Starting phenix.real_space_refine on Sun Sep 29 19:35:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/09_2024/5gmk_9525.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/09_2024/5gmk_9525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/09_2024/5gmk_9525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/09_2024/5gmk_9525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/09_2024/5gmk_9525.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/09_2024/5gmk_9525.cif" } resolution = 3.4 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 7 6.06 5 P 407 5.49 5 Mg 6 5.21 5 S 242 5.16 5 C 46149 2.51 5 N 13144 2.21 5 O 15318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 75273 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 15775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1910, 15775 Classifications: {'peptide': 1910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 99, 'TRANS': 1809} Chain breaks: 3 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: "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: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2673 Classifications: {'RNA': 127} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 15, 'rna3p_pur': 48, 'rna3p_pyr': 58} Link IDs: {'rna2p': 21, 'rna3p': 105} Chain breaks: 6 Chain: "M" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 608 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 14} Link IDs: {'rna2p': 4, 'rna3p': 24} 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_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 6, 'rna3p': 8} 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: "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: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 1535 Classifications: {'peptide': 309} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 299} Link IDs: {'TRANS': 308} Chain breaks: 20 Unresolved non-hydrogen bonds: 628 Unresolved non-hydrogen angles: 947 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'UNK:plan-1': 309} Unresolved non-hydrogen planarities: 309 Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 937 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "G" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 342 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "H" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 810 Classifications: {'peptide': 95} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 92} 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: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 3580 Classifications: {'peptide': 673} Incomplete info: {'backbone_only': 19, 'truncation_to_alanine': 535} Link IDs: {'PTRANS': 6, 'TRANS': 666} Chain breaks: 38 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1329 Unresolved non-hydrogen angles: 1967 Unresolved non-hydrogen dihedrals: 725 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 2, 'TYR:plan': 2, 'UNK:plan-1': 540, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 4, 'PHE:plan': 4, 'GLU:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 675 Chain: "n" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1890 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 280} Chain breaks: 9 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 472 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 338 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: 119 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: 624 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: 312 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: "s" 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: "u" 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: "w" 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: "x" 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: "y" 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: "z" 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: "e" 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: "a" 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: "b" 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: "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: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35823 SG CYS Q 13 69.815 144.140 124.941 1.00 0.00 S ATOM 36281 SG CYS Q 71 73.089 143.621 126.646 1.00 0.00 S ATOM 36296 SG CYS Q 73 71.485 146.721 127.323 1.00 0.00 S ATOM 36302 SG CYS Q 74 69.631 143.633 128.467 1.00 0.00 S ATOM 35981 SG CYS Q 34 83.818 147.023 133.999 1.00 0.00 S ATOM 36004 SG CYS Q 37 87.226 146.867 135.407 1.00 0.00 S ATOM 36203 SG CYS Q 61 86.441 147.413 131.701 1.00 0.00 S ATOM 36227 SG CYS Q 64 86.063 144.014 133.465 1.00 0.00 S ATOM 37792 SG CYS R 73 59.002 159.945 145.543 1.00 0.00 S ATOM 37854 SG CYS R 81 57.608 163.270 146.449 1.00 0.00 S ATOM 37894 SG CYS R 87 57.410 162.088 142.893 1.00 0.00 S ATOM 40747 SG CYS T 104 59.896 180.190 126.868 1.00 0.00 S ATOM 40753 SG CYS T 105 63.123 182.250 127.516 1.00 0.00 S ATOM 40778 SG CYS T 108 63.233 178.977 125.292 1.00 0.00 S ATOM 41092 SG CYS T 148 63.042 179.021 128.630 1.00 0.00 S ATOM 40747 SG CYS T 104 59.896 180.190 126.868 1.00 0.00 S ATOM 40881 SG CYS T 122 60.361 176.888 124.978 1.00 0.00 S ATOM 41102 SG CYS T 150 56.923 177.988 126.082 1.00 0.00 S ATOM 41123 SG CYS T 153 58.694 179.952 123.587 1.00 0.00 S ATOM 40778 SG CYS T 108 63.233 178.977 125.292 1.00 0.00 S ATOM 40867 SG CYS T 120 64.071 175.549 124.133 1.00 0.00 S ATOM 40881 SG CYS T 122 60.361 176.888 124.978 1.00 0.00 S ATOM 41069 SG CYS T 145 62.857 175.772 127.531 1.00 0.00 S ATOM 51772 SG CYS F 51 115.943 144.711 185.579 1.00 20.00 S ATOM 51795 SG CYS F 54 116.189 142.385 182.637 1.00 20.00 S ATOM 52084 SG CYS F 88 115.173 145.961 182.110 1.00 20.00 S ATOM 52108 SG CYS F 91 112.849 143.505 183.681 1.00 20.00 S Time building chain proxies: 31.22, per 1000 atoms: 0.41 Number of scatterers: 75273 At special positions: 0 Unit cell: (245.528, 304.298, 300.38, 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 7 29.99 S 242 16.00 P 407 15.00 Mg 6 11.99 O 15318 8.00 N 13144 7.00 C 46149 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=0, symmetry=0 Time building additional restraints: 14.12 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 300 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 91 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 54 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 88 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 51 " pdb=" ZN Q 400 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 71 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 74 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 13 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 73 " pdb=" ZN Q 401 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 34 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 37 " 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 81 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 73 " pdb="ZN ZN R 400 " - pdb=" NE2 HIS R 91 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 87 " 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 153 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 150 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 104 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 145 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 120 " Number of angles added : 39 15620 Ramachandran restraints generated. 7810 Oldfield, 0 Emsley, 7810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17218 Finding SS restraints... Secondary structure from input PDB file: 325 helices and 69 sheets defined 54.8% alpha, 14.4% beta 105 base pairs and 179 stacking pairs defined. Time for finding SS restraints: 19.76 Creating SS restraints... Processing helix chain 'A' and resid 135 through 147 removed outlier: 4.210A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 154 through 165 removed outlier: 3.597A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 209 through 231 removed outlier: 3.605A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.713A pdb=" N TYR A 327 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.704A pdb=" N LYS A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.515A pdb=" N TYR A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.558A 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 483 through 489 removed outlier: 3.881A pdb=" N ASN A 487 " --> pdb=" O PRO A 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 489' Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.810A pdb=" N PHE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 535 removed outlier: 3.558A pdb=" N LYS A 519 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 616 through 641 Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.724A pdb=" N ALA A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLN A 662 " --> pdb=" O ASN A 658 " (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: 3.774A pdb=" N LYS A 684 " --> pdb=" O CYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 736 removed outlier: 3.515A pdb=" N THR A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 749 through 770 removed outlier: 3.578A pdb=" N ASP A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 795 Processing helix chain 'A' and resid 805 through 836 removed outlier: 4.056A pdb=" N ARG A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 871 removed outlier: 3.611A pdb=" N VAL A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 893 Processing helix chain 'A' and resid 907 through 925 removed outlier: 3.501A pdb=" N LEU A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 removed outlier: 3.537A pdb=" N ASN A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 985 through 1006 Processing helix chain 'A' and resid 1020 through 1035 removed outlier: 3.585A pdb=" N LEU A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1074 removed outlier: 3.920A pdb=" N ARG A1068 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1086 Processing helix chain 'A' and resid 1109 through 1127 removed outlier: 3.694A pdb=" N LEU A1124 " --> pdb=" O VAL A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1135 Processing helix chain 'A' and resid 1149 through 1155 Processing helix chain 'A' and resid 1175 through 1190 Processing helix chain 'A' and resid 1195 through 1199 removed outlier: 4.281A pdb=" N SER A1198 " --> pdb=" O PHE A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1234 removed outlier: 3.674A pdb=" N VAL A1234 " --> pdb=" O ILE A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1276 removed outlier: 3.567A pdb=" N GLU A1276 " --> pdb=" O GLN A1273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1273 through 1276' Processing helix chain 'A' and resid 1305 through 1323 removed outlier: 3.522A pdb=" N SER A1323 " --> pdb=" O ILE A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1347 removed outlier: 3.838A 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: 3.656A pdb=" N LEU A1357 " --> pdb=" O THR A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1390 Processing helix chain 'A' and resid 1391 through 1395 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 1497 removed outlier: 6.353A pdb=" N ARG A1497 " --> pdb=" O LEU A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1503 Processing helix chain 'A' and resid 1507 through 1519 removed outlier: 4.452A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A1518 " --> pdb=" O PHE A1514 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A1519 " --> pdb=" O LYS A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1534 Processing helix chain 'A' and resid 1540 through 1550 Processing helix chain 'A' and resid 1551 through 1557 removed outlier: 3.902A pdb=" N THR A1555 " --> pdb=" O GLY A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1610 Processing helix chain 'A' and resid 1610 through 1615 Processing helix chain 'A' and resid 1638 through 1649 removed outlier: 4.045A pdb=" N LYS A1642 " --> pdb=" O ILE A1638 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A1643 " --> pdb=" O PRO A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1652 through 1672 removed outlier: 3.507A pdb=" N GLU A1672 " --> pdb=" O ILE A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1677 removed outlier: 3.562A pdb=" N GLN A1677 " --> pdb=" O LEU A1673 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1762 removed outlier: 4.014A pdb=" N TYR A1751 " --> pdb=" O ASP A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1809 removed outlier: 3.662A pdb=" N LEU A1797 " --> pdb=" O GLY A1793 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A1800 " --> pdb=" O PRO A1796 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A1807 " --> pdb=" O ARG A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1824 removed outlier: 3.781A pdb=" N ARG A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1840 through 1845 removed outlier: 3.944A pdb=" N LEU A1843 " --> pdb=" O TYR A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1902 removed outlier: 4.300A pdb=" N GLY A1901 " --> pdb=" O VAL A1898 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A1902 " --> pdb=" O TRP A1899 " (cutoff:3.500A) Processing helix chain 'A' and resid 1904 through 1922 removed outlier: 3.737A pdb=" N LEU A1908 " --> pdb=" O ARG A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1923 through 1924 No H-bonds generated for 'chain 'A' and resid 1923 through 1924' Processing helix chain 'A' and resid 1925 through 1929 Processing helix chain 'A' and resid 1940 through 1948 Processing helix chain 'A' and resid 1949 through 1951 No H-bonds generated for 'chain 'A' and resid 1949 through 1951' Processing helix chain 'A' and resid 1965 through 1970 removed outlier: 3.576A pdb=" N ALA A1968 " --> pdb=" O PHE A1965 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A1969 " --> pdb=" O SER A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1980 Processing helix chain 'A' and resid 2000 through 2018 Processing helix chain 'A' and resid 2019 through 2028 Processing helix chain 'A' and resid 2044 through 2068 removed outlier: 3.869A pdb=" N ILE A2059 " --> pdb=" O MET A2055 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A2060 " --> pdb=" O ARG A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2074 Processing helix chain 'A' and resid 2075 through 2085 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.749A pdb=" N MET C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 158 Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.604A pdb=" N LEU C 170 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.773A pdb=" N VAL C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.629A 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 270 through 275 removed outlier: 3.637A pdb=" N ILE C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.657A pdb=" N TYR C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.695A 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 Processing helix chain 'C' and resid 331 through 336 removed outlier: 4.334A pdb=" N SER C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 331 through 336' 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: 3.679A 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 403 removed outlier: 3.827A pdb=" N ARG C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 432 through 441 removed outlier: 4.063A pdb=" N VAL C 436 " --> pdb=" O GLN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.626A pdb=" N LEU C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 507 No H-bonds generated for 'chain 'C' and resid 505 through 507' Processing helix chain 'C' and resid 567 through 571 removed outlier: 3.952A pdb=" N TYR C 571 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 589 removed outlier: 3.907A pdb=" N LYS C 587 " --> pdb=" O LYS C 583 " (cutoff:3.500A) removed outlier: 3.881A 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: 3.531A pdb=" N LEU C 618 " --> pdb=" O GLU C 614 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP C 620 " --> pdb=" O PRO C 616 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 662 Processing helix chain 'C' and resid 716 through 724 Processing helix chain 'C' and resid 736 through 740 removed outlier: 3.705A pdb=" N GLY C 739 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 756 removed outlier: 3.828A pdb=" N GLY C 756 " --> pdb=" O ARG C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 765 removed outlier: 3.898A pdb=" N ARG C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 784 removed outlier: 4.085A pdb=" N GLU C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 804 removed outlier: 3.807A pdb=" N LEU C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 837 removed outlier: 3.542A pdb=" N SER C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 852 removed outlier: 3.910A pdb=" N LEU C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 852 " --> pdb=" O VAL C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 884 removed outlier: 3.528A pdb=" N ARG C 884 " --> pdb=" O MET C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 912 removed outlier: 4.032A pdb=" N ALA C 912 " --> pdb=" O ILE C 909 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 909 through 912' 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: 3.760A pdb=" N ARG C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 118 Processing helix chain 'O' and resid 396 through 400 removed outlier: 3.756A pdb=" N ARG O 400 " --> pdb=" O GLU O 397 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 35 removed outlier: 4.513A 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 83 removed outlier: 3.832A pdb=" N ALA P 68 " --> pdb=" O GLN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 94 removed outlier: 3.666A pdb=" N TYR P 93 " --> pdb=" O SER P 90 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL P 94 " --> pdb=" O SER P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 164 removed outlier: 3.723A pdb=" N GLU P 162 " --> pdb=" O ALA P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 186 Processing helix chain 'P' and resid 198 through 245 removed outlier: 3.880A pdb=" N MET P 202 " --> pdb=" O ASN P 198 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS P 226 " --> pdb=" O LYS P 222 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU P 241 " --> pdb=" O LYS P 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 67 Processing helix chain 'Q' and resid 83 through 94 removed outlier: 3.519A pdb=" N ASP Q 88 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N HIS Q 89 " --> pdb=" O GLN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 114 Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.946A pdb=" N ILE Q 125 " --> pdb=" O GLY Q 121 " (cutoff:3.500A) removed outlier: 4.010A 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 255 through 263 Processing helix chain 'R' and resid 14 through 18 Processing helix chain 'R' and resid 54 through 59 Processing helix chain 'R' and resid 62 through 68 removed outlier: 3.902A pdb=" N ASN R 66 " --> pdb=" O THR R 62 " (cutoff:3.500A) 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 Processing helix chain 'R' and resid 141 through 146 Processing helix chain 'R' and resid 152 through 168 removed outlier: 4.223A pdb=" N ILE R 156 " --> pdb=" O LYS R 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG R 166 " --> pdb=" O PHE R 162 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU R 167 " --> pdb=" O VAL R 163 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY R 168 " --> pdb=" O PHE R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 Processing helix chain 'R' and resid 209 through 218 removed outlier: 4.653A pdb=" N ASP R 213 " --> pdb=" O LYS R 210 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG R 216 " --> pdb=" O ASP R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 261 removed outlier: 3.521A pdb=" N GLN R 235 " --> pdb=" O ASP R 231 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS R 252 " --> pdb=" O ASN R 248 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 20 removed outlier: 3.683A pdb=" N TYR S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 131 Processing helix chain 'S' and resid 163 through 174 removed outlier: 3.738A pdb=" N GLN S 167 " --> pdb=" O SER S 163 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL S 174 " --> pdb=" O LEU S 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 35 removed outlier: 4.275A pdb=" N ILE T 19 " --> pdb=" O GLY T 15 " (cutoff:3.500A) Proline residue: T 21 - end of helix removed outlier: 3.935A pdb=" N PHE T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN T 29 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP T 32 " --> pdb=" O ILE T 28 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS T 35 " --> pdb=" O ARG T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 69 removed outlier: 3.590A 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 Processing helix chain 'T' and resid 120 through 124 Processing helix chain 'T' and resid 125 through 137 removed outlier: 3.770A pdb=" N GLU T 131 " --> pdb=" O ALA T 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 31 Proline residue: Z 27 - end of helix Processing helix chain 'Z' and resid 36 through 47 Processing helix chain 'Z' and resid 52 through 66 Processing helix chain 'Z' and resid 72 through 87 Processing helix chain 'Z' and resid 87 through 109 removed outlier: 3.666A pdb=" N GLY Z 91 " --> pdb=" O ILE Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 110 through 127 Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.957A pdb=" N ILE Z 135 " --> pdb=" O HIS Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 166 removed outlier: 5.529A pdb=" N TRP Z 160 " --> pdb=" O LYS Z 156 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS Z 161 " --> pdb=" O ILE Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 184 removed outlier: 3.634A pdb=" N LEU Z 181 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Z 183 " --> pdb=" O TYR Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 204 removed outlier: 3.634A pdb=" N SER Z 193 " --> pdb=" O THR Z 189 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE Z 198 " --> pdb=" O LEU Z 194 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN Z 202 " --> pdb=" O PHE Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 241 Processing helix chain 'Z' and resid 285 through 301 removed outlier: 3.658A pdb=" N PHE Z 291 " --> pdb=" O ASN Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 307 through 315 Processing helix chain 'Z' and resid 323 through 336 removed outlier: 3.785A pdb=" N ASP Z 327 " --> pdb=" O LYS Z 323 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN Z 335 " --> pdb=" O LYS Z 331 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU Z 336 " --> pdb=" O SER Z 332 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 352 removed outlier: 3.966A pdb=" N SER Z 344 " --> pdb=" O SER Z 340 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 371 removed outlier: 3.639A pdb=" N GLN Z 358 " --> pdb=" O HIS Z 354 " (cutoff:3.500A) Processing helix chain 'Z' and resid 372 through 376 removed outlier: 3.564A pdb=" N ASP Z 375 " --> pdb=" O ASP Z 372 " (cutoff:3.500A) Processing helix chain 'Z' and resid 379 through 394 removed outlier: 3.537A pdb=" N ILE Z 383 " --> pdb=" O ASP Z 379 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS Z 386 " --> pdb=" O ARG Z 382 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU Z 391 " --> pdb=" O PHE Z 387 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR Z 394 " --> pdb=" O HIS Z 390 " (cutoff:3.500A) Processing helix chain 'Z' and resid 398 through 405 removed outlier: 3.519A pdb=" N CYS Z 401 " --> pdb=" O PRO Z 398 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE Z 404 " --> pdb=" O CYS Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 432 removed outlier: 4.089A pdb=" N ASN Z 429 " --> pdb=" O GLN Z 425 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU Z 430 " --> pdb=" O GLU Z 426 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU Z 431 " --> pdb=" O LEU Z 427 " (cutoff:3.500A) Processing helix chain 'Z' and resid 433 through 443 removed outlier: 3.797A pdb=" N GLN Z 437 " --> pdb=" O LEU Z 433 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Z 438 " --> pdb=" O ASP Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 454 through 469 Processing helix chain 'Z' and resid 474 through 485 removed outlier: 3.694A pdb=" N ARG Z 480 " --> pdb=" O ASP Z 476 " (cutoff:3.500A) Processing helix chain 'c' and resid 14 through 29 Processing helix chain 'c' and resid 32 through 34 No H-bonds generated for 'chain 'c' and resid 32 through 34' Processing helix chain 'c' and resid 35 through 40 removed outlier: 3.700A pdb=" N LEU c 39 " --> pdb=" O LYS c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 66 through 80 removed outlier: 3.529A pdb=" N ASP c 70 " --> pdb=" O SER c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 92 Processing helix chain 'c' and resid 94 through 107 Processing helix chain 'c' and resid 146 through 160 removed outlier: 3.612A pdb=" N LEU c 160 " --> pdb=" O ARG c 156 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 194 Processing helix chain 'c' and resid 232 through 249 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: 3.577A pdb=" N UNK c 469 " --> pdb=" O UNK c 465 " (cutoff:3.500A) Processing helix chain 'c' and resid 483 through 582 removed outlier: 3.596A pdb=" N HIS c 487 " --> pdb=" O SER c 483 " (cutoff:3.500A) Proline residue: c 504 - end of helix removed outlier: 4.514A 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: 3.703A pdb=" N LYS c 526 " --> pdb=" O GLN c 522 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU c 527 " --> pdb=" O LEU c 523 " (cutoff:3.500A) Proline residue: c 532 - end of helix removed outlier: 3.687A 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: 4.383A 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: 3.509A 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: 3.705A pdb=" N SER c 586 " --> pdb=" O ALA c 582 " (cutoff:3.500A) removed outlier: 3.645A 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: 3.710A pdb=" N GLU d 45 " --> pdb=" O GLU d 41 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS d 50 " --> pdb=" O