLIER) cc_final: 0.4203 (mm) REVERT: h 16 LYS cc_start: 0.8244 (pttt) cc_final: 0.7704 (tttm) REVERT: j 19 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7035 (mt) REVERT: j 20 ASN cc_start: 0.7412 (t0) cc_final: 0.5407 (m110) REVERT: j 69 ILE cc_start: 0.7503 (mm) cc_final: 0.6537 (mm) REVERT: l 15 GLN cc_start: 0.6647 (tm-30) cc_final: 0.5906 (tt0) REVERT: l 22 GLU cc_start: 0.4972 (mp0) cc_final: 0.4181 (mp0) REVERT: l 32 LYS cc_start: 0.3516 (tmtt) cc_final: 0.3093 (ttpt) REVERT: l 41 ASN cc_start: 0.6590 (m-40) cc_final: 0.6324 (m-40) REVERT: g 61 PHE cc_start: 0.4975 (OUTLIER) cc_final: 0.4520 (t80) REVERT: G 10 MET cc_start: 0.0037 (ttm) cc_final: -0.1086 (mtm) REVERT: K 44 MET cc_start: 0.2696 (mmm) cc_final: 0.2390 (mmm) REVERT: f 184 MET cc_start: 0.5446 (mmm) cc_final: 0.5092 (mmm) REVERT: f 247 HIS cc_start: 0.6498 (OUTLIER) cc_final: 0.4918 (t-90) outliers start: 300 outliers final: 204 residues processed: 1081 average time/residue: 0.6804 time to fit residues: 1307.4577 Evaluate side-chains 986 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 765 time to evaluate : 5.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1940 MET Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain A residue 2054 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 346 GLU Chi-restraints excluded: chain O residue 355 THR Chi-restraints excluded: chain O residue 377 ASP Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain O residue 393 VAL Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 81 HIS Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 289 PHE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 169 ASP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 239 GLN Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 150 CYS Chi-restraints excluded: chain Z residue 19 GLU Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 200 ILE Chi-restraints excluded: chain Z residue 281 TYR Chi-restraints excluded: chain Z residue 295 ILE Chi-restraints excluded: chain Z residue 390 HIS Chi-restraints excluded: chain Z residue 481 LEU Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 218 VAL Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 59 LYS Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 641 PRO Chi-restraints excluded: chain v residue 649 GLU Chi-restraints excluded: chain v residue 687 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 258 THR Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 286 VAL Chi-restraints excluded: chain n residue 295 SER Chi-restraints excluded: chain n residue 306 SER Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 27 LEU Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 137 LEU Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 20 LEU Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 47 ASP Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain h residue 76 ASN Chi-restraints excluded: chain j residue 19 ILE Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 69 ILE Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain g residue 99 ASP Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 236 LEU Chi-restraints excluded: chain f residue 247 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 712 optimal weight: 6.9990 chunk 485 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 636 optimal weight: 20.0000 chunk 352 optimal weight: 6.9990 chunk 729 optimal weight: 7.9990 chunk 591 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 436 optimal weight: 0.7980 chunk 767 optimal weight: 0.1980 chunk 215 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 636 HIS A 648 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN A1087 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2054 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 683 ASN C 830 ASN ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN P 37 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 46 ASN T 112 ASN T 128 GLN ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 24 GLN ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 HIS ** f 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5478 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 78599 Z= 0.184 Angle : 0.643 13.053 108122 Z= 0.327 Chirality : 0.042 0.307 12968 Planarity : 0.004 0.064 12497 Dihedral : 16.547 175.140 15691 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.71 % Favored : 93.00 % Rotamer: Outliers : 4.11 % Allowed : 17.08 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.09), residues: 8400 helix: 0.91 (0.09), residues: 3498 sheet: -1.22 (0.14), residues: 1296 loop : -1.77 (0.10), residues: 3606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP Q 217 HIS 0.010 0.001 HIS A1431 PHE 0.028 0.001 PHE i 20 TYR 0.025 0.001 TYR O 376 ARG 0.005 0.000 ARG l 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 885 time to evaluate : 5.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 196 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7436 (tt) REVERT: A 179 MET cc_start: 0.8007 (mtm) cc_final: 0.7702 (mtm) REVERT: A 210 GLU cc_start: 0.7362 (tt0) cc_final: 0.6974 (tm-30) REVERT: A 275 TYR cc_start: 0.8702 (m-80) cc_final: 0.8334 (m-80) REVERT: A 289 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6675 (m-30) REVERT: A 304 ASP cc_start: 0.7550 (t0) cc_final: 0.7158 (t0) REVERT: A 458 PHE cc_start: 0.8144 (t80) cc_final: 0.7388 (t80) REVERT: A 551 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 581 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7532 (mp) REVERT: A 625 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7072 (tt) REVERT: A 769 MET cc_start: 0.8679 (mmm) cc_final: 0.7809 (mtp) REVERT: A 775 ARG cc_start: 0.7147 (ttm170) cc_final: 0.6335 (tmm160) REVERT: A 788 GLU cc_start: 0.8588 (tp30) cc_final: 0.7647 (tm-30) REVERT: A 848 ASN cc_start: 0.8679 (t0) cc_final: 0.8335 (m-40) REVERT: A 988 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7788 (mt-10) REVERT: A 992 ASP cc_start: 0.8577 (m-30) cc_final: 0.8095 (m-30) REVERT: A 1056 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8029 (pt0) REVERT: A 1095 MET cc_start: 0.9122 (mtt) cc_final: 0.8894 (mtm) REVERT: A 1145 MET cc_start: 0.8961 (mmp) cc_final: 0.8684 (mmm) REVERT: A 1217 ARG cc_start: 0.8446 (mmt-90) cc_final: 0.7347 (ttp-170) REVERT: A 1244 GLU cc_start: 0.9109 (mp0) cc_final: 0.8843 (pp20) REVERT: A 1383 PHE cc_start: 0.9165 (m-80) cc_final: 0.8602 (m-10) REVERT: A 1422 ILE cc_start: 0.8414 (pp) cc_final: 0.7981 (mp) REVERT: A 1424 HIS cc_start: 0.8970 (m-70) cc_final: 0.8326 (m-70) REVERT: A 1429 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: A 1451 PHE cc_start: 0.8106 (m-80) cc_final: 0.7802 (m-80) REVERT: A 1455 GLN cc_start: 0.9177 (tt0) cc_final: 0.8827 (tm-30) REVERT: A 1499 ARG cc_start: 0.8022 (ptt180) cc_final: 0.6345 (tpt-90) REVERT: A 1521 ARG cc_start: 0.8516 (ptp90) cc_final: 0.8046 (mmt180) REVERT: A 1659 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8243 (mm-30) REVERT: A 1682 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7422 (p) REVERT: A 1927 GLU cc_start: 0.8233 (tm-30) cc_final: 0.8012 (pt0) REVERT: A 2024 MET cc_start: 0.7250 (mmt) cc_final: 0.6769 (ppp) REVERT: C 78 MET cc_start: 0.6614 (mmm) cc_final: 0.6356 (mmm) REVERT: C 126 MET cc_start: 0.7860 (mmt) cc_final: 0.7601 (tpp) REVERT: C 208 ARG cc_start: 0.7344 (mtt180) cc_final: 0.7107 (mtt90) REVERT: C 243 GLU cc_start: 0.8630 (tt0) cc_final: 0.8177 (mm-30) REVERT: C 334 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7286 (t70) REVERT: C 347 ARG cc_start: 0.8339 (mmt180) cc_final: 0.8069 (mmm160) REVERT: C 538 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8469 (tp30) REVERT: C 542 ILE cc_start: 0.8433 (mt) cc_final: 0.8162 (mp) REVERT: C 586 MET cc_start: 0.7517 (tpt) cc_final: 0.6992 (tpp) REVERT: C 635 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8047 (mtmm) REVERT: C 649 GLU cc_start: 0.9190 (mp0) cc_final: 0.8342 (mt-10) REVERT: C 741 MET cc_start: 0.4117 (mmm) cc_final: 0.3512 (ppp) REVERT: C 745 