TYR d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 78 removed outlier: 3.982A pdb=" N TRP d 68 " --> pdb=" O ASP d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 95 removed outlier: 3.688A pdb=" N ALA d 84 " --> pdb=" O ASP d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 112 removed outlier: 3.887A pdb=" N TRP d 102 " --> pdb=" O PHE d 98 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU d 109 " --> pdb=" O TYR d 105 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL d 112 " --> pdb=" O ALA d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 129 removed outlier: 3.820A pdb=" N ALA d 118 " --> pdb=" O CYS d 114 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER d 127 " --> pdb=" O ASN d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 145 removed outlier: 4.030A pdb=" N TRP d 136 " --> pdb=" O VAL d 132 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 162 removed outlier: 3.877A pdb=" N VAL d 152 " --> pdb=" O ASN d 148 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU d 162 " --> pdb=" O LYS d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 179 removed outlier: 3.910A pdb=" N ARG d 178 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 196 removed outlier: 3.742A pdb=" N ARG d 186 " --> pdb=" O TRP d 182 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU d 187 " --> pdb=" O ASN d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 213 removed outlier: 3.569A pdb=" N TRP d 202 " --> pdb=" O GLN d 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU d 209 " --> pdb=" O TRP d 205 " (cutoff:3.500A) Processing helix chain 'd' and resid 214 through 233 removed outlier: 3.756A pdb=" N THR d 218 " --> pdb=" O ASN d 214 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE d 226 " --> pdb=" O TYR d 222 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR d 228 " --> pdb=" O LEU d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 236 No H-bonds generated for 'chain 'd' and resid 234 through 236' Processing helix chain 'd' and resid 239 through 257 Processing helix chain 'd' and resid 259 through 274 Processing helix chain 'd' and resid 297 through 311 removed outlier: 3.801A 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: 3.813A pdb=" N UNK d 366 " --> pdb=" O UNK d 362 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.951A pdb=" N UNK d 418 " --> pdb=" O UNK d 414 " (cutoff:3.500A) Processing helix chain 'd' and resid 429 through 444 removed outlier: 3.502A pdb=" N UNK d 443 " --> pdb=" O UNK d 439 " (cutoff:3.500A) removed outlier: 3.526A 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: 3.897A 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: 3.671A 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: 3.693A 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 'd' and resid 626 through 641 Processing helix chain 'F' and resid 16 through 31 removed outlier: 4.385A pdb=" N LYS F 29 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS F 30 " --> pdb=" O LYS F 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU F 31 " --> pdb=" O MET F 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 10 removed outlier: 3.524A pdb=" N LEU G 8 " --> pdb=" O ASP G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 42 removed outlier: 3.547A pdb=" N LYS G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 8 removed outlier: 3.943A pdb=" N LYS H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 24 removed outlier: 4.815A pdb=" N GLN H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU H 17 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER H 22 " --> pdb=" O GLN H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 64 removed outlier: 3.593A pdb=" N ALA H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU H 49 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU H 57 " --> pdb=" O GLN H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 96 Processing helix chain 'I' and resid 96 through 123 removed outlier: 3.575A pdb=" N ALA I 101 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 190 removed outlier: 4.267A pdb=" N TYR I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 211 removed outlier: 3.595A pdb=" N SER I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'v' and resid 67 through 71 Processing helix chain 'v' and resid 75 through 88 Processing helix chain 'v' and resid 91 through 103 Processing helix chain 'v' and resid 107 through 120 removed outlier: 3.728A pdb=" N UNK v 120 " --> pdb=" O UNK v 116 " (cutoff:3.500A) Processing helix chain 'v' and resid 125 through 137 Processing helix chain 'v' and resid 140 through 152 removed outlier: 3.607A pdb=" N UNK v 146 " --> pdb=" O UNK v 142 " (cutoff:3.500A) Processing helix chain 'v' and resid 156 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: 3.867A 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: 3.538A 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: 3.523A pdb=" N UNK v 557 " --> pdb=" O UNK v 553 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N UNK v 558 " --> pdb=" O UNK v 554 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK v 560 " --> pdb=" O UNK v 556 " (cutoff:3.500A) Processing helix chain 'v' and resid 570 through 579 removed outlier: 4.379A 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: 3.854A pdb=" N GLU v 622 " --> pdb=" O GLU v 618 " (cutoff:3.500A) removed outlier: 4.645A 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: 3.943A pdb=" N GLN v 730 " --> pdb=" O ARG v 726 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU v 731 " --> pdb=" O GLU v 727 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN v 734 " --> pdb=" O GLN v 730 " (cutoff:3.500A) Processing helix chain 'v' and resid 741 through 756 removed outlier: 4.291A pdb=" N UNK v 751 " --> pdb=" O UNK v 747 " (cutoff:3.500A) Processing helix chain 'v' and resid 759 through 773 removed outlier: 3.866A 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: 4.061A pdb=" N LYS n 61 " --> pdb=" O LYS n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 423 through 427 removed outlier: 3.756A 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: 3.677A 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: 4.408A 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: 3.693A 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: 3.655A pdb=" N ALA q 90 " --> pdb=" O ASN q 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS q 97 " --> pdb=" O LEU q 93 " (cutoff:3.500A) removed outlier: 3.546A 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: 3.599A 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: 3.544A pdb=" N LYS q 135 " --> pdb=" O ASN q 131 " (cutoff:3.500A) Proline residue: q 138 - end of helix removed outlier: 3.708A 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: 3.716A pdb=" N THR r 82 " --> pdb=" O PRO r 78 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU r 93 " --> pdb=" O ASP r 89 " (cutoff:3.500A) removed outlier: 3.936A 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: 3.505A 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: 3.707A 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: 4.245A pdb=" N THR t 56 " --> pdb=" O ASN t 52 " (cutoff:3.500A) Processing helix chain 't' and resid 82 through 103 removed outlier: 3.580A 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: 3.655A pdb=" N VAL t 117 " --> pdb=" O LEU t 113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR t 120 " --> pdb=" O ILE t 116 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL t 127 " --> pdb=" O HIS t 123 " (cutoff:3.500A) removed outlier: 3.936A 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: 3.740A 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: 3.878A 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: 3.780A pdb=" N ASN g 35 " --> pdb=" O MET g 31 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 16 Processing helix chain 'u' and resid 12 through 24 Processing helix chain 'u' and resid 84 through 87 Processing helix chain 'w' and resid 14 through 22 removed outlier: 3.668A pdb=" N PHE w 18 " --> pdb=" O ASN w 14 " (cutoff:3.500A) Processing helix chain 'y' and resid 5 through 15 Processing helix chain 'y' and resid 65 through 67 No H-bonds generated for 'chain 'y' and resid 65 through 67' Processing helix chain 'y' and resid 75 through 80 Processing helix chain 'z' and resid 2 through 10 removed outlier: 3.877A pdb=" N PHE z 6 " --> pdb=" O LYS z 2 " (cutoff:3.500A) Processing helix chain 'z' and resid 102 through 108 Processing helix chain 'a' and resid 40 through 54 removed outlier: 4.195A pdb=" N THR a 54 " --> pdb=" O LEU a 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 78 through 89 removed outlier: 3.518A pdb=" N ALA a 82 " --> pdb=" O THR a 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 10 removed outlier: 3.512A pdb=" N ASP b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 51 removed outlier: 3.907A pdb=" N HIS b 49 " --> pdb=" O SER b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 110 through 120 removed outlier: 4.607A pdb=" N ARG b 116 " --> pdb=" O ASP b 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG b 119 " --> pdb=" O ARG b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 137 Processing helix chain 'b' and resid 139 through 148 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: 3.630A pdb=" N VAL A 494 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 591 through 593 Processing sheet with id=AA4, first strand: chain 'A' and resid 982 through 983 removed outlier: 6.073A pdb=" N VAL A 967 " --> pdb=" O ASN A1091 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 972 through 973 Processing sheet with id=AA6, first strand: chain 'A' and resid 1158 through 1164 removed outlier: 6.063A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A1160 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1258 through 1262 removed outlier: 3.744A pdb=" N ALA A1298 " --> pdb=" O LEU A1288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1407 through 1408 Processing sheet with id=AA9, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id=AB1, first strand: chain 'A' and resid 1682 through 1683 removed outlier: 3.689A pdb=" N THR A1682 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A1701 " --> pdb=" O PHE A1734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id=AB3, first strand: chain 'A' and resid 1955 through 1958 removed outlier: 6.415A pdb=" N ILE A1933 " --> pdb=" O ARG A1957 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A1850 " --> pdb=" O ILE A1934 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A1880 " --> pdb=" O ASP A1853 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A1985 " --> pdb=" O ILE A1893 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1859 through 1863 removed outlier: 4.062A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 75 through 77 removed outlier: 5.737A pdb=" N GLU C 75 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU O 131 " --> pdb=" O LYS O 427 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS O 427 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER O 422 " --> pdb=" O GLU O 418 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 194 through 201 removed outlier: 6.176A pdb=" N VAL C 235 " --> pdb=" O CYS C 264 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL C 266 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 237 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN C 268 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 239 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB8, first strand: chain 'C' and resid 536 through 537 removed outlier: 6.556A pdb=" N TRP C 469 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C 485 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR C 475 " --> pdb=" O TRP C 483 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP C 483 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE C 542 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC2, first strand: chain 'C' and resid 678 through 681 removed outlier: 3.680A pdb=" N TYR C 931 " --> pdb=" O GLU C 863 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 887 through 893 removed outlier: 5.667A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 714 removed outlier: 6.366A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL C 773 " --> pdb=" O TYR C 818 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU C 820 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 775 " --> pdb=" O LEU C 820 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER C 822 " --> pdb=" O ILE C 775 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 145 through 147 Processing sheet with id=AC6, first strand: chain 'O' and resid 165 through 167 removed outlier: 6.558A pdb=" N VAL O 166 " --> pdb=" O LYS O 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 187 through 190 removed outlier: 3.820A pdb=" N VAL O 206 " --> pdb=" O TYR O 220 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG O 218 " --> pdb=" O CYS O 208 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP O 210 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE O 216 " --> pdb=" O ASP O 210 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 229 through 232 removed outlier: 3.530A pdb=" N ILE O 248 " --> pdb=" O LEU O 262 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 269 through 274 removed outlier: 4.214A pdb=" N VAL O 281 " --> pdb=" O TRP O 293 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP O 294 " --> pdb=" O THR O 300 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR O 300 " --> pdb=" O ASP O 294 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 314 through 316 Processing sheet with id=AD2, first strand: chain 'O' and resid 353 through 358 removed outlier: 3.997A pdb=" N THR O 355 " --> pdb=" O GLY O 367 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL O 372 " --> pdb=" O GLY O 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN O 385 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP O 377 " --> pdb=" O LYS O 383 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS O 383 " --> pdb=" O ASP O 377 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 113 through 115 removed outlier: 6.148A pdb=" N GLU P 113 " --> pdb=" O MET Q 25 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS Q 27 " --> pdb=" O GLU P 113 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL P 115 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 204 through 207 Processing sheet with id=AD5, first strand: chain 'R' and resid 170 through 176 removed outlier: 4.061A pdb=" N CYS R 181 " --> pdb=" O VAL R 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 41 through 43 removed outlier: 7.234A pdb=" N ASN F 65 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER F 87 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR F 82 " --> pdb=" O THR F 99 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 84 " --> pdb=" O PHE F 97 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AD8, first strand: chain 'I' and resid 144 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: 5.989A 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: 6.559A 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: 3.820A pdb=" N VAL n 230 " --> pdb=" O LEU n 244 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR n 242 " --> pdb=" O ILE n 232 " (cutoff:3.500A) removed outlier: 6.343A 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: 3.531A 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) removed outlier: 5.574A pdb=" N GLU n 321 " --> pdb=" O PRO n 327 " (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: 3.748A pdb=" N TRP n 410 " --> pdb=" O SER n 400 " (cutoff:3.500A) removed outlier: 6.869A 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: 3.610A 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: 3.953A 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: 3.836A pdb=" N SER q 335 " --> pdb=" O TYR q 348 " (cutoff:3.500A) removed outlier: 6.594A 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: 6.870A 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: 4.187A 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: 6.548A pdb=" N ILE l 48 " --> pdb=" O HIS l 58 " (cutoff:3.500A) removed outlier: 6.683A 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: 4.519A 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: 6.493A 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: 6.766A 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: 6.403A 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: 6.707A 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: 4.185A 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: 6.482A 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: 6.699A 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: 5.642A pdb=" N GLN m 30 " --> pdb=" O LEU m 40 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP m 42 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 4.288A 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: 4.358A pdb=" N ILE h 81 " --> pdb=" O GLY h 28 " (cutoff:3.500A) removed outlier: 6.447A 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: 4.965A pdb=" N GLU h 58 " --> pdb=" O GLU h 37 " (cutoff:3.500A) removed outlier: 6.356A 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: 6.163A 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: 4.382A 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: 6.741A 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: 7.106A pdb=" N LEU g 75 " --> pdb=" O GLU g 88 " (cutoff:3.500A) removed outlier: 7.111A 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 'y' and resid 56 through 64 removed outlier: 6.667A pdb=" N VAL y 56 " --> pdb=" O THR y 50 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR y 50 " --> pdb=" O VAL y 56 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS y 58 " --> pdb=" O ILE y 48 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE y 48 " --> pdb=" O HIS y 58 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP y 60 " --> pdb=" O ASP y 46 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN y 43 " --> pdb=" O VAL y 34 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL y 47 " --> pdb=" O ARG y 30 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG y 30 " --> pdb=" O VAL y 47 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE y 18 " --> pdb=" O VAL y 74 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL y 74 " --> pdb=" O ILE y 18 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER y 20 " --> pdb=" O ILE y 72 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE y 72 " --> pdb=" O SER y 20 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU y 22 " --> pdb=" O LYS y 70 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU s 84 " --> pdb=" O VAL y 74 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS s 48 " --> pdb=" O LEU s 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU s 84 " --> pdb=" O ASN s 46 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN s 46 " --> pdb=" O LEU s 84 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE s 86 " --> pdb=" O VAL s 44 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL s 44 " --> pdb=" O ILE s 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA s 36 " --> pdb=" O VAL s 44 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN s 46 " --> pdb=" O LEU s 34 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU s 34 " --> pdb=" O ASN s 46 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS s 48 " --> pdb=" O GLY s 32 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY s 32 " --> pdb=" O CYS s 48 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU s 50 " --> pdb=" O TYR s 30 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR s 30 " --> pdb=" O GLU s 50 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL s 97 " --> pdb=" O TYR z 84 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR z 84 " --> pdb=" O VAL s 97 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER z 81 " --> pdb=" O LYS z 44 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS z 44 " --> pdb=" O SER z 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN z 83 " --> pdb=" O ASP z 42 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA z 38 " --> pdb=" O VAL z 32 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL z 32 " --> pdb=" O ALA z 38 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU z 40 " --> pdb=" O GLN z 30 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN z 30 " --> pdb=" O LEU z 40 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP z 42 " --> pdb=" O THR z 28 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR z 28 " --> pdb=" O ASP z 42 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU z 13 " --> pdb=" O LEU z 29 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'u' and resid 27 through 31 removed outlier: 4.260A pdb=" N LEU u 31 " --> pdb=" O ILE u 37 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE u 37 " --> pdb=" O LEU u 31 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS u 42 " --> pdb=" O GLU u 56 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU u 56 " --> pdb=" O LYS u 42 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL u 52 " --> pdb=" O LEU u 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU u 82 " --> pdb=" O VAL u 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU u 81 " --> pdb=" O ILE w 81 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS w 30 " --> pdb=" O LEU w 79 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE w 81 " --> pdb=" O GLY w 28 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY w 28 " --> pdb=" O ILE w 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL w 29 " --> pdb=" O TYR w 38 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU w 37 " --> pdb=" O GLU w 58 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU w 58 " --> pdb=" O GLU w 37 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG w 39 " --> pdb=" O ALA w 56 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA w 56 " --> pdb=" O ARG w 39 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN w 52 " --> pdb=" O VAL w 43 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN w 52 " --> pdb=" O PHE w 72 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE w 72 " --> pdb=" O GLN w 52 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN w 54 " --> pdb=" O GLU w 70 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU w 70 " --> pdb=" O ASN w 54 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA w 56 " --> pdb=" O LEU w 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY w 66 " --> pdb=" O GLU w 58 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU w 70 " --> pdb=" O LYS e 106 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL e 103 " --> pdb=" O SER e 47 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS e 53 " --> pdb=" O GLU e 74 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU e 74 " --> pdb=" O LYS e 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE e 55 " --> pdb=" O VAL e 72 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL e 72 " --> pdb=" O ILE e 55 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER e 92 " --> pdb=" O ASN e 71 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS e 73 " --> pdb=" O PHE e 90 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE e 90 " --> pdb=" O LYS e 73 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU e 75 " --> pdb=" O GLU e 88 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU e 88 " --> pdb=" O LEU e 75 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'u' and resid 89 through 90 removed outlier: 6.049A pdb=" N ASP x 41 " --> pdb=" O LEU x 29 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU x 29 " --> pdb=" O ASP x 41 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'x' and resid 23 through 25 Processing sheet with id=AH2, first strand: chain 'x' and resid 44 through 45 removed outlier: 3.605A pdb=" N GLU x 45 " --> pdb=" O HIS x 55 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS x 55 " --> pdb=" O GLU x 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'a' and resid 72 through 74 Processing sheet with id=AH4, first strand: chain 'a' and resid 93 through 94 Processing sheet with id=AH5, first strand: chain 'b' and resid 13 through 15 removed outlier: 6.180A pdb=" N LEU b 34 " --> pdb=" O ILE b 56 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP b 58 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU b 36 " --> pdb=" O ASP b 58 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU b 79 " --> pdb=" O THR b 102 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 66 through 67 3465 hydrogen bonds defined for protein. 