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7657 (mmt180) REVERT: C 775 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8272 (mm) REVERT: C 832 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7092 (p0) REVERT: C 931 TYR cc_start: 0.8733 (p90) cc_final: 0.8053 (p90) REVERT: C 947 LYS cc_start: 0.7446 (mptt) cc_final: 0.6922 (tppt) REVERT: C 955 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8275 (mtmm) REVERT: J 9 LYS cc_start: 0.8069 (mmpt) cc_final: 0.7764 (mmtt) REVERT: O 221 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.8049 (t80) REVERT: O 343 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8981 (m) REVERT: O 404 CYS cc_start: 0.7456 (p) cc_final: 0.7139 (p) REVERT: R 110 ASP cc_start: 0.7480 (p0) cc_final: 0.6379 (m-30) REVERT: S 127 TRP cc_start: 0.6916 (p-90) cc_final: 0.6271 (p-90) REVERT: S 175 ARG cc_start: 0.6196 (mtm180) cc_final: 0.5861 (mmm160) REVERT: Z 390 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7525 (m-70) REVERT: I 205 GLU cc_start: 0.6536 (pp20) cc_final: 0.5933 (tm-30) REVERT: v 687 LEU cc_start: 0.2180 (OUTLIER) cc_final: 0.1882 (tt) REVERT: n 184 ASP cc_start: 0.3940 (p0) cc_final: 0.3480 (p0) REVERT: o 1 MET cc_start: -0.0117 (mmm) cc_final: -0.1285 (mpp) REVERT: o 81 LEU cc_start: 0.3314 (mt) cc_final: 0.2541 (tt) REVERT: q 10 PRO cc_start: 0.0399 (Cg_endo) cc_final: 0.0052 (Cg_exo) REVERT: r 26 SER cc_start: 0.2021 (p) cc_final: 0.1769 (m) REVERT: k 51 GLU cc_start: 0.3573 (mm-30) cc_final: 0.2486 (tm-30) REVERT: i 83 LYS cc_start: 0.6087 (tttt) cc_final: 0.5442 (pttt) REVERT: i 90 ILE cc_start: 0.4578 (OUTLIER) cc_final: 0.4339 (mm) REVERT: h 16 LYS cc_start: 0.7919 (pttt) cc_final: 0.7440 (tttm) REVERT: h 77 ASN cc_start: 0.3166 (m110) cc_final: 0.2910 (m-40) REVERT: j 19 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7096 (mt) REVERT: j 20 ASN cc_start: 0.7154 (t0) cc_final: 0.5503 (m110) REVERT: j 69 ILE cc_start: 0.7487 (mm) cc_final: 0.6445 (mm) REVERT: l 15 GLN cc_start: 0.6298 (tm-30) cc_final: 0.5632 (tt0) REVERT: l 32 LYS cc_start: 0.3746 (tmtt) cc_final: 0.3458 (ttpt) REVERT: l 71 PHE cc_start: 0.7602 (p90) cc_final: 0.7335 (p90) REVERT: g 61 PHE cc_start: 0.4892 (OUTLIER) cc_final: 0.4317 (t80) REVERT: F 15 LEU cc_start: 0.2183 (OUTLIER) cc_final: 0.1101 (mp) REVERT: G 10 MET cc_start: -0.0276 (ttm) cc_final: -0.1252 (mtm) REVERT: K 44 MET cc_start: 0.2725 (mmm) cc_final: 0.2474 (mmm) REVERT: U 40 MET cc_start: 0.1222 (ppp) cc_final: 0.0275 (ttm) REVERT: f 184 MET cc_start: 0.5682 (mmm) cc_final: 0.5209 (mmm) REVERT: f 247 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.4792 (t-90) outliers start: 292 outliers final: 185 residues processed: 1099 average time/residue: 0.6781 time to fit residues: 1326.2270 Evaluate side-chains 991 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 787 time to evaluate : 5.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 688 TYR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1429 MET Chi-restraints excluded: chain A residue 1529 ASN Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1940 MET Chi-restraints excluded: chain A residue 1961 LEU Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 830 ASN Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 346 GLU Chi-restraints excluded: chain O residue 355 THR Chi-restraints excluded: chain O residue 377 ASP Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain O residue 393 VAL Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 81 HIS Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 289 PHE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 135 LYS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 239 GLN Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain Z residue 19 GLU Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 390 HIS Chi-restraints excluded: chain Z residue 481 LEU Chi-restraints excluded: chain c residue 16 VAL Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 218 VAL Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 59 LYS Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 641 PRO Chi-restraints excluded: chain v residue 649 GLU Chi-restraints excluded: chain v residue 684 ILE Chi-restraints excluded: chain v residue 687 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 295 SER Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 196 PRO Chi-restraints excluded: chain q residue 233 THR Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 137 LEU Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain h residue 76 ASN Chi-restraints excluded: chain j residue 19 ILE Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 69 ILE Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain g residue 99 ASP Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 143 LEU Chi-restraints excluded: chain f residue 149 GLN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 247 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 287 optimal weight: 9.9990 chunk 770 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 502 optimal weight: 0.6980 chunk 211 optimal weight: 0.9990 chunk 856 optimal weight: 0.0020 chunk 710 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 449 optimal weight: 20.0000 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 GLN A1086 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1254 ASN ** A1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN C 407 ASN C 830 ASN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN P 37 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 46 ASN T 57 HIS ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 HIS K 20 ASN U 61 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5508 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 78599 Z= 0.214 Angle : 0.653 13.810 108122 Z= 0.331 Chirality : 0.042 0.563 12968 Planarity : 0.004 0.065 12497 Dihedral : 16.466 176.615 15690 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.81 % Favored : 92.90 % Rotamer: Outliers : 4.63 % Allowed : 17.45 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.09), residues: 8400 helix: 1.03 (0.09), residues: 3506 sheet: -1.13 (0.14), residues: 1297 loop : -1.74 (0.10), residues: 3597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP Q 217 HIS 0.009 0.001 HIS A1431 PHE 0.046 0.002 PHE C 364 TYR 0.025 0.002 TYR O 384 ARG 0.008 0.000 ARG A 749 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 830 time to evaluate : 6.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 196 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7602 (tt) REVERT: A 177 GLU cc_start: 0.8879 (pt0) cc_final: 0.8592 (tt0) REVERT: A 210 GLU cc_start: 0.7476 (tt0) cc_final: 0.7072 (tm-30) REVERT: A 275 TYR cc_start: 0.8736 (m-80) cc_final: 0.8357 (m-80) REVERT: A 289 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6678 (m-30) REVERT: A 304 ASP cc_start: 0.7527 (t0) cc_final: 0.7227 (t0) REVERT: A 308 MET cc_start: 0.7967 (tpp) cc_final: 0.7228 (tpt) REVERT: A 405 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8279 (m110) REVERT: A 458 PHE cc_start: 0.8168 (t80) cc_final: 0.7473 (t80) REVERT: A 551 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 581 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7638 (mp) REVERT: A 769 MET cc_start: 0.8624 (mmm) cc_final: 0.7843 (mtp) REVERT: A 775 ARG cc_start: 0.7138 (ttm170) cc_final: 0.6340 (tmm160) REVERT: A 788 GLU cc_start: 0.8576 (tp30) cc_final: 0.7660 (tm-30) REVERT: A 992 ASP cc_start: 0.8596 (m-30) cc_final: 0.8113 (m-30) REVERT: A 997 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8819 (mm-40) REVERT: A 1056 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8075 (pt0) REVERT: A 1145 MET cc_start: 0.9037 (mmp) cc_final: 0.8679 (mmm) REVERT: A 1217 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.7429 (ttp-170) REVERT: A 1244 GLU cc_start: 0.9118 (mp0) cc_final: 0.8852 (pp20) REVERT: A 1307 GLU cc_start: 0.8986 (mp0) cc_final: 0.8737 (mp0) REVERT: A 1424 HIS cc_start: 0.8778 (m-70) cc_final: 0.8303 (m170) REVERT: A 1429 MET cc_start: 0.8356 (mtm) cc_final: 0.8023 (mtm) REVERT: A 1440 ILE