9855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 466 hydrogen bond angles 0 basepair planarities 105 basepair parallelities 179 stacking parallelities Total time for adding SS restraints: 42.30 Time building geometry restraints manager: 16.88 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: 75978 1.56 - 1.92: 1250 1.92 - 2.27: 0 2.27 - 2.63: 0 2.63 - 2.99: 1 Bond restraints: 77229 Sorted by residual: bond pdb=" C ALA q 247 " pdb=" N ARG q 256 " ideal model delta sigma weight residual 1.335 2.990 -1.654 1.97e-02 2.58e+03 7.05e+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 1.430 0.378 3.30e-02 9.18e+02 1.31e+02 bond pdb=" CA ASP b 69 " pdb=" CB ASP b 69 " ideal model delta sigma weight residual 1.532 1.382 0.150 1.42e-02 4.96e+03 1.12e+02 bond pdb=" CB CYS n 454 " pdb=" SG CYS n 454 " ideal model delta sigma weight residual 1.808 1.478 0.330 3.30e-02 9.18e+02 9.98e+01 ... (remaining 77224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.03: 106122 9.03 - 18.07: 140 18.07 - 27.10: 3 27.10 - 36.13: 0 36.13 - 45.17: 2 Bond angle restraints: 106267 Sorted by residual: angle pdb=" O PRO A 483 " pdb=" C PRO A 483 " pdb=" N PHE A 484 " ideal model delta sigma weight residual 122.64 77.47 45.17 1.35e+00 5.49e-01 1.12e+03 angle pdb=" O ALA q 247 " pdb=" C ALA q 247 " pdb=" N ARG q 256 " ideal model delta sigma weight residual 122.59 84.56 38.03 1.33e+00 5.65e-01 8.17e+02 angle pdb=" O3' C M 502 " pdb=" P A M 503 " pdb=" O5' A M 503 " ideal model delta sigma weight residual 104.00 79.95 24.05 1.50e+00 4.44e-01 2.57e+02 angle pdb=" N PRO b 44 " pdb=" CA PRO b 44 " pdb=" CB PRO b 44 " ideal model delta sigma weight residual 103.23 113.89 -10.66 6.70e-01 2.23e+00 2.53e+02 angle pdb=" C ALA q 247 " pdb=" N ARG q 256 " pdb=" CA ARG q 256 " ideal model delta sigma weight residual 120.17 141.06 -20.89 1.54e+00 4.22e-01 1.84e+02 ... (remaining 106262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 46014 35.81 - 71.63: 1346 71.63 - 107.44: 143 107.44 - 143.25: 28 143.25 - 179.07: 19 Dihedral angle restraints: 47550 sinusoidal: 21273 harmonic: 26277 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 -50.95 -129.05 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 -52.75 -127.25 0 5.00e+00 4.00e-02 6.48e+02 dihedral pdb=" CA ALA y 81 " pdb=" C ALA y 81 " pdb=" N PRO y 82 " pdb=" CA PRO y 82 " ideal model delta harmonic sigma weight residual -180.00 -52.77 -127.23 0 5.00e+00 4.00e-02 6.47e+02 ... (remaining 47547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 11653 0.114 - 0.228: 876 0.228 - 0.342: 107 0.342 - 0.457: 10 0.457 - 0.571: 3 Chirality restraints: 12649 Sorted by residual: chirality pdb=" CA LYS e 82 " pdb=" N LYS e 82 " pdb=" C LYS e 82 " pdb=" CB LYS e 82 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CA LYS g 82 " pdb=" N LYS g 82 " pdb=" C LYS g 82 " pdb=" CB LYS g 82 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" CA ILE Z 123 " pdb=" N ILE Z 123 " pdb=" C ILE Z 123 " pdb=" CB ILE Z 123 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 5.98e+00 ... (remaining 12646 not shown) Planarity restraints: 12082 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 PRO A 483 " 0.116 2.00e-02 2.50e+03 1.67e-01 2.79e+02 pdb=" C PRO A 483 " -0.288 2.00e-02 2.50e+03 pdb=" O PRO A 483 " 0.072 2.00e-02 2.50e+03 pdb=" N PHE A 484 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Z 227 " -0.121 2.00e-02 2.50e+03 6.63e-02 8.78e+01 pdb=" CG TYR Z 227 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR Z 227 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR Z 227 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR Z 227 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR Z 227 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR Z 227 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR Z 227 " -0.103 2.00e-02 2.50e+03 ... (remaining 12079 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 35 2.08 - 2.79: 17026 2.79 - 3.49: 105580 3.49 - 4.20: 177011 4.20 - 4.90: 294859 Nonbonded interactions: 594511 Sorted by model distance: nonbonded pdb=" O ARG A 488 " pdb=" OD1 ASP C 416 " model vdw 1.378 3.040 nonbonded pdb=" O2' A M 501 " pdb=" P G N 100 " model vdw 1.612 3.400 nonbonded pdb=" CA GLU Z 192 " pdb=" OE2 GLU Z 195 " model vdw 1.699 3.470 nonbonded pdb=" O ALA Q 212 " pdb=" NH2 ARG R 237 " model vdw 1.707 3.120 nonbonded pdb=" OP2 U E 21 " pdb=" OG SER n 54 " model vdw 1.727 3.040 ... (remaining 594506 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 'h' selection = chain 'w' } ncs_group { reference = chain 'i' selection = chain 'u' } ncs_group { reference = chain 'j' selection = chain 'x' } ncs_group { reference = (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)) selection = chain 's' } ncs_group { reference = chain 'l' selection = chain 'y' } ncs_group { reference = chain 'm' selection = chain 'z' } 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 individual isotropic 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: 5.660 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: 0.070 Extract box with map and model: 2.270 Check model and map are aligned: 0.420 Set scattering table: 0.510 Process input model: 162.610 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 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 : 0.012 1.654 77229 Z= 0.696 Angle : 1.249 45.166 106267 Z= 0.768 Chirality : 0.067 0.571 12649 Planarity : 0.007 0.229 12082 Dihedral : 16.169 179.068 30332 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.73 % Favored : 91.22 % Rotamer: Outliers : 2.77 % Allowed : 3.70 % Favored : 93.53 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 2.34 % Twisted General : 0.34 % 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: -3.71 (0.08), residues: 7810 helix: -2.55 (0.07), residues: 3086 sheet: -1.98 (0.13), residues: 1111 loop : -2.45 (0.09), residues: 3613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP Z 18 HIS 0.026 0.002 HIS A1431 PHE 0.093 0.003 PHE Z 102 TYR 0.121 0.004 TYR Z 227 ARG 0.026 0.001 ARG Z 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15620 Ramachandran restraints generated. 7810 Oldfield, 0 Emsley, 7810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15620 Ramachandran restraints generated. 7810 Oldfield, 0 Emsley, 7810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1944 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1729 time to evaluate : 5.571 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 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 revert: symmetry clash 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: b residue: PRO 44 >>> skipping REVERT: A 187 LYS cc_start: 0.6953 (tttp) cc_final: 0.6720 (ttmm) REVERT: A 245 ASP cc_start: 0.8761 (m-30) cc_final: 0.8447 (m-30) REVERT: A 249 LEU cc_start: 0.7879 (pp) cc_final: 0.7502 (pt) REVERT: A 261 LEU cc_start: 0.8021 (tp) cc_final: 0.7580 (tp) REVERT: A 272 ASP cc_start: 0.8235 (m-30) cc_final: 0.7899 (t0) REVERT: A 351 LYS cc_start: 0.8246 (mttt) cc_final: 0.7933 (mmtt) REVERT: A 379 ILE cc_start: 0.8323 (mm) cc_final: 0.7997 (tt) REVERT: A 397 SER cc_start: 0.9236 (m) cc_final: 0.9033 (p) REVERT: A 467 GLU cc_start: 0.7959 (pt0) cc_final: 0.7602 (pm20) REVERT: A 468 LEU cc_start: 0.8687 (pp) cc_final: 0.8362 (pp) REVERT: A 763 MET cc_start: 0.7969 (mmm) cc_final: 0.7678 (tpt) REVERT: A 792 CYS cc_start: 0.8068 (m) cc_final: 0.7801 (m) REVERT: A 800 ASP cc_start: 0.8098 (m-30) cc_final: 0.7876 (p0) REVERT: A 1056 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8247 (pt0) REVERT: A 1156 HIS cc_start: 0.8306 (t70) cc_final: 0.7993 (t70) REVERT: A 1205 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8567 (mmtp) REVERT: A 1242 LYS cc_start: 0.8258 (mttt) cc_final: 0.7819 (mmmt) REVERT: A 1278 VAL cc_start: 0.7550 (t) cc_final: 0.7235 (p) REVERT: A 1405 ILE cc_start: 0.8373 (mm) cc_final: 0.8103 (pt) REVERT: A 1422 ILE cc_start: 0.7478 (pp) cc_final: 0.6957 (mt) REVERT: A 1568 ASN cc_start: 0.8571 (m-40) cc_final: 0.8237 (p0) REVERT: A 1618 ASN cc_start: 0.8183 (t0) cc_final: 0.7861 (m-40) REVERT: A 1628 ASP cc_start: 0.8480 (m-30) cc_final: 0.8234 (t0) REVERT: A 1790 TRP cc_start: 0.7561 (m100) cc_final: 0.7243 (m100) REVERT: A 1802 MET cc_start: 0.8546 (mmm) cc_final: 0.8152 (mtt) REVERT: A 1804 THR cc_start: 0.8600 (p) cc_final: 0.8324 (p) REVERT: A 1969 MET cc_start: 0.3008 (mmm) cc_final: 0.1932 (tmm) REVERT: C 110 LYS cc_start: 0.7919 (mmtp) cc_final: 0.7512 (ttmm) REVERT: C 156 ASP cc_start: 0.6776 (m-30) cc_final: 0.6377 (m-30) REVERT: C 186 ASP cc_start: 0.8337 (m-30) cc_final: 0.8050 (m-30) REVERT: C 263 MET cc_start: 0.6952 (mtm) cc_final: 0.6751 (mtp) REVERT: C 347 ARG cc_start: 0.7929 (mmt180) cc_final: 0.7529 (mmt180) REVERT: C 366 ASN cc_start: 0.4371 (t0) cc_final: 0.4038 (t0) REVERT: C 382 TYR cc_start: 0.7077 (m-10) cc_final: 0.6790 (m-80) REVERT: C 386 SER cc_start: 0.7944 (t) cc_final: 0.7669 (p) REVERT: C 446 PHE cc_start: 0.8273 (m-10) cc_final: 0.7507 (m-10) REVERT: C 450 ASP cc_start: 0.8518 (m-30) cc_final: 0.8138 (p0) REVERT: C 490 SER cc_start: 0.7336 (m) cc_final: 0.7081 (p) REVERT: C 538 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7419 (tt0) REVERT: C 540 GLU cc_start: 0.8632 (tt0) cc_final: 0.8375 (mp0) REVERT: C 698 LEU cc_start: 0.8497 (mt) cc_final: 0.8092 (tp) REVERT: C 878 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8115 (tp30) REVERT: C 889 TYR cc_start: 0.6535 (m-10) cc_final: 0.6000 (m-80) REVERT: C 909 ILE cc_start: 0.8659 (tp) cc_final: 0.8401 (tp) REVERT: C 927 MET cc_start: 0.7248 (tpp) cc_final: 0.7029 (tpt) REVERT: C 943 ASP cc_start: 0.7223 (m-30) cc_final: 0.6118 (p0) REVERT: C 948 ASP cc_start: 0.8778 (m-30) cc_final: 0.8470 (t0) REVERT: C 960 ASN cc_start: 0.7075 (m110) cc_final: 0.6536 (p0) REVERT: O 187 ASP cc_start: 0.6596 (t0) cc_final: 0.6318 (t70) REVERT: O 392 MET cc_start: 0.6553 (tpp) cc_final: 0.6262 (tpt) REVERT: S 31 LEU cc_start: 0.8691 (mt) cc_final: 0.8411 (mt) REVERT: S 167 GLN cc_start: 0.5978 (mt0) cc_final: 0.5682 (mt0) REVERT: Z 67 LYS cc_start: 0.3869 (OUTLIER) cc_final: 0.1609 (pttt) REVERT: Z 197 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7458 (tp) REVERT: c 218 VAL cc_start: 0.5543 (t) cc_final: 0.4121 (t) REVERT: d 155 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8291 (tt) REVERT: d 183 ASN cc_start: 0.5834 (m-40) cc_final: 0.5258 (m110) REVERT: H 3 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.5074 (mmt180) REVERT: p 1 MET cc_start: 0.2813 (mtt) cc_final: 0.2510 (tpt) REVERT: p 85 GLN cc_start: 0.1816 (OUTLIER) cc_final: 0.1533 (mt0) REVERT: r 1 MET cc_start: 0.2440 (mtt) cc_final: 0.0825 (tpt) REVERT: k 24 THR cc_start: 0.4773 (p) cc_final: 0.3927 (p) REVERT: k 40 HIS cc_start: 0.6888 (m-70) cc_final: 0.6484 (m-70) REVERT: k 49 ILE cc_start: 0.6080 (mt) cc_final: 0.5626 (tt) REVERT: k 80 ARG cc_start: 0.7813 (ttm110) cc_final: 0.7494 (ttp80) REVERT: k 82 LEU cc_start: 0.5744 (mt) cc_final: 0.4685 (mp) REVERT: k 91 GLN cc_start: 0.7394 (mm-40) cc_final: 0.6202 (tp-100) REVERT: i 24 GLN cc_start: 0.7455 (mt0) cc_final: 0.7204 (mm-40) REVERT: i 40 LYS cc_start: 0.2995 (mttt) cc_final: 0.2795 (tptp) REVERT: i 54 ILE cc_start: 0.7484 (tt) cc_final: 0.7170 (pt) REVERT: i 81 LEU cc_start: 0.3343 (OUTLIER) cc_final: 0.3136 (pp) REVERT: h 75 CYS cc_start: 0.5481 (p) cc_final: 0.5239 (p) REVERT: j 12 ASP cc_start: 0.5692 (m-30) cc_final: 0.4927 (m-30) REVERT: m 1 MET cc_start: 0.2165 (mmt) cc_final: 0.1831 (ttp) REVERT: m 10 LEU cc_start: 0.7850 (mt) cc_final: 0.7051 (mm) REVERT: m 36 MET cc_start: 0.5667 (ttm) cc_final: 0.5209 (ttt) REVERT: m 85 ILE cc_start: 0.8750 (mt) cc_final: 0.8446 (tt) REVERT: m 91 THR cc_start: 0.8001 (p) cc_final: 0.7718 (p) REVERT: m 101 LEU cc_start: 0.4257 (tp) cc_final: 0.3646 (tp) REVERT: m 106 LEU cc_start: 0.6282 (mt) cc_final: 0.5815 (tp) REVERT: g 50 ASN cc_start: 0.6549 (p0) cc_final: 0.6343 (p0) REVERT: g 68 VAL cc_start: 0.6747 (t) cc_final: 0.6386 (t) REVERT: u 50 MET cc_start: 0.1288 (mmm) cc_final: 0.0311 (ttm) REVERT: w 79 LEU cc_start: 0.1498 (OUTLIER) cc_final: 0.1249 (mt) REVERT: z 1 MET cc_start: 0.1514 (mmt) cc_final: -0.0539 (pmm) REVERT: e 49 ARG cc_start: -0.0184 (OUTLIER) cc_final: -0.0454 (mtp-110) REVERT: e 99 ASP cc_start: 0.3053 (OUTLIER) cc_final: 0.2643 (m-30) REVERT: b 71 SER cc_start: 0.4460 (OUTLIER) cc_final: 0.4137 (p) outliers start: 215 outliers final: 109 residues processed: 1921 average time/residue: 0.7607 time to fit residues: 2462.3455 Evaluate side-chains 1060 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 941 time to evaluate : 5.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 640 ARG Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 213 SER Chi-restraints excluded: chain Q residue 217 TRP Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 222 THR Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 248 CYS Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain T residue 31 ARG Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain T residue 120 CYS Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 174 TRP Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 192 GLU Chi-restraints excluded: chain Z residue 193 SER Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 197 LEU Chi-restraints excluded: chain Z residue 199 GLU Chi-restraints excluded: chain Z residue 203 LYS Chi-restraints excluded: chain Z residue 229 VAL 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 d residue 155 LEU Chi-restraints excluded: chain H residue 3 ARG 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 722 PRO Chi-restraints excluded: chain n residue 57 LYS 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 306 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 o residue 63 THR Chi-restraints excluded: chain o residue 134 SER 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 p residue 85 GLN Chi-restraints excluded: chain p residue 109 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 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 t residue 5 SER 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 108 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain i residue 18 PHE Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain g residue 99 ASP Chi-restraints excluded: chain g residue 100 SER Chi-restraints excluded: chain w residue 79 LEU Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain e residue 49 ARG Chi-restraints excluded: chain e residue 99 ASP Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 44 PRO Chi-restraints excluded: chain b residue 71 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 700 optimal weight: 30.0000 chunk 628 optimal weight: 7.9990 chunk 348 optimal weight: 0.8980 chunk 214 optimal weight: 0.0030 chunk 423 optimal weight: 0.9980 chunk 335 optimal weight: 0.9990 chunk 649 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 395 optimal weight: 0.9990 chunk 483 optimal weight: 2.9990 chunk 752 optimal weight: 6.