cc_start: 0.8848 (mt) cc_final: 0.8637 (tp) REVERT: A 1455 GLN cc_start: 0.9189 (tt0) cc_final: 0.8834 (tm-30) REVERT: A 1499 ARG cc_start: 0.8021 (ptt180) cc_final: 0.6345 (tpt-90) REVERT: A 1521 ARG cc_start: 0.8554 (ptp90) cc_final: 0.8081 (mmt180) REVERT: A 1529 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7609 (m-40) REVERT: A 1659 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8256 (mm-30) REVERT: A 2024 MET cc_start: 0.7276 (mmt) cc_final: 0.6788 (ppp) REVERT: C 126 MET cc_start: 0.8025 (mmt) cc_final: 0.7811 (tpp) REVERT: C 208 ARG cc_start: 0.7303 (mtt180) cc_final: 0.7069 (mtt90) REVERT: C 243 GLU cc_start: 0.8562 (tt0) cc_final: 0.8169 (mm-30) REVERT: C 334 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7162 (t70) REVERT: C 586 MET cc_start: 0.7616 (tpt) cc_final: 0.7187 (tpp) REVERT: C 635 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8037 (mtmm) REVERT: C 649 GLU cc_start: 0.9157 (mp0) cc_final: 0.8329 (mt-10) REVERT: C 745 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7484 (tpp-160) REVERT: C 775 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8301 (mm) REVERT: C 800 TYR cc_start: 0.8582 (m-10) cc_final: 0.8293 (m-10) REVERT: C 832 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7058 (p0) REVERT: C 931 TYR cc_start: 0.8750 (p90) cc_final: 0.8094 (p90) REVERT: C 947 LYS cc_start: 0.7450 (mptt) cc_final: 0.6924 (tppt) REVERT: C 955 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8259 (mtmm) REVERT: O 221 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8091 (t80) REVERT: O 343 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8951 (m) REVERT: O 404 CYS cc_start: 0.7673 (p) cc_final: 0.7315 (p) REVERT: O 426 TRP cc_start: 0.8310 (m100) cc_final: 0.7898 (m100) REVERT: R 110 ASP cc_start: 0.7584 (p0) cc_final: 0.6619 (m-30) REVERT: S 175 ARG cc_start: 0.6289 (mtm180) cc_final: 0.5854 (mmm160) REVERT: Z 34 MET cc_start: 0.4531 (mtt) cc_final: 0.4079 (ttt) REVERT: Z 390 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7503 (m-70) REVERT: d 187 GLU cc_start: 0.6124 (tm-30) cc_final: 0.5874 (tm-30) REVERT: I 205 GLU cc_start: 0.6562 (pp20) cc_final: 0.5940 (tm-30) REVERT: v 687 LEU cc_start: 0.2283 (OUTLIER) cc_final: 0.2020 (tt) REVERT: n 184 ASP cc_start: 0.4140 (p0) cc_final: 0.3653 (p0) REVERT: o 1 MET cc_start: 0.0034 (mmm) cc_final: -0.1114 (mpp) REVERT: o 81 LEU cc_start: 0.3659 (mt) cc_final: 0.2914 (tt) REVERT: p 1 MET cc_start: 0.2402 (mmt) cc_final: 0.1721 (mtt) REVERT: q 10 PRO cc_start: 0.0472 (Cg_endo) cc_final: 0.0134 (Cg_exo) REVERT: k 33 GLN cc_start: 0.6497 (tt0) cc_final: 0.6176 (tp40) REVERT: k 41 MET cc_start: 0.6940 (mtt) cc_final: 0.6602 (mtm) REVERT: i 83 LYS cc_start: 0.6194 (tttt) cc_final: 0.5570 (pttt) REVERT: h 16 LYS cc_start: 0.7997 (pttt) cc_final: 0.7498 (tttm) REVERT: h 77 ASN cc_start: 0.3310 (m110) cc_final: 0.3099 (m-40) REVERT: j 19 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7074 (mt) REVERT: j 20 ASN cc_start: 0.7107 (t0) cc_final: 0.5648 (m110) REVERT: j 57 LEU cc_start: 0.4723 (OUTLIER) cc_final: 0.3444 (tt) REVERT: j 69 ILE cc_start: 0.7584 (mm) cc_final: 0.6550 (mm) REVERT: l 15 GLN cc_start: 0.6589 (tm-30) cc_final: 0.5978 (tt0) REVERT: l 22 GLU cc_start: 0.5248 (mp0) cc_final: 0.4291 (mp0) REVERT: g 61 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.4463 (t80) REVERT: F 15 LEU cc_start: 0.2242 (OUTLIER) cc_final: 0.1134 (mp) REVERT: G 10 MET cc_start: -0.0389 (ttm) cc_final: -0.1108 (mtm) REVERT: K 44 MET cc_start: 0.2201 (mmm) cc_final: 0.1956 (mmm) REVERT: U 40 MET cc_start: 0.1196 (ppp) cc_final: 0.0323 (ttm) REVERT: f 184 MET cc_start: 0.5677 (mmm) cc_final: 0.5203 (mmm) REVERT: f 247 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.4732 (t70) outliers start: 323 outliers final: 228 residues processed: 1066 average time/residue: 0.6869 time to fit residues: 1310.9263 Evaluate side-chains 1022 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 775 time to evaluate : 5.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 688 TYR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1529 ASN Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1802 MET Chi-restraints excluded: chain A residue 1812 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1940 MET Chi-restraints excluded: chain A residue 1961 LEU Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain A residue 2002 TYR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 830 ASN Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 355 THR Chi-restraints excluded: chain O residue 377 ASP Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain O residue 393 VAL Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 81 HIS Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 289 PHE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 135 LYS Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 169 ASP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain Z residue 19 GLU Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 281 TYR Chi-restraints excluded: chain Z residue 390 HIS Chi-restraints excluded: chain Z residue 422 PHE Chi-restraints excluded: chain Z residue 481 LEU Chi-restraints excluded: chain c residue 16 VAL Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 218 VAL Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 59 LYS Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain v residue 577 VAL Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 641 PRO Chi-restraints excluded: chain v residue 649 GLU Chi-restraints excluded: chain v residue 684 ILE Chi-restraints excluded: chain v residue 687 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 258 THR Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 276 ASP Chi-restraints excluded: chain n residue 295 SER Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 196 PRO Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 3 CYS Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 101 THR Chi-restraints excluded: chain r residue 137 LEU Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 20 LEU Chi-restraints excluded: chain k residue 50 GLU Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain h residue 76 ASN Chi-restraints excluded: chain j residue 19 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 67 SER Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 99 ASP Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain W residue 52 HIS Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 143 LEU Chi-restraints excluded: chain f residue 149 GLN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 247 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 825 optimal weight: 50.0000 chunk 96 optimal weight: 7.9990 chunk 487 optimal weight: 6.9990 chunk 625 optimal weight: 6.9990 chunk 484 optimal weight: 6.9990 chunk 720 optimal weight: 6.9990 chunk 478 optimal weight: 9.9990 chunk 852 optimal weight: 50.0000 chunk 533 optimal weight: 40.0000 chunk 520 optimal weight: 4.9990 chunk 393 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 523 GLN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 588 GLN C 830 ASN C 869 HIS C 960 ASN ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN ** Q 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 GLN ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 57 HIS ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 143 ASN j 55 HIS ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS W 64 HIS ** f 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 190 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 78599 Z= 0.466 Angle : 0.874 17.990 108122 Z= 0.446 Chirality : 0.049 0.402 12968 Planarity : 0.006 0.072 12497 Dihedral : 16.815 177.627 15689 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.24 % Favored : 90.43 % Rotamer: Outliers : 5.37 % Allowed : 17.94 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.09), residues: 8400 helix: 0.21 (0.08), residues: 3540 sheet: -1.29 (0.15), residues: 1132 loop : -2.13 (0.10), residues: 3728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP n 69 HIS 0.013 0.002 HIS R 91 PHE 0.027 0.003 PHE A1756 TYR 0.028 0.003 TYR v 669 ARG 0.010 0.001 ARG H 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 748 time to evaluate : 5.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 196 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping revert: symmetry clash REVERT: A 149 MET cc_start: 0.5346 (pmm) cc_final: 0.4754 (pmm) REVERT: A 176 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7493 (tt) REVERT: A 177 GLU cc_start: 0.9050 (pt0) cc_final: 0.8579 (tt0) REVERT: A 210 GLU cc_start: 0.7430 (tt0) cc_final: 0.7035 (tm-30) REVERT: A 235 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7216 (ptpt) REVERT: A 275 TYR cc_start: 0.8806 (m-80) cc_final: 0.8382 (m-80) REVERT: A 289 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: A 304 ASP cc_start: 0.7473 (t0) cc_final: 0.7122 (t0) REVERT: A 547 LEU cc_start: 0.7451 (tp) cc_final: 0.7162 (tt) REVERT: A 551 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 581 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 769 MET cc_start: 0.8810 (mmm) cc_final: 0.8222 (ttp) REVERT: A 775 ARG cc_start: 0.7081 (ttm170) cc_final: 0.6362 (tmm160) REVERT: A 776 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5246 (pm20) REVERT: A 788 GLU cc_start: 0.8542 (tp30) cc_final: 0.8001 (tp30) REVERT: A 1020 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8457 (pt) REVERT: A 1056 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8142 (pt0) REVERT: A 1169 TYR cc_start: 0.8608 (m-80) cc_final: 0.8301 (m-10) REVERT: A 1217 ARG cc_start: 0.8443 (mmt-90) cc_final: 0.8091 (tpp80) REVERT: A 1307 GLU cc_start: 0.9106 (mp0) cc_final: 0.8843 (mp0) REVERT: A 1429 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: A 1455 GLN cc_start: 0.9309 (tt0) cc_final: 0.9041 (tm-30) REVERT: A 1499 ARG cc_start: 0.8388 (ptt180) cc_final: 0.6832 (tpt-90) REVERT: A 1521 ARG cc_start: 0.8656 (ptp90) cc_final: 0.8181 (mmt180) REVERT: A 1659 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8315 (mm-30) REVERT: A 1806 MET cc_start: 0.7835 (mmm) cc_final: 0.6969 (ppp) REVERT: A 1888 HIS cc_start: 0.5642 (OUTLIER) cc_final: 0.4673 (p90) REVERT: A 1946 VAL cc_start: 0.8950 (t) cc_final: 0.8569 (m) REVERT: A 2024 MET cc_start: 0.7435 (mmt) cc_final: 0.6836 (ppp) REVERT: C 208 ARG cc_start: 0.7293 (mtt180) cc_final: 0.6992 (mtt90) REVERT: C 243 GLU cc_start: 0.8657 (tt0) cc_final: 0.8196 (mm-30) REVERT: C 334 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7074 (t70) REVERT: C 347 ARG cc_start: 0.8465 (mmt180) cc_final: 0.8228 (mmm160) REVERT: C 538 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8271 (tp30) REVERT: C 586 MET cc_start: 0.7550 (tpt) cc_final: 0.7071 (tpp) REVERT: C 649 GLU cc_start: 0.9262 (mp0) cc_final: 0.8503 (mt-10) REVERT: C 655 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7967 (tt) REVERT: C 715 MET cc_start: 0.8415 (ttp) cc_final: 0.7852 (tmm) REVERT: C 745 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7476 (tpp-160) REVERT: C 775 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8369 (mm) REVERT: C 811 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8732 (mp0) REVERT: C 931 TYR cc_start: 0.8821 (p90) cc_final: 0.8064 (p90) REVERT: C 947 LYS cc_start: 0.7545 (mptt) cc_final: 0.6863 (tppt) REVERT: C 955 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8261 (mtmm) REVERT: O 221 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7866 (t80) REVERT: O 343 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8905 (m) REVERT: O 426 TRP cc_start: 0.8194 (m100) cc_final: 0.7749 (m100) REVERT: Q 53 ASN cc_start: 0.7937 (p0) cc_final: 0.7534 (t0) REVERT: Q 244 HIS cc_start: 0.6687 (m90) cc_final: 0.6109 (m90) REVERT: R 110 ASP cc_start: 0.8064 (p0) cc_final: 0.7022 (m-30) REVERT: S 175 ARG cc_start: 0.6171 (mtm180) cc_final: 0.5814 (mmm160) REVERT: Z 390 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7830 (m-70) REVERT: c 151 MET cc_start: 0.5399 (ptp) cc_final: 0.5184 (ptp) REVERT: I 156 ASP cc_start: 0.7191 (t0) cc_final: 0.6630 (t0) REVERT: v 687 LEU cc_start: 0.2498 (OUTLIER) cc_final: 0.1698 (tt) REVERT: o 1 MET cc_start: -0.0189 (mmm) cc_final: -0.1718 (mtm) REVERT: o 81 LEU cc_start: 0.3750 (mt) cc_final: 0.3001 (tt) REVERT: p 1 MET cc_start: 0.3691 (mmt) cc_final: 0.3334 (mtt) REVERT: q 10 PRO cc_start: 0.1202 (Cg_endo) cc_final: 0.0821 (Cg_exo) REVERT: q 140 SER cc_start: 0.1373 (OUTLIER) cc_final: 0.0999 (p) REVERT: k 21 ARG cc_start: 0.2358 (ttt180) cc_final: 0.1606 (mtt180) REVERT: k 76 LYS cc_start: 0.5317 (tttt) cc_final: 0.4959 (mmtm) REVERT: i 82 LEU cc_start: 0.3752 (tp) cc_final: 0.3427 (pt) REVERT: i 83 LYS cc_start: 0.6061 (tttt) cc_final: 0.5419 (pttt) REVERT: j 20 ASN cc_start: 0.7182 (t0) cc_final: 0.5883 (m110) REVERT: j 69 ILE cc_start: 0.7217 (mm) cc_final: 0.6027 (mm) REVERT: l 15 GLN cc_start: 0.7113 (tm-30) cc_final: 0.6518 (tt0) REVERT: l 29 TYR cc_start: 0.7128 (m-80) cc_final: 0.6856 (m-10) REVERT: m 6 PHE cc_start: 0.6572 (t80) cc_final: 0.6251 (t80) REVERT: g 61 PHE cc_start: 0.5399 (OUTLIER) cc_final: 0.4728 (t80) REVERT: g 73 LYS cc_start: 0.3499 (OUTLIER) cc_final: 0.3295 (ptpp) REVERT: G 10 MET cc_start: -0.0231 (ttm) cc_final: -0.0986 (mtm) REVERT: U 40 MET cc_start: 0.2170 (ppp) cc_final: 0.0719 (ttm) REVERT: V 20 LYS cc_start: -0.0713 (OUTLIER) cc_final: -0.4363 (pptt) REVERT: f 184 MET cc_start: 0.6000 (mmm) cc_final: 0.5470 (mmm) REVERT: f 247 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.5036 (t70) outliers start: 364 outliers final: 267 residues processed: 1024 average time/residue: 0.6857 time to fit residues: 1251.4405 Evaluate side-chains 980 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 692 time to evaluate : 6.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 MET Chi-restraints excluded: chain A residue 1529 ASN Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1645 LEU Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1802 MET Chi-restraints excluded: chain A residue 1812 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1888 HIS Chi-restraints excluded: chain A residue 1940 MET Chi-restraints excluded: chain A residue 1961 LEU Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain A residue 2002 TYR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 830 ASN Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain O residue 164 MET Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 265 HIS Chi-restraints excluded: chain O residue 328 THR Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 355 THR Chi-restraints excluded: chain O residue 377 ASP Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain O residue 393 VAL Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 79 ASN Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 81 HIS Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 289 PHE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 135 LYS Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 169 ASP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 150 CYS Chi-restraints excluded: chain Z residue 19 GLU Chi-restraints excluded: chain Z residue 116 ASN Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 281 TYR Chi-restraints excluded: chain Z residue 295 ILE Chi-restraints excluded: chain Z residue 390 HIS Chi-restraints excluded: chain Z residue 422 PHE Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 59 LYS Chi-restraints excluded: chain d residue 76 ILE Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 266 LEU Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain v residue 577 VAL Chi-restraints excluded: chain v residue 608 TYR Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 641 PRO Chi-restraints excluded: chain v residue 649 GLU Chi-restraints excluded: chain v residue 684 ILE Chi-restraints excluded: chain v residue 687 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 276 ASP Chi-restraints excluded: chain n residue 295 SER Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 27 LEU Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 