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 146 HIS A 181 HIS ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 405 ASN A 429 ASN A 574 GLN A 592 HIS A 638 GLN A 659 HIS A 685 HIS A 705 GLN A 760 ASN A 784 GLN A 848 ASN A 961 GLN A 976 GLN A1011 ASN A1087 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1254 ASN A1369 ASN A1449 ASN A1532 HIS A1559 HIS ** A1635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1652 HIS ** A1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 GLN A1863 HIS A1947 HIS A2018 ASN C 101 GLN C 158 HIS ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN C 289 ASN C 647 ASN C 764 ASN C 776 ASN C 794 GLN C 817 GLN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 344 ASN O 382 HIS O 428 GLN P 37 ASN P 195 ASN Q 106 ASN Q 225 GLN R 58 HIS ** R 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 HIS R 150 HIS R 155 GLN R 201 ASN R 248 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 HIS S 173 HIS T 54 GLN T 116 ASN T 143 HIS T 147 HIS Z 54 ASN ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 354 HIS Z 457 HIS c 83 GLN d 78 GLN ** d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN v 590 ASN i 15 ASN h 24 ASN h 54 ASN j 18 ASN g 35 ASN g 52 HIS ** s 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 15 ASN u 34 GLN u 86 ASN w 24 ASN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5324 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 77229 Z= 0.215 Angle : 0.734 18.296 106267 Z= 0.377 Chirality : 0.044 0.266 12649 Planarity : 0.005 0.083 12082 Dihedral : 17.281 179.081 15787 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.75 % Favored : 94.75 % Rotamer: Outliers : 2.98 % Allowed : 12.09 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 1.75 % Twisted General : 0.18 % 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: -1.63 (0.09), residues: 7812 helix: -0.02 (0.09), residues: 3165 sheet: -1.46 (0.14), residues: 1163 loop : -1.92 (0.10), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 823 HIS 0.013 0.001 HIS A1431 PHE 0.033 0.002 PHE C 364 TYR 0.036 0.002 TYR C 285 ARG 0.008 0.001 ARG R 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1166 time to evaluate : 5.713 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 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 revert: symmetry clash 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 revert: symmetry clash 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 Corrupt residue: chain: b residue: PRO 44 >>> skipping REVERT: A 245 ASP cc_start: 0.8577 (m-30) cc_final: 0.8268 (m-30) REVERT: A 249 LEU cc_start: 0.7627 (pp) cc_final: 0.7402 (pt) REVERT: A 272 ASP cc_start: 0.8130 (m-30) cc_final: 0.7840 (t0) REVERT: A 313 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8220 (ttp-110) REVERT: A 321 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 351 LYS cc_start: 0.8631 (mttt) cc_final: 0.7961 (mmtt) REVERT: A 397 SER cc_start: 0.9345 (m) cc_final: 0.9112 (p) REVERT: A 468 LEU cc_start: 0.8649 (pp) cc_final: 0.8374 (pp) REVERT: A 495 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7953 (mtp85) REVERT: A 540 THR cc_start: 0.7815 (p) cc_final: 0.7606 (p) REVERT: A 618 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7454 (p) REVERT: A 763 MET cc_start: 0.8045 (mmm) cc_final: 0.7813 (tpt) REVERT: A 780 ARG cc_start: 0.6808 (mmt90) cc_final: 0.6527 (mmt90) REVERT: A 792 CYS cc_start: 0.8159 (m) cc_final: 0.7826 (m) REVERT: A 800 ASP cc_start: 0.8130 (m-30) cc_final: 0.7787 (t70) REVERT: A 832 GLU cc_start: 0.8890 (tp30) cc_final: 0.8376 (mm-30) REVERT: A 1116 TYR cc_start: 0.8489 (t80) cc_final: 0.8131 (t80) REVERT: A 1151 GLU cc_start: 0.8278 (mp0) cc_final: 0.7106 (tp30) REVERT: A 1205 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8589 (mmtp) REVERT: A 1242 LYS cc_start: 0.8344 (mttt) cc_final: 0.7987 (mmmt) REVERT: A 1422 ILE cc_start: 0.7815 (pp) cc_final: 0.6666 (mt) REVERT: A 1451 PHE cc_start: 0.8512 (m-80) cc_final: 0.8110 (m-80) REVERT: A 1568 ASN cc_start: 0.8598 (m-40) cc_final: 0.8229 (p0) REVERT: A 1618 ASN cc_start: 0.8437 (t0) cc_final: 0.8183 (m-40) REVERT: A 1628 ASP cc_start: 0.8532 (m-30) cc_final: 0.7954 (t0) REVERT: A 1679 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7001 (tm-30) REVERT: A 1700 ASP cc_start: 0.8307 (m-30) cc_final: 0.8021 (m-30) REVERT: A 1746 HIS cc_start: 0.8699 (p-80) cc_final: 0.8444 (p-80) REVERT: A 1783 MET cc_start: 0.8228 (mtm) cc_final: 0.7983 (ptp) REVERT: A 1969 MET cc_start: 0.2625 (mmm) cc_final: 0.1633 (ppp) REVERT: C 110 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7624 (tppt) REVERT: C 186 ASP cc_start: 0.8096 (m-30) cc_final: 0.7851 (m-30) REVERT: C 233 ASP cc_start: 0.7831 (m-30) cc_final: 0.7462 (m-30) REVERT: C 294 ASN cc_start: 0.8128 (t0) cc_final: 0.7887 (t0) REVERT: C 347 ARG cc_start: 0.7557 (mmt180) cc_final: 0.7226 (mmt180) REVERT: C 362 LYS cc_start: 0.8399 (tttt) cc_final: 0.8074 (ttmm) REVERT: C 382 TYR cc_start: 0.7194 (m-10) cc_final: 0.6941 (m-80) REVERT: C 446 PHE cc_start: 0.8547 (m-10) cc_final: 0.7579 (m-10) REVERT: C 450 ASP cc_start: 0.8435 (m-30) cc_final: 0.8052 (p0) REVERT: C 540 GLU cc_start: 0.8501 (tt0) cc_final: 0.8276 (mp0) REVERT: C 609 PRO cc_start: 0.8018 (Cg_exo) cc_final: 0.7778 (Cg_endo) REVERT: C 614 GLU cc_start: 0.8491 (tp30) cc_final: 0.8265 (tp30) REVERT: C 757 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.5696 (m-90) REVERT: C 878 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8310 (tp30) REVERT: C 943 ASP cc_start: 0.7139 (m-30) cc_final: 0.6644 (t0) REVERT: C 948 ASP cc_start: 0.8779 (m-30) cc_final: 0.8462 (t0) REVERT: C 954 LEU cc_start: 0.7962 (mt) cc_final: 0.7738 (mt) REVERT: C 959 ILE cc_start: 0.7082 (pp) cc_final: 0.6864 (mp) REVERT: C 960 ASN cc_start: 0.7329 (m110) cc_final: 0.6863 (p0) REVERT: O 124 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7228 (mm-30) REVERT: O 221 TYR cc_start: 0.8291 (t80) cc_final: 0.8018 (t80) REVERT: P 210 ASN cc_start: 0.5154 (m-40) cc_final: 0.4949 (m-40) REVERT: S 6 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6398 (mmt180) REVERT: S 167 GLN cc_start: 0.5936 (mt0) cc_final: 0.5578 (mt0) REVERT: Z 67 LYS cc_start: 0.2725 (OUTLIER) cc_final: 0.1395 (mttp) REVERT: Z 99 MET cc_start: 0.5056 (tmm) cc_final: 0.4820 (tmm) REVERT: Z 179 TYR cc_start: 0.4847 (t80) cc_final: 0.4628 (t80) REVERT: c 218 VAL cc_start: 0.5622 (t) cc_final: 0.4939 (t) REVERT: F 93 ASN cc_start: 0.5905 (t0) cc_final: 0.5570 (t0) REVERT: H 3 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.5268 (mmt180) REVERT: H 6 ASP cc_start: 0.7582 (m-30) cc_final: 0.7309 (m-30) REVERT: p 1 MET cc_start: 0.3344 (mtt) cc_final: 0.3071 (tpt) REVERT: r 1 MET cc_start: 0.2478 (mtt) cc_final: 0.1023 (tpt) REVERT: k 80 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7634 (ttm170) REVERT: k 87 LEU cc_start: 0.7615 (mt) cc_final: 0.6949 (tp) REVERT: k 90 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7761 (tm-30) REVERT: h 31 LEU cc_start: 0.6945 (mm) cc_final: 0.6659 (mt) REVERT: j 28 ILE cc_start: 0.5819 (pt) cc_final: 0.5551 (tt) REVERT: j 32 TYR cc_start: 0.5216 (p90) cc_final: 0.4675 (p90) REVERT: j 35 PHE cc_start: 0.7290 (m-80) cc_final: 0.7036 (m-80) REVERT: l 22 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5859 (tp30) REVERT: l 29 TYR cc_start: 0.7262 (m-80) cc_final: 0.6806 (m-80) REVERT: l 40 MET cc_start: 0.7066 (mtt) cc_final: 0.6778 (mtm) REVERT: l 59 MET cc_start: 0.7617 (mmt) cc_final: 0.7273 (mmp) REVERT: m 28 THR cc_start: 0.4619 (m) cc_final: 0.4409 (p) REVERT: m 36 MET cc_start: 0.5607 (ttm) cc_final: 0.5139 (tmm) REVERT: m 47 LEU cc_start: 0.2237 (pt) cc_final: 0.1841 (mm) REVERT: g 96 LEU cc_start: 0.6195 (tp) cc_final: 0.5821 (tt) REVERT: s 35 MET cc_start: 0.3670 (mtt) cc_final: 0.2249 (tpp) REVERT: u 50 MET cc_start: 0.1146 (mmm) cc_final: 0.0493 (ttm) REVERT: w 79 LEU cc_start: 0.1393 (OUTLIER) cc_final: 0.1119 (mt) REVERT: z 1 MET cc_start: 0.1648 (mmt) cc_final: -0.0297 (pmm) REVERT: b 36 LEU cc_start: 0.3987 (tp) cc_final: 0.3559 (pp) outliers start: 227 outliers final: 135 residues processed: 1335 average time/residue: 0.7222 time to fit residues: 1691.1034 Evaluate side-chains 1017 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 875 time to evaluate : 5.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1369 ASN Chi-restraints excluded: chain A residue 1418 THR Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 757 TRP Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 277 VAL Chi-restraints excluded: chain O residue 350 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 199 GLU Chi-restraints excluded: chain Z residue 229 VAL Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 54 GLU Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 215 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 228 THR Chi-restraints excluded: chain d residue 259 GLU Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 154 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 706 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain v residue 725 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 306 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 o residue 134 SER 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 p residue 109 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 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 r residue 109 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 t residue 136 VAL Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 100 SER Chi-restraints excluded: chain u residue 18 PHE Chi-restraints excluded: chain w residue 79 LEU Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 44 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 418 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 626 optimal weight: 5.9990 chunk 512 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 754 optimal weight: 0.9980 chunk 814 optimal weight: 40.0000 chunk 671 optimal weight: 6.9990 chunk 747 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 605 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 343 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN A 952 ASN A 961 GLN A1005 GLN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1254 ASN A1368 GLN A1635 HIS ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 215 GLN ** O 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 GLN ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 ASN P 195 ASN Q 106 ASN Q 124 GLN Q 209 ASN S 8 GLN T 147 HIS Z 241 ASN ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN F 65 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 85 GLN k 33 GLN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 GLN l 17 HIS l 41 ASN l 61 GLN y 41 ASN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 77229 Z= 0.432 Angle : 0.776 12.577 106267 Z= 0.399 Chirality : 0.047 0.306 12649 Planarity : 0.006 0.121 12082 Dihedral : 16.825 179.783 15691 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.05 % Favored : 93.54 % Rotamer: Outliers : 4.03 % Allowed : 14.07 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 1.75 % 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: -1.18 (0.09), residues: 7812 helix: 0.52 (0.09), residues: 3168 sheet: -1.27 (0.14), residues: 1198 loop : -1.84 (0.10), residues: 3446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP Q 217 HIS 0.021 0.002 HIS A1431 PHE 0.034 0.003 PHE d 172 TYR 0.038 0.003 TYR d 139 ARG 0.011 0.001 ARG Z 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 886 time to evaluate : 5.651 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 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 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 Corrupt residue: chain: b residue: PRO 44 >>> skipping REVERT: A 245 ASP cc_start: 0.8675 (m-30) cc_final: 0.8386 (m-30) REVERT: A 249 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7248 (pt) REVERT: A 272 ASP cc_start: 0.8127 (m-30) cc_final: 0.7814 (t0) REVERT: A 291 LYS cc_start: 0.8561 (mmtm) cc_final: 0.8334 (mmtm) REVERT: A 397 SER cc_start: 0.9163 (m) cc_final: 0.8889 (p) REVERT: A 495 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7920 (mtp85) REVERT: A 612 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7296 (tmtp) REVERT: A 618 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7442 (p) REVERT: A 763 MET cc_start: 0.7780 (mmm) cc_final: 0.7447 (tpt) REVERT: A 780 ARG cc_start: 0.6902 (mmt90) cc_final: 0.6678 (mmt90) REVERT: A 832 GLU cc_start: 0.9029 (tp30) cc_final: 0.8611 (mm-30) REVERT: A 1056 GLU cc_start: 0.8450 (pt0) cc_final: 0.8066 (pt0) REVERT: A 1210 ASP cc_start: 0.9127 (t0) cc_final: 0.8862 (m-30) REVERT: A 1242 LYS cc_start: 0.8823 (mttt) cc_final: 0.8342 (mmmt) REVERT: A 1422 ILE cc_start: 0.8055 (pp) cc_final: 0.7697 (mt) REVERT: A 1518 SER cc_start: 