21 THR Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 109 LEU Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 140 SER Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 196 PRO Chi-restraints excluded: chain q residue 233 THR Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 3 CYS Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 101 THR Chi-restraints excluded: chain r residue 134 SER Chi-restraints excluded: chain r residue 137 LEU Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 50 GLU Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 47 ASP Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain h residue 76 ASN Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 19 ILE Chi-restraints excluded: chain j residue 67 SER Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 107 LEU Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 73 LYS Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain W residue 52 HIS Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 143 LEU Chi-restraints excluded: chain f residue 149 GLN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 247 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 527 optimal weight: 20.0000 chunk 340 optimal weight: 0.9990 chunk 509 optimal weight: 0.7980 chunk 256 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 542 optimal weight: 30.0000 chunk 581 optimal weight: 20.0000 chunk 421 optimal weight: 30.0000 chunk 79 optimal weight: 0.2980 chunk 670 optimal weight: 30.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 ASN C 869 HIS C 923 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN Q 54 ASN ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 57 HIS ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 115 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 GLN g 64 HIS ** f 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 78599 Z= 0.180 Angle : 0.667 15.715 108122 Z= 0.337 Chirality : 0.042 0.345 12968 Planarity : 0.004 0.069 12497 Dihedral : 16.498 178.342 15680 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.07 % Favored : 93.64 % Rotamer: Outliers : 3.59 % Allowed : 20.20 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.09), residues: 8400 helix: 0.90 (0.09), residues: 3522 sheet: -1.10 (0.15), residues: 1155 loop : -1.91 (0.10), residues: 3723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP Q 217 HIS 0.010 0.001 HIS A1431 PHE 0.036 0.002 PHE d 250 TYR 0.024 0.001 TYR A 356 ARG 0.008 0.000 ARG l 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 816 time to evaluate : 6.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 196 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping revert: symmetry clash REVERT: A 149 MET cc_start: 0.4902 (pmm) cc_final: 0.4545 (pmm) REVERT: A 177 GLU cc_start: 0.8843 (pt0) cc_final: 0.8571 (tt0) REVERT: A 210 GLU cc_start: 0.7326 (tt0) cc_final: 0.6909 (tm-30) REVERT: A 275 TYR cc_start: 0.8767 (m-80) cc_final: 0.8360 (m-80) REVERT: A 289 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: A 304 ASP cc_start: 0.7266 (t0) cc_final: 0.6882 (t0) REVERT: A 334 LYS cc_start: 0.7977 (mttm) cc_final: 0.7559 (mttp) REVERT: A 458 PHE cc_start: 0.8178 (t80) cc_final: 0.7461 (t80) REVERT: A 581 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7462 (mp) REVERT: A 769 MET cc_start: 0.8798 (mmm) cc_final: 0.8077 (ttm) REVERT: A 775 ARG cc_start: 0.6902 (ttm170) cc_final: 0.6203 (tmm160) REVERT: A 776 GLN cc_start: 0.6208 (OUTLIER) cc_final: 0.5408 (tt0) REVERT: A 788 GLU cc_start: 0.8551 (tp30) cc_final: 0.7693 (tm-30) REVERT: A 1056 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: A 1217 ARG cc_start: 0.8473 (mmt-90) cc_final: 0.7473 (tpt-90) REVERT: A 1244 GLU cc_start: 0.8941 (mp0) cc_final: 0.8688 (tm-30) REVERT: A 1424 HIS cc_start: 0.8632 (m-70) cc_final: 0.8409 (m-70) REVERT: A 1455 GLN cc_start: 0.9179 (tt0) cc_final: 0.8867 (tm-30) REVERT: A 1499 ARG cc_start: 0.8007 (ptt180) cc_final: 0.6347 (tpt-90) REVERT: A 1521 ARG cc_start: 0.8644 (ptp90) cc_final: 0.8056 (mmt180) REVERT: A 1888 HIS cc_start: 0.5753 (OUTLIER) cc_final: 0.4848 (p90) REVERT: A 1946 VAL cc_start: 0.8951 (t) cc_final: 0.8691 (m) REVERT: A 2024 MET cc_start: 0.7430 (mmt) cc_final: 0.6853 (ppp) REVERT: C 126 MET cc_start: 0.8055 (tpp) cc_final: 0.7747 (tpp) REVERT: C 150 MET cc_start: 0.7942 (tpp) cc_final: 0.7642 (mtt) REVERT: C 208 ARG cc_start: 0.7283 (mtt180) cc_final: 0.7034 (mtt90) REVERT: C 243 GLU cc_start: 0.8538 (tt0) cc_final: 0.8041 (mm-30) REVERT: C 334 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7078 (t70) REVERT: C 347 ARG cc_start: 0.8362 (mmt180) cc_final: 0.7828 (mmm160) REVERT: C 538 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8271 (tp30) REVERT: C 586 MET cc_start: 0.7551 (tpt) cc_final: 0.7212 (tpp) REVERT: C 635 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8136 (mtmm) REVERT: C 715 MET cc_start: 0.8389 (ttp) cc_final: 0.8029 (tmm) REVERT: C 745 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7495 (tpp-160) REVERT: C 775 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8304 (mm) REVERT: C 811 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8655 (mp0) REVERT: C 931 TYR cc_start: 0.8709 (p90) cc_final: 0.8118 (p90) REVERT: C 947 LYS cc_start: 0.7519 (mptt) cc_final: 0.6928 (tppt) REVERT: C 955 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8278 (mtmm) REVERT: O 202 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6591 (mm-30) REVERT: O 221 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8083 (t80) REVERT: O 343 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8972 (m) REVERT: O 404 CYS cc_start: 0.7465 (p) cc_final: 0.7132 (p) REVERT: P 75 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7563 (mm110) REVERT: Q 53 ASN cc_start: 0.7865 (p0) cc_final: 0.7441 (t0) REVERT: R 110 ASP cc_start: 0.7541 (p0) cc_final: 0.6394 (m-30) REVERT: S 175 ARG cc_start: 0.6521 (mtm180) cc_final: 0.5955 (mmm160) REVERT: T 48 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7620 (mp10) REVERT: Z 34 MET cc_start: 0.4633 (mtt) cc_final: 0.4125 (ttt) REVERT: Z 199 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7824 (tm-30) REVERT: Z 390 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7420 (m-70) REVERT: c 90 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6667 (ttt) REVERT: I 205 GLU cc_start: 0.6815 (pp20) cc_final: 0.6247 (tm-30) REVERT: v 687 LEU cc_start: 0.2183 (OUTLIER) cc_final: 0.1946 (tp) REVERT: o 1 MET cc_start: -0.1050 (mmm) cc_final: -0.1253 (mtm) REVERT: o 81 LEU cc_start: 0.3353 (mt) cc_final: 0.2682 (tt) REVERT: p 1 MET cc_start: 0.3845 (mmt) cc_final: 0.3458 (mtt) REVERT: q 10 PRO cc_start: 0.0976 (Cg_endo) cc_final: 0.0666 (Cg_exo) REVERT: q 81 LEU cc_start: -0.2718 (tp) cc_final: -0.3265 (pp) REVERT: k 19 LYS cc_start: 0.7452 (tptm) cc_final: 0.7076 (mmtm) REVERT: k 21 ARG cc_start: 0.2560 (ttt180) cc_final: 0.1826 (mtt180) REVERT: k 30 TYR cc_start: 0.7014 (m-80) cc_final: 0.6777 (m-80) REVERT: k 33 GLN cc_start: 0.6242 (tt0) cc_final: 0.5949 (tt0) REVERT: k 41 MET cc_start: 0.6992 (mtt) cc_final: 0.6686 (mtt) REVERT: k 76 LYS cc_start: 0.5152 (tttt) cc_final: 0.4704 (mmtm) REVERT: i 83 LYS cc_start: 0.6104 (tttt) cc_final: 0.5512 (pttt) REVERT: h 77 ASN cc_start: 0.2900 (m-40) cc_final: 0.1910 (t0) REVERT: j 20 ASN cc_start: 0.7353 (t0) cc_final: 0.6053 (m110) REVERT: j 69 ILE cc_start: 0.7196 (mm) cc_final: 0.5972 (mm) REVERT: l 15 GLN cc_start: 0.6916 (tm-30) cc_final: 0.6508 (tt0) REVERT: l 71 PHE cc_start: 0.6890 (p90) cc_final: 0.6500 (p90) REVERT: m 6 PHE cc_start: 0.6748 (t80) cc_final: 0.6393 (t80) REVERT: g 61 PHE cc_start: 0.5651 (OUTLIER) cc_final: 0.5110 (t80) REVERT: g 99 ASP cc_start: 0.2360 (p0) cc_final: 0.0982 (p0) REVERT: G 10 MET cc_start: -0.0219 (ttm) cc_final: -0.0626 (mtm) REVERT: K 44 MET cc_start: 0.2431 (mmm) cc_final: 0.2219 (mmm) REVERT: U 40 MET cc_start: 0.1977 (OUTLIER) cc_final: 0.0626 (ttm) REVERT: V 20 LYS cc_start: -0.0811 (OUTLIER) cc_final: -0.4739 (mmtt) REVERT: V 36 MET cc_start: 0.2624 (tpt) cc_final: 0.0907 (mtt) outliers start: 253 outliers final: 200 residues processed: 1001 average time/residue: 0.6946 time to fit residues: 1237.4906 Evaluate side-chains 990 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 775 time to evaluate : 5.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 688 TYR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 MET Chi-restraints excluded: chain A residue 1529 ASN Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1579 SER Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1645 LEU Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1888 HIS Chi-restraints excluded: chain A residue 1940 MET Chi-restraints excluded: chain A residue 1961 LEU Chi-restraints excluded: chain A residue 1986 MET Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain A residue 2002 TYR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 830 ASN Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 377 ASP Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain O residue 393 VAL Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 81 HIS Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 289 PHE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 135 LYS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain Z residue 19 GLU Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 281 TYR Chi-restraints excluded: chain Z residue 390 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 59 LYS Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain v residue 608 TYR Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 649 GLU Chi-restraints excluded: chain v residue 684 ILE Chi-restraints excluded: chain v residue 687 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 276 ASP Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 21 THR Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 80 LEU Chi-restraints excluded: chain q residue 109 LEU Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 196 PRO Chi-restraints excluded: chain q residue 233 THR Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 3 CYS Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 101 THR Chi-restraints excluded: chain r residue 137 LEU Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 50 GLU Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain h residue 76 ASN Chi-restraints excluded: chain j residue 19 ILE Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain W residue 52 HIS Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 143 LEU Chi-restraints excluded: chain f residue 149 GLN Chi-restraints excluded: chain f residue 188 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 775 optimal weight: 4.9990 chunk 817 optimal weight: 40.0000 chunk 745 optimal weight: 5.9990 chunk 794 optimal weight: 1.9990 chunk 816 optimal weight: 5.9990 chunk 478 optimal weight: 0.0870 chunk 346 optimal weight: 0.9980 chunk 624 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 718 optimal weight: 8.9990 chunk 751 optimal weight: 20.0000 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1626 GLN ** A1824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 ASN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN O 214 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 GLN ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 78599 Z= 0.197 Angle : 0.664 16.581 108122 Z= 0.334 Chirality : 0.042 0.311 12968 Planarity : 0.004 0.120 12497 Dihedral : 16.350 179.861 15679 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.21 % Favored : 92.52 % Rotamer: Outliers : 3.72 % Allowed : 20.36 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.09), residues: 8400 helix: 1.03 (0.09), residues: 3548 sheet: -1.07 (0.15), residues: 1142 loop : -1.84 (0.10), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP Q 217 HIS 0.030 0.001 HIS C 869 PHE 0.023 0.002 PHE A1574 TYR 0.028 0.001 TYR d 222 ARG 0.013 0.000 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 813 time to evaluate : 5.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 196 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping revert: symmetry clash REVERT: A 134 MET cc_start: 0.7224 (mtm) cc_final: 0.6734 (mtm) REVERT: A 149 MET cc_start: 0.4974 (pmm) cc_final: 0.4519 (pmm) REVERT: A 177 GLU cc_start: 0.8700 (pt0) cc_final: 0.8449 (tt0) REVERT: A 210 GLU cc_start: 0.7292 (tt0) cc_final: 0.6892 (tm-30) REVERT: A 275 TYR cc_start: 0.8792 (m-80) cc_final: 0.8401 (m-80) REVERT: A 289 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6728 (m-30) REVERT: A 304 ASP cc_start: 0.7556 (t0) cc_final: 0.7174 (t0) REVERT: A 458 PHE cc_start: 0.8307 (t80) cc_final: 0.7555 (t80) REVERT: A 581 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7532 (mp) REVERT: A 625 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7076 (tt) REVERT: A 769 MET cc_start: 0.8736 (mmm) cc_final: 0.8109 (ttp) REVERT: A 775 ARG cc_start: 0.6774 (ttm170) cc_final: 0.6013 (tmm160) REVERT: A 776 GLN cc_start: 0.6149 (OUTLIER) cc_final: 0.5321 (tt0) REVERT: A 788 GLU cc_start: 0.8540 (tp30) cc_final: 0.7744 (tm-30) REVERT: A 1056 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8109 (pt0) REVERT: A 1217 ARG cc_start: 0.8468 (mmt-90) cc_final: 0.7472 (ttp-170) REVERT: A 1375 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7804 (mt) REVERT: A 1424 HIS cc_start: 0.8808 (m-70) cc_final: 0.8529 (m-70) REVERT: A 1455 GLN cc_start: 0.9201 (tt0) cc_final: 0.8864 (tm-30) REVERT: A 1499 ARG cc_start: 0.8087 (ptt180) cc_final: 0.6348 (tpt-90) REVERT: A 1521 ARG cc_start: 0.8629 (ptp90) cc_final: 0.8046 (mmt180) REVERT: A 1529 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7618 (m-40) REVERT: A 1888 HIS cc_start: 0.5720 (OUTLIER) cc_final: 0.4899 (p90) REVERT: A 1946 VAL cc_start: 0.8960 (t) cc_final: 0.8698 (m) REVERT: A 2024 MET cc_start: 0.7361 (mmt) cc_final: 0.6853 (ppp) REVERT: C 150 MET cc_start: 0.7961 (tpp) cc_final: 0.7729 (mtt) REVERT: C 184 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6774 (tt0) REVERT: C 208 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6981 (mtt90) REVERT: C 243 GLU cc_start: 0.8571 (tt0) cc_final: 0.7998 (mm-30) REVERT: C 263 MET cc_start: 0.7505 (mtt) cc_final: 0.7179 (mmm) REVERT: C 334 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.7076 (t70) REVERT: C 347 ARG cc_start: 0.8393 (mmt180) cc_final: 0.8167 (mmm160) REVERT: C 641 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8544 (pp20) REVERT: C 715 MET cc_start: 0.8402 (ttp) cc_final: 0.8019 (tmm) REVERT: C 745 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7575 (tpp-160) REVERT: C 775 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8292 (mm) REVERT: C 905 GLN cc_start: 0.8969 (mt0) cc_final: 0.8739 (mt0) REVERT: C 931 TYR cc_start: 0.8713 (p90) cc_final: 0.8071 (p90) REVERT: C 947 LYS cc_start: 0.7484 (mptt) cc_final: 0.6914 (tppt) REVERT: C 955 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8187 (mtmm) REVERT: O 183 MET cc_start: 0.7344 (ptp) cc_final: 0.6594 (mtm) REVERT: O 221 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8081 (t80) REVERT: O 343 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8979 (m) REVERT: O 404 CYS cc_start: 0.7942 (p) cc_final: 0.7736 (p) REVERT: Q 53 ASN cc_start: 0.7827 (p0) cc_final: 0.7326 (t0) REVERT: Q 215 PRO cc_start: 0.6042 (Cg_endo) cc_final: 0.5729 (Cg_exo) REVERT: R 110 ASP cc_start: 0.7465 (p0) cc_final: 0.6416 (m-30) REVERT: T 48 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7581 (mp10) REVERT: Z 34 MET cc_start: 0.4462 (mtt) cc_final: 0.3826 (ttt) REVERT: Z 390 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7559 (m-70) REVERT: c 44 THR cc_start: 0.8658 (p) cc_final: 0.8371 (p) REVERT: c 90 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6605 (ttt) REVERT: I 156 ASP cc_start: 0.7196 (t0) cc_final: 0.6843 (t0) REVERT: I 205 GLU cc_start: 0.6761 (pp20) cc_final: 0.6054 (tm-30) REVERT: v 687 LEU cc_start: 0.2544 (OUTLIER) cc_final: 0.2195 (tp) REVERT: n 51 PHE cc_start: 0.5927 (m-10) cc_final: 0.5698 (m-10) REVERT: o 1 MET cc_start: -0.0539 (mmm) cc_final: -0.0827 (mtm) REVERT: o 