0.9309 (p) cc_final: 0.9088 (m) REVERT: A 1543 ARG cc_start: 0.8992 (ttp80) cc_final: 0.8717 (ttt90) REVERT: A 1618 ASN cc_start: 0.8248 (t0) cc_final: 0.7826 (t0) REVERT: A 1679 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7337 (tm-30) REVERT: A 1803 ARG cc_start: 0.8520 (ttp-110) cc_final: 0.7702 (mtt90) REVERT: A 1969 MET cc_start: 0.2954 (mmm) cc_final: 0.1597 (tmm) REVERT: C 110 LYS cc_start: 0.8085 (mmtp) cc_final: 0.7516 (ttmm) REVERT: C 233 ASP cc_start: 0.7696 (m-30) cc_final: 0.7254 (m-30) REVERT: C 342 ASP cc_start: 0.8223 (m-30) cc_final: 0.7784 (t0) REVERT: C 347 ARG cc_start: 0.7641 (mmt180) cc_final: 0.7438 (mmt90) REVERT: C 362 LYS cc_start: 0.8451 (tttt) cc_final: 0.8099 (mtpp) REVERT: C 446 PHE cc_start: 0.8912 (m-10) cc_final: 0.8504 (m-10) REVERT: C 450 ASP cc_start: 0.8409 (m-30) cc_final: 0.8020 (p0) REVERT: C 538 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7212 (tt0) REVERT: C 540 GLU cc_start: 0.8419 (tt0) cc_final: 0.8202 (mp0) REVERT: C 614 GLU cc_start: 0.8712 (tp30) cc_final: 0.8219 (tp30) REVERT: C 810 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8575 (mp0) REVERT: C 859 GLU cc_start: 0.8554 (pt0) cc_final: 0.8287 (pt0) REVERT: C 862 TYR cc_start: 0.8867 (m-80) cc_final: 0.8616 (m-10) REVERT: C 878 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8466 (tp30) REVERT: C 888 ILE cc_start: 0.8285 (pp) cc_final: 0.8062 (mt) REVERT: C 943 ASP cc_start: 0.7440 (m-30) cc_final: 0.6206 (p0) REVERT: C 948 ASP cc_start: 0.9079 (m-30) cc_final: 0.8526 (t0) REVERT: P 122 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8580 (mp) REVERT: P 176 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7612 (m-40) REVERT: Q 17 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7425 (tt) REVERT: S 162 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7115 (mtmm) REVERT: S 167 GLN cc_start: 0.6190 (mt0) cc_final: 0.5975 (mt0) REVERT: T 34 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7389 (mt0) REVERT: Z 67 LYS cc_start: 0.2975 (OUTLIER) cc_final: 0.1601 (mtmm) REVERT: Z 99 MET cc_start: 0.5121 (tmm) cc_final: 0.4907 (tmm) REVERT: c 217 ILE cc_start: 0.8625 (mm) cc_final: 0.7631 (mt) REVERT: H 3 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.5633 (mmt180) REVERT: o 61 SER cc_start: 0.1941 (p) cc_final: 0.1374 (t) REVERT: p 1 MET cc_start: 0.3472 (mtt) cc_final: 0.3132 (tpt) REVERT: r 1 MET cc_start: 0.2970 (mtt) cc_final: 0.1091 (tpt) REVERT: k 15 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7397 (pp) REVERT: k 28 ARG cc_start: 0.6148 (mtt90) cc_final: 0.5758 (mtm-85) REVERT: k 34 LEU cc_start: 0.7919 (tt) cc_final: 0.7690 (tp) REVERT: k 90 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7776 (tm-30) REVERT: i 16 CYS cc_start: 0.5226 (m) cc_final: 0.5016 (m) REVERT: i 91 THR cc_start: -0.0010 (OUTLIER) cc_final: -0.0314 (p) REVERT: h 31 LEU cc_start: 0.6865 (mm) cc_final: 0.6619 (mt) REVERT: h 70 GLU cc_start: 0.4246 (tt0) cc_final: 0.3899 (tm-30) REVERT: l 29 TYR cc_start: 0.7620 (m-80) cc_final: 0.6954 (m-10) REVERT: l 35 GLU cc_start: 0.7993 (tp30) cc_final: 0.7443 (tp30) REVERT: l 36 SER cc_start: 0.7599 (t) cc_final: 0.7271 (t) REVERT: l 68 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7480 (mm-40) REVERT: m 36 MET cc_start: 0.5566 (ttm) cc_final: 0.5312 (tmm) REVERT: m 47 LEU cc_start: 0.2254 (pt) cc_final: 0.1817 (mm) REVERT: s 35 MET cc_start: 0.2908 (mtt) cc_final: 0.1865 (tpp) REVERT: u 50 MET cc_start: 0.1235 (mmm) cc_final: 0.0668 (ttm) REVERT: y 59 MET cc_start: 0.2995 (ptp) cc_final: 0.1977 (ppp) REVERT: z 1 MET cc_start: 0.0880 (mmt) cc_final: -0.1103 (pmm) REVERT: b 36 LEU cc_start: 0.4233 (tp) cc_final: 0.3513 (pp) outliers start: 292 outliers final: 185 residues processed: 1108 average time/residue: 0.7095 time to fit residues: 1383.2697 Evaluate side-chains 977 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 779 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1619 VAL Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 231 SER Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 277 VAL Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 301 MET Chi-restraints excluded: chain O residue 350 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 208 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 45 HIS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 223 VAL Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 245 GLU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 162 LYS Chi-restraints excluded: chain S residue 163 SER Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 114 THR Chi-restraints excluded: chain T residue 122 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain Z residue 34 MET Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 199 GLU Chi-restraints excluded: chain Z residue 229 VAL Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain Z residue 378 THR Chi-restraints excluded: chain Z residue 481 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 248 VAL 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 52 THR Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 228 THR Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 154 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 706 LEU Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain n residue 60 ARG 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 260 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 44 PRO Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 134 SER Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 109 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 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 17 PRO Chi-restraints excluded: chain r residue 44 PRO 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 133 PRO Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain k residue 15 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 39 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain h residue 75 CYS Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 100 SER Chi-restraints excluded: chain u residue 80 ILE Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 44 PRO Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 745 optimal weight: 0.1980 chunk 567 optimal weight: 20.0000 chunk 391 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 359 optimal weight: 2.9990 chunk 506 optimal weight: 0.6980 chunk 756 optimal weight: 0.4980 chunk 801 optimal weight: 2.9990 chunk 395 optimal weight: 0.9980 chunk 717 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 GLN A1295 GLN A1368 GLN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN C 403 ASN C 776 ASN C 869 HIS ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 106 ASN R 66 ASN ** Z 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 368 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN k 33 GLN k 91 GLN j 66 ASN x 18 ASN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5494 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 77229 Z= 0.177 Angle : 0.623 12.094 106267 Z= 0.320 Chirality : 0.041 0.271 12649 Planarity : 0.005 0.105 12082 Dihedral : 16.493 177.885 15673 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.21 % Favored : 94.43 % Rotamer: Outliers : 2.95 % Allowed : 16.06 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 1.17 % Twisted General : 0.13 % 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: -0.61 (0.09), residues: 7812 helix: 1.12 (0.09), residues: 3173 sheet: -1.06 (0.14), residues: 1191 loop : -1.64 (0.10), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP Q 217 HIS 0.018 0.001 HIS A1431 PHE 0.035 0.001 PHE C 364 TYR 0.029 0.001 TYR C 862 ARG 0.013 0.001 ARG c 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 902 time to evaluate : 5.625 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 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 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 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 Corrupt residue: chain: b residue: PRO 44 >>> skipping REVERT: A 245 ASP cc_start: 0.8673 (m-30) cc_final: 0.8389 (m-30) REVERT: A 272 ASP cc_start: 0.8105 (m-30) cc_final: 0.7874 (t0) REVERT: A 305 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6515 (tp) REVERT: A 321 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 397 SER cc_start: 0.9256 (m) cc_final: 0.8939 (p) REVERT: A 495 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7845 (mtp85) REVERT: A 612 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7210 (tmtp) REVERT: A 618 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7502 (p) REVERT: A 651 ASP cc_start: 0.7604 (t70) cc_final: 0.7191 (t0) REVERT: A 763 MET cc_start: 0.7663 (mmm) cc_final: 0.7453 (tpt) REVERT: A 800 ASP cc_start: 0.8551 (m-30) cc_final: 0.8158 (t70) REVERT: A 832 GLU cc_start: 0.8950 (tp30) cc_final: 0.8447 (mm-30) REVERT: A 841 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6924 (mt-10) REVERT: A 842 LYS cc_start: 0.8644 (tptm) cc_final: 0.8004 (ttpt) REVERT: A 978 ILE cc_start: 0.7997 (mt) cc_final: 0.7719 (mm) REVERT: A 1151 GLU cc_start: 0.8473 (mp0) cc_final: 0.7601 (tp30) REVERT: A 1242 LYS cc_start: 0.8764 (mttt) cc_final: 0.8305 (mmmt) REVERT: A 1286 TRP cc_start: 0.8802 (m-10) cc_final: 0.8501 (m-10) REVERT: A 1422 ILE cc_start: 0.8177 (pp) cc_final: 0.7678 (mt) REVERT: A 1543 ARG cc_start: 0.8764 (ttp80) cc_final: 0.8555 (ttt90) REVERT: A 1545 ASP cc_start: 0.8619 (m-30) cc_final: 0.8218 (m-30) REVERT: A 1618 ASN cc_start: 0.8257 (t0) cc_final: 0.7847 (t0) REVERT: A 1679 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7149 (tm-30) REVERT: A 1700 ASP cc_start: 0.8627 (t0) cc_final: 0.8406 (t0) REVERT: C 110 LYS cc_start: 0.8033 (mmtp) cc_final: 0.7490 (tppt) REVERT: C 204 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7524 (mp0) REVERT: C 362 LYS cc_start: 0.8592 (tttt) cc_final: 0.8206 (mtpp) REVERT: C 446 PHE cc_start: 0.8984 (m-10) cc_final: 0.8570 (m-10) REVERT: C 450 ASP cc_start: 0.8339 (m-30) cc_final: 0.8068 (p0) REVERT: C 540 GLU cc_start: 0.8426 (tt0) cc_final: 0.8223 (mp0) REVERT: C 614 GLU cc_start: 0.8723 (tp30) cc_final: 0.8144 (tp30) REVERT: C 671 SER cc_start: 0.8980 (t) cc_final: 0.8772 (p) REVERT: C 674 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7636 (mt) REVERT: C 810 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8569 (mp0) REVERT: C 822 SER cc_start: 0.7596 (t) cc_final: 0.7196 (p) REVERT: C 859 GLU cc_start: 0.8638 (pt0) cc_final: 0.8353 (pt0) REVERT: C 878 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8441 (tp30) REVERT: C 943 ASP cc_start: 0.7284 (m-30) cc_final: 0.6342 (p0) REVERT: C 948 ASP cc_start: 0.9081 (m-30) cc_final: 0.8562 (t0) REVERT: C 972 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7212 (mtm-85) REVERT: S 6 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6015 (mmt180) REVERT: S 167 GLN cc_start: 0.6342 (mt0) cc_final: 0.6114 (mt0) REVERT: T 136 LYS cc_start: 0.6263 (mmtm) cc_final: 0.5865 (mptt) REVERT: T 153 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7653 (m) REVERT: Z 67 LYS cc_start: 0.2315 (OUTLIER) cc_final: 0.1485 (mtmm) REVERT: c 82 ASN cc_start: 0.7321 (p0) cc_final: 0.6648 (p0) REVERT: d 235 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7738 (tt) REVERT: H 3 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.5553 (mmt180) REVERT: I 99 GLN cc_start: 0.7411 (pm20) cc_final: 0.7167 (pm20) REVERT: I 181 ARG cc_start: 0.7071 (mpt-90) cc_final: 0.6621 (mtt-85) REVERT: p 1 MET cc_start: 0.3368 (mtt) cc_final: 0.3101 (tpt) REVERT: r 1 MET cc_start: 0.3117 (mtt) cc_final: 0.1067 (tpt) REVERT: k 28 ARG cc_start: 0.6191 (mtt90) cc_final: 0.5871 (mtm-85) REVERT: k 49 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.6967 (tp) REVERT: k 87 LEU cc_start: 0.7385 (mt) cc_final: 0.6885 (tp) REVERT: k 90 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7342 (tm-30) REVERT: k 91 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6927 (mm-40) REVERT: i 16 CYS cc_start: 0.5338 (m) cc_final: 0.5100 (m) REVERT: h 31 LEU cc_start: 0.6733 (mm) cc_final: 0.6425 (mt) REVERT: h 70 GLU cc_start: 0.4264 (tt0) cc_final: 0.3781 (tm-30) REVERT: j 12 ASP cc_start: 0.6642 (m-30) cc_final: 0.6329 (p0) REVERT: l 29 TYR cc_start: 0.7289 (m-80) cc_final: 0.6710 (m-80) REVERT: l 35 GLU cc_start: 0.8104 (tp30) cc_final: 0.7684 (tp30) REVERT: l 80 ASN cc_start: 0.9183 (t0) cc_final: 0.8734 (p0) REVERT: m 36 MET cc_start: 0.5732 (ttm) cc_final: 0.5472 (tmm) REVERT: m 47 LEU cc_start: 0.2166 (pt) cc_final: 0.1788 (tp) REVERT: g 96 LEU cc_start: 0.6369 (tp) cc_final: 0.6102 (tt) REVERT: s 35 MET cc_start: 0.3003 (mtt) cc_final: 0.1956 (tpp) REVERT: u 50 MET cc_start: 0.1346 (mmm) cc_final: 0.0471 (ttm) REVERT: y 59 MET cc_start: 0.2968 (ptp) cc_final: 0.1858 (ppp) REVERT: z 1 MET cc_start: 0.0728 (mmt) cc_final: -0.1162 (pmm) REVERT: e 67 MET cc_start: -0.1323 (mtm) cc_final: -0.1556 (tpp) REVERT: b 36 LEU cc_start: 0.3912 (tp) cc_final: 0.3095 (pp) outliers start: 226 outliers final: 149 residues processed: 1068 average time/residue: 0.6726 time to fit residues: 1263.1095 Evaluate side-chains 947 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 