81 LEU cc_start: 0.3345 (mt) cc_final: 0.2694 (tt) REVERT: o 93 LEU cc_start: 0.1987 (pp) cc_final: 0.1589 (tp) REVERT: p 1 MET cc_start: 0.3736 (mmt) cc_final: 0.3416 (mtt) REVERT: q 10 PRO cc_start: 0.0972 (Cg_endo) cc_final: 0.0609 (Cg_exo) REVERT: k 19 LYS cc_start: 0.7293 (tptm) cc_final: 0.6755 (mmtm) REVERT: k 21 ARG cc_start: 0.2524 (ttt180) cc_final: 0.1853 (mtt180) REVERT: k 33 GLN cc_start: 0.6044 (tt0) cc_final: 0.5528 (tp40) REVERT: k 76 LYS cc_start: 0.5395 (tttt) cc_final: 0.5055 (mmtm) REVERT: i 83 LYS cc_start: 0.6119 (tttt) cc_final: 0.5513 (pttt) REVERT: j 20 ASN cc_start: 0.7324 (t0) cc_final: 0.6035 (m110) REVERT: j 69 ILE cc_start: 0.7233 (mm) cc_final: 0.5991 (mm) REVERT: l 15 GLN cc_start: 0.7020 (tm-30) cc_final: 0.6636 (tt0) REVERT: l 22 GLU cc_start: 0.5196 (mp0) cc_final: 0.4122 (mp0) REVERT: m 6 PHE cc_start: 0.6672 (t80) cc_final: 0.6306 (t80) REVERT: g 61 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.4960 (t80) REVERT: g 99 ASP cc_start: 0.2248 (p0) cc_final: 0.1169 (p0) REVERT: K 44 MET cc_start: 0.2140 (mmm) cc_final: 0.1863 (mmm) REVERT: U 40 MET cc_start: 0.1832 (OUTLIER) cc_final: 0.0339 (ttm) REVERT: V 20 LYS cc_start: -0.0889 (OUTLIER) cc_final: -0.4422 (pttt) REVERT: V 36 MET cc_start: 0.2660 (tpt) cc_final: 0.0947 (mtt) REVERT: f 184 MET cc_start: 0.5896 (mmm) cc_final: 0.5036 (mmm) REVERT: f 247 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.4191 (t70) outliers start: 261 outliers final: 203 residues processed: 1004 average time/residue: 0.6866 time to fit residues: 1233.7069 Evaluate side-chains 992 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 769 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 MET Chi-restraints excluded: chain A residue 1529 ASN Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1579 SER Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1888 HIS Chi-restraints excluded: chain A residue 1961 LEU Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain A residue 2002 TYR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 869 HIS Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 355 THR Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain O residue 393 VAL Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain P residue 180 VAL Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 81 HIS Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 223 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 289 PHE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 135 LYS Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain Z residue 19 GLU Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 281 TYR Chi-restraints excluded: chain Z residue 384 LEU Chi-restraints excluded: chain Z residue 390 HIS Chi-restraints excluded: chain Z residue 422 PHE Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 59 LYS Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain v residue 608 TYR Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 684 ILE Chi-restraints excluded: chain v residue 687 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 276 ASP Chi-restraints excluded: chain n residue 306 SER Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 21 THR Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 80 LEU Chi-restraints excluded: chain q residue 109 LEU Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 196 PRO Chi-restraints excluded: chain q residue 233 THR Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 101 THR Chi-restraints excluded: chain r residue 137 LEU Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain h residue 76 ASN Chi-restraints excluded: chain j residue 19 ILE Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain W residue 52 HIS Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 143 LEU Chi-restraints excluded: chain f residue 149 GLN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 247 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 792 optimal weight: 0.0980 chunk 521 optimal weight: 10.0000 chunk 840 optimal weight: 40.0000 chunk 513 optimal weight: 3.9990 chunk 398 optimal weight: 0.0670 chunk 584 optimal weight: 2.9990 chunk 881 optimal weight: 0.6980 chunk 811 optimal weight: 20.0000 chunk 702 optimal weight: 6.9990 chunk 72 optimal weight: 0.0570 chunk 542 optimal weight: 30.0000 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 543 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN A 861 GLN ** A1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 426 GLN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN C 929 GLN O 214 ASN Q 72 GLN R 150 HIS ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 78599 Z= 0.166 Angle : 0.648 14.511 108122 Z= 0.323 Chirality : 0.041 0.282 12968 Planarity : 0.004 0.069 12497 Dihedral : 16.242 178.917 15677 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.05 % Favored : 93.69 % Rotamer: Outliers : 3.04 % Allowed : 20.99 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.09), residues: 8400 helix: 1.26 (0.09), residues: 3514 sheet: -0.98 (0.15), residues: 1144 loop : -1.69 (0.10), residues: 3742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP Q 217 HIS 0.011 0.001 HIS A1431 PHE 0.023 0.001 PHE A1574 TYR 0.031 0.001 TYR d 222 ARG 0.013 0.000 ARG d 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 839 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping Corrupt residue: chain: v residue: PRO 641 >>> skipping Corrupt residue: chain: v residue: PRO 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 172 >>> skipping Corrupt residue: chain: q residue: PRO 175 >>> skipping Corrupt residue: chain: q residue: PRO 196 >>> skipping Corrupt residue: chain: q residue: PRO 239 >>> skipping Corrupt residue: chain: q residue: PRO 262 >>> skipping Corrupt residue: chain: q residue: PRO 350 >>> skipping Corrupt residue: chain: q residue: PRO 412 >>> skipping Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: Y residue: PRO 44 >>> skipping revert: symmetry clash REVERT: A 149 MET cc_start: 0.4955 (pmm) cc_final: 0.4601 (pmm) REVERT: A 210 GLU cc_start: 0.7251 (tt0) cc_final: 0.6854 (tm-30) REVERT: A 275 TYR cc_start: 0.8767 (m-80) cc_final: 0.8405 (m-80) REVERT: A 289 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6381 (m-30) REVERT: A 303 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7440 (m-10) REVERT: A 304 ASP cc_start: 0.7564 (t0) cc_final: 0.7157 (t0) REVERT: A 397 SER cc_start: 0.8938 (t) cc_final: 0.8484 (p) REVERT: A 458 PHE cc_start: 0.8311 (t80) cc_final: 0.7673 (t80) REVERT: A 581 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 769 MET cc_start: 0.8474 (mmm) cc_final: 0.7627 (ttm) REVERT: A 775 ARG cc_start: 0.6680 (ttm170) cc_final: 0.6066 (tmm160) REVERT: A 776 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.5447 (tt0) REVERT: A 788 GLU cc_start: 0.8527 (tp30) cc_final: 0.7706 (tm-30) REVERT: A 1056 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: A 1145 MET cc_start: 0.8657 (mmp) cc_final: 0.8292 (mmm) REVERT: A 1217 ARG cc_start: 0.8422 (mmt-90) cc_final: 0.7428 (tpt-90) REVERT: A 1455 GLN cc_start: 0.9180 (tt0) cc_final: 0.8852 (tm-30) REVERT: A 1499 ARG cc_start: 0.8082 (ptt180) cc_final: 0.6257 (tpt-90) REVERT: A 1521 ARG cc_start: 0.8597 (ptp90) cc_final: 0.8014 (mmt180) REVERT: A 1718 HIS cc_start: 0.6825 (m170) cc_final: 0.5267 (t70) REVERT: A 1774 MET cc_start: 0.6801 (ttt) cc_final: 0.6566 (ttt) REVERT: A 1806 MET cc_start: 0.7845 (mmm) cc_final: 0.7066 (ppp) REVERT: A 1813 TYR cc_start: 0.7484 (t80) cc_final: 0.7253 (t80) REVERT: A 1888 HIS cc_start: 0.5571 (OUTLIER) cc_final: 0.4759 (p90) REVERT: A 1946 VAL cc_start: 0.8946 (t) cc_final: 0.8674 (p) REVERT: A 2024 MET cc_start: 0.7411 (mmt) cc_final: 0.6925 (ppp) REVERT: C 126 MET cc_start: 0.8135 (tpp) cc_final: 0.7819 (tpp) REVERT: C 150 MET cc_start: 0.7909 (tpp) cc_final: 0.7628 (mtt) REVERT: C 208 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6961 (mtt90) REVERT: C 243 GLU cc_start: 0.8428 (tt0) cc_final: 0.7942 (mm-30) REVERT: C 334 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7082 (t70) REVERT: C 538 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8166 (tp30) REVERT: C 600 GLU cc_start: 0.8103 (tt0) cc_final: 0.7505 (tp30) REVERT: C 635 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8028 (mtmm) REVERT: C 715 MET cc_start: 0.8351 (ttp) cc_final: 0.7929 (tmm) REVERT: C 745 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7535 (tpp-160) REVERT: C 775 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8256 (mm) REVERT: C 905 GLN cc_start: 0.8919 (mt0) cc_final: 0.8699 (mt0) REVERT: C 931 TYR cc_start: 0.8678 (p90) cc_final: 0.8177 (p90) REVERT: C 947 LYS cc_start: 0.7493 (mptt) cc_final: 0.6916 (tppt) REVERT: C 955 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8084 (mtmm) REVERT: O 177 THR cc_start: 0.9373 (m) cc_final: 0.9085 (p) REVERT: O 183 MET cc_start: 0.7467 (ptp) cc_final: 0.6602 (mtm) REVERT: O 221 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8105 (t80) REVERT: O 343 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8956 (m) REVERT: O 404 CYS cc_start: 0.7903 (p) cc_final: 0.7656 (p) REVERT: P 75 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7553 (mm110) REVERT: Q 53 ASN cc_start: 0.7809 (p0) cc_final: 0.7372 (t0) REVERT: Q 215 PRO cc_start: 0.5917 (Cg_endo) cc_final: 0.5628 (Cg_exo) REVERT: Q 261 ARG cc_start: 0.5170 (tpp80) cc_final: 0.4815 (tpm170) REVERT: R 110 ASP cc_start: 0.7156 (p0) cc_final: 0.6010 (m-30) REVERT: R 135 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7620 (mtmm) REVERT: T 48 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7472 (mp10) REVERT: Z 34 MET cc_start: 0.4554 (mtt) cc_final: 0.3614 (ttt) REVERT: Z 101 MET cc_start: 0.6036 (mtt) cc_final: 0.5683 (mtt) REVERT: Z 195 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5714 (mt-10) REVERT: c 44 THR cc_start: 0.8638 (p) cc_final: 0.8336 (p) REVERT: I 156 ASP cc_start: 0.7107 (t0) cc_final: 0.6827 (t0) REVERT: I 205 GLU cc_start: 0.6716 (pp20) cc_final: 0.6275 (tm-30) REVERT: v 687 LEU cc_start: 0.2509 (OUTLIER) cc_final: 0.2124 (tp) REVERT: o 81 LEU cc_start: 0.3223 (mt) cc_final: 0.2580 (tt) REVERT: p 1 MET cc_start: 0.3915 (mmt) cc_final: 0.3629 (mtt) REVERT: q 10 PRO cc_start: 0.0938 (Cg_endo) cc_final: 0.0615 (Cg_exo) REVERT: k 19 LYS cc_start: 0.7275 (tptm) cc_final: 0.6747 (mmtm) REVERT: k 21 ARG cc_start: 0.2564 (ttt180) cc_final: 0.1925 (mtt180) REVERT: k 33 GLN cc_start: 0.5980 (tt0) cc_final: 0.5506 (tp40) REVERT: k 41 MET cc_start: 0.6956 (mtt) cc_final: 0.6688 (mtm) REVERT: k 76 LYS cc_start: 0.5586 (tttt) cc_final: 0.5305 (mmtm) REVERT: i 83 LYS cc_start: 0.5870 (tttt) cc_final: 0.5322 (pttt) REVERT: h 77 ASN cc_start: 0.2494 (m-40) cc_final: 0.1181 (t0) REVERT: j 9 LYS cc_start: 0.7433 (mmtm) cc_final: 0.6711 (mmmt) REVERT: j 20 ASN cc_start: 0.7295 (t0) cc_final: 0.5995 (m110) REVERT: j 67 SER cc_start: 0.4190 (OUTLIER) cc_final: 0.3770 (m) REVERT: j 69 ILE cc_start: 0.7284 (mm) cc_final: 0.6040 (mm) REVERT: l 15 GLN cc_start: 0.7018 (tm-30) cc_final: 0.6599 (tt0) REVERT: l 30 ARG cc_start: 0.8889 (ttt-90) cc_final: 0.8318 (tmt-80) REVERT: l 71 PHE cc_start: 0.6982 (p90) cc_final: 0.6615 (p90) REVERT: m 6 PHE cc_start: 0.6649 (t80) cc_final: 0.6291 (t80) REVERT: g 38 MET cc_start: 0.0595 (mmm) cc_final: 0.0382 (mmm) REVERT: g 61 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.4976 (t80) REVERT: g 99 ASP cc_start: 0.1786 (p0) cc_final: 0.0706 (p0) REVERT: K 44 MET cc_start: 0.1887 (mmm) cc_final: 0.1578 (mmm) REVERT: U 40 MET cc_start: 0.1782 (OUTLIER) cc_final: 0.0279 (ttm) REVERT: V 20 LYS cc_start: -0.0875 (OUTLIER) cc_final: -0.4342 (pttm) REVERT: V 36 MET cc_start: 0.2835 (tpt) cc_final: 0.1214 (mtt) REVERT: f 184 MET cc_start: 0.5799 (mmm) cc_final: 0.4949 (mmm) REVERT: f 247 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.3892 (t70) outliers start: 220 outliers final: 178 residues processed: 1001 average time/residue: 0.7036 time to fit residues: 1258.7215 Evaluate side-chains 974 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 779 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 MET Chi-restraints excluded: chain A residue 1570 TRP Chi-restraints excluded: chain A residue 1579 SER Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1888 HIS Chi-restraints excluded: chain A residue 1986 MET Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2002 TYR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 301 MET Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 355 THR Chi-restraints excluded: chain O residue 365 PHE Chi-restraints excluded: chain O residue 392 MET Chi-restraints excluded: chain O residue 393 VAL Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 223 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 289 PHE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 135 LYS Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain Z residue 19 GLU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 281 TYR Chi-restraints excluded: chain Z residue 384 LEU Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 59 LYS Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain v residue 608 TYR Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 687 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 276 ASP Chi-restraints excluded: chain n residue 306 SER Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 21 THR Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 80 LEU Chi-restraints excluded: chain q residue 109 LEU Chi-restraints excluded: chain q residue 172 PRO Chi-restraints excluded: chain q residue 175 PRO Chi-restraints excluded: chain q residue 196 PRO Chi-restraints excluded: chain q residue 233 THR Chi-restraints excluded: chain q residue 239 PRO Chi-restraints excluded: chain q residue 262 PRO Chi-restraints excluded: chain q residue 350 PRO Chi-restraints excluded: chain q residue 412 PRO Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 101 THR Chi-restraints excluded: chain r residue 137 LEU Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 90 GLU Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain h residue 59 PHE Chi-restraints excluded: chain h residue 76 ASN Chi-restraints excluded: chain j residue 19 ILE Chi-restraints excluded: chain j residue 67 SER Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain W residue 52 HIS Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 44 PRO Chi-restraints excluded: chain f residue 143 LEU Chi-restraints excluded: chain f residue 149 GLN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 247 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 430 optimal weight: 1.9990 chunk 557 optimal weight: 1.9990 chunk 747 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 647 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 703 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 722 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1529 ASN ** A1824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN S 8 GLN ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.186337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.161590 restraints weight = 190330.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.159555 restraints weight = 420540.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.160387 restraints weight = 374237.466| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 78599 Z= 0.194 Angle : 0.661 12.673 108122 Z= 0.328 Chirality : 0.042 0.266 12968 Planarity : 0.004 0.092 12497 Dihedral : 16.171 179.156 15675 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.95 % Favored : 92.76 % Rotamer: Outliers : 3.04 % Allowed : 21.37 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.09), residues: 8400 helix: 1.23 (0.09), residues: 3545 sheet: -1.02 (0.15), residues: 1135 loop : -1.71 (0.10), residues: 3720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP Q 217 HIS 0.014 0.001 HIS A1424 PHE 0.026 0.001 PHE d 250 TYR 0.036 0.001 TYR d 222 ARG 0.009 0.000 ARG F 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20572.48 seconds wall clock time: 356 minutes 13.41 seconds (21373.41 seconds total)