787 time to evaluate : 5.520 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ASN Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 277 VAL Chi-restraints excluded: chain O residue 350 THR Chi-restraints excluded: chain P residue 208 LEU Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 25 ILE Chi-restraints excluded: chain S residue 162 LYS Chi-restraints excluded: chain S residue 163 SER Chi-restraints excluded: chain T residue 98 THR Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain T residue 122 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain T residue 153 CYS Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 199 GLU Chi-restraints excluded: chain Z residue 229 VAL Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain Z residue 378 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 248 VAL 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 235 LEU Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 154 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 722 PRO Chi-restraints excluded: chain n residue 57 LYS 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 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 35 THR Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 134 SER Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 109 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 137 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 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 109 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 16 ILE Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 72 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain u residue 80 ILE Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 44 PRO Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 667 optimal weight: 50.0000 chunk 454 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 596 optimal weight: 7.9990 chunk 330 optimal weight: 0.6980 chunk 683 optimal weight: 0.0970 chunk 553 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 409 optimal weight: 0.9980 chunk 719 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 overall best weight: 1.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 638 GLN A 658 ASN ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1369 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 428 GLN P 64 GLN ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 119 GLN Z 310 HIS F 65 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN k 33 GLN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 77229 Z= 0.215 Angle : 0.613 13.979 106267 Z= 0.313 Chirality : 0.041 0.284 12649 Planarity : 0.005 0.100 12082 Dihedral : 16.266 178.152 15665 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.72 % Favored : 93.91 % Rotamer: Outliers : 3.17 % Allowed : 16.60 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 1.46 % 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: -0.36 (0.09), residues: 7812 helix: 1.37 (0.09), residues: 3154 sheet: -0.92 (0.14), residues: 1208 loop : -1.53 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP Q 217 HIS 0.019 0.001 HIS A1431 PHE 0.031 0.002 PHE C 364 TYR 0.024 0.002 TYR C 862 ARG 0.006 0.000 ARG c 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 827 time to evaluate : 5.791 Fit side-chains 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 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 revert: symmetry clash 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 Corrupt residue: chain: b residue: PRO 44 >>> skipping REVERT: A 245 ASP cc_start: 0.8710 (m-30) cc_final: 0.8401 (p0) REVERT: A 249 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7470 (pt) REVERT: A 272 ASP cc_start: 0.8149 (m-30) cc_final: 0.7881 (t0) REVERT: A 321 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 397 SER cc_start: 0.9180 (m) cc_final: 0.8882 (p) REVERT: A 495 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7894 (mtp85) REVERT: A 612 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7185 (tmtp) REVERT: A 618 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7521 (p) REVERT: A 800 ASP cc_start: 0.8438 (m-30) cc_final: 0.8124 (t70) REVERT: A 832 GLU cc_start: 0.8933 (tp30) cc_final: 0.8410 (mm-30) REVERT: A 841 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6584 (mp0) REVERT: A 842 LYS cc_start: 0.8666 (tptm) cc_final: 0.8065 (ttpt) REVERT: A 866 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7608 (mm110) REVERT: A 1014 LYS cc_start: 0.8274 (ttmt) cc_final: 0.8052 (tppt) REVERT: A 1151 GLU cc_start: 0.8579 (mp0) cc_final: 0.7859 (tp30) REVERT: A 1242 LYS cc_start: 0.8790 (mttt) cc_final: 0.8318 (mmmt) REVERT: A 1276 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: A 1286 TRP cc_start: 0.8932 (m-10) cc_final: 0.8504 (m-10) REVERT: A 1335 TRP cc_start: 0.8074 (t60) cc_final: 0.7862 (t60) REVERT: A 1422 ILE cc_start: 0.8344 (pp) cc_final: 0.7092 (mt) REVERT: A 1545 ASP cc_start: 0.8637 (m-30) cc_final: 0.8219 (m-30) REVERT: A 1618 ASN cc_start: 0.8092 (t0) cc_final: 0.7611 (t0) REVERT: C 110 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7436 (ttmm) REVERT: C 204 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7509 (mp0) REVERT: C 342 ASP cc_start: 0.8175 (m-30) cc_final: 0.7766 (t0) REVERT: C 362 LYS cc_start: 0.8624 (tttt) cc_final: 0.8314 (mtpp) REVERT: C 446 PHE cc_start: 0.8992 (m-10) cc_final: 0.8603 (m-10) REVERT: C 450 ASP cc_start: 0.8397 (m-30) cc_final: 0.8138 (p0) REVERT: C 614 GLU cc_start: 0.8708 (tp30) cc_final: 0.8142 (tp30) REVERT: C 641 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: C 804 LYS cc_start: 0.7941 (tttt) cc_final: 0.7561 (mtmt) REVERT: C 810 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8650 (mp0) REVERT: C 822 SER cc_start: 0.7530 (t) cc_final: 0.7161 (p) REVERT: C 859 GLU cc_start: 0.8670 (pt0) cc_final: 0.8393 (pt0) REVERT: C 878 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8471 (tp30) REVERT: C 943 ASP cc_start: 0.7262 (m-30) cc_final: 0.6119 (p0) REVERT: C 948 ASP cc_start: 0.9100 (m-30) cc_final: 0.8558 (t0) REVERT: C 972 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7268 (mtm-85) REVERT: R 120 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7227 (t80) REVERT: S 6 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6174 (mmt180) REVERT: S 162 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6909 (mtmm) REVERT: S 167 GLN cc_start: 0.6295 (mt0) cc_final: 0.5928 (mt0) REVERT: T 136 LYS cc_start: 0.6376 (mmtm) cc_final: 0.5968 (mptt) REVERT: T 153 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7799 (m) REVERT: Z 67 LYS cc_start: 0.3030 (OUTLIER) cc_final: 0.2176 (mtmm) REVERT: c 82 ASN cc_start: 0.7464 (p0) cc_final: 0.6916 (p0) REVERT: d 60 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7615 (mtm180) REVERT: H 3 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.5476 (mmt180) REVERT: o 61 SER cc_start: 0.1228 (OUTLIER) cc_final: 0.0699 (t) REVERT: p 1 MET cc_start: 0.3190 (mtt) cc_final: 0.2913 (tpt) REVERT: r 1 MET cc_start: 0.3194 (mtt) cc_final: 0.2586 (mpp) REVERT: k 28 ARG cc_start: 0.6166 (mtt90) cc_final: 0.5692 (mtm-85) REVERT: k 37 PHE cc_start: 0.7101 (p90) cc_final: 0.6702 (p90) REVERT: k 49 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7018 (tp) REVERT: k 90 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7452 (tm-30) REVERT: k 91 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7088 (mm-40) REVERT: i 16 CYS cc_start: 0.5432 (m) cc_final: 0.5211 (m) REVERT: i 91 THR cc_start: -0.0488 (OUTLIER) cc_final: -0.0744 (p) REVERT: h 31 LEU cc_start: 0.6793 (mm) cc_final: 0.6465 (mt) REVERT: h 70 GLU cc_start: 0.4326 (tt0) cc_final: 0.3831 (tm-30) REVERT: j 12 ASP cc_start: 0.6736 (m-30) cc_final: 0.6358 (p0) REVERT: j 35 PHE cc_start: 0.7594 (m-80) cc_final: 0.7239 (t80) REVERT: l 29 TYR cc_start: 0.7354 (m-80) cc_final: 0.6759 (m-80) REVERT: l 35 GLU cc_start: 0.8168 (tp30) cc_final: 0.7696 (tp30) REVERT: m 36 MET cc_start: 0.5740 (ttm) cc_final: 0.5480 (tmm) REVERT: m 47 LEU cc_start: 0.1624 (pt) cc_final: 0.1268 (tp) REVERT: g 96 LEU cc_start: 0.6504 (tp) cc_final: 0.6224 (tp) REVERT: s 35 MET cc_start: 0.3036 (mtt) cc_final: 0.1991 (tpp) REVERT: u 50 MET cc_start: 0.1641 (mmm) cc_final: 0.0792 (ttm) REVERT: y 59 MET cc_start: 0.2930 (ptp) cc_final: 0.1761 (ppp) REVERT: z 20 LYS cc_start: 0.0203 (OUTLIER) cc_final: -0.0726 (tptt) REVERT: b 36 LEU cc_start: 0.3830 (tp) cc_final: 0.2947 (pp) outliers start: 240 outliers final: 175 residues processed: 1010 average time/residue: 0.6884 time to fit residues: 1225.7719 Evaluate side-chains 959 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 766 time to evaluate : 5.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ASN Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 350 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 208 LEU Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 120 TYR Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 25 ILE Chi-restraints excluded: chain S residue 162 LYS Chi-restraints excluded: chain S residue 163 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 98 THR Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain T residue 122 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain T residue 153 CYS Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 199 GLU Chi-restraints excluded: chain Z residue 229 VAL Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain Z residue 378 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 248 VAL 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 60 ARG Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 228 THR Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 154 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 722 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain n residue 61 LYS 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 292 HIS 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 35 THR Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain q residue 137 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 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 109 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 40 HIS Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 54 ASN Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 25 THR Chi-restraints excluded: chain l residue 72 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain u residue 80 ILE Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain b residue 44 PRO Chi-restraints excluded: chain b residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 269 optimal weight: 7.9990 chunk 721 optimal weight: 0.3980 chunk 158 optimal weight: 0.6980 chunk 470 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 802 optimal weight: 20.0000 chunk 665 optimal weight: 30.0000 chunk 371 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 421 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 638 GLN ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1369 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1548 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN C 776 ASN ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 194 HIS ** O 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 GLN ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 ASN P 198 ASN Q 124 GLN Z 66 ASN Z 105 GLN d 210 ASN F 35 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 23 GLN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 77229 Z= 0.265 Angle : 0.637 11.743 106267 Z= 0.326 Chirality : 0.042 0.294 12649 Planarity : 0.005 0.100 12082 Dihedral : 16.184 178.220 15663 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.05 % Favored : 93.56 % Rotamer: Outliers : 3.55 % Allowed : 17.08 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 1.17 % 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: -0.29 (0.09), residues: 7812 helix: 1.44 (0.09), residues: 3158 sheet: -0.74 (0.14), residues: 1171 loop : -1.56 (0.10), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Q 217 HIS 0.020 0.001 HIS A1431 PHE 0.063 0.002 PHE C 364 TYR 0.022 0.002 TYR O 221 ARG 0.009 0.001 ARG e 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 822 time to evaluate : 5.693 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 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 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 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 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: b residue: PRO 44 >>> skipping REVERT: A 249 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7482 (pt) REVERT: A 272 ASP cc_start: 0.8113 (m-30) cc_final: 0.7750 (t0) REVERT: A 495 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7837 (mtp85) REVERT: A 612 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7197 (tmtp) REVERT: A 618 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7576 (p) REVERT: A 800 ASP cc_start: 0.8516 (m-30) cc_final: 0.8299 (t70) REVERT: A 832 GLU cc_start: 0.8929 (tp30) cc_final: 0.8410 (mm-30) REVERT: A 841 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6553 (mp0) REVERT: A 842 LYS cc_start: 0.8695 (tptm) cc_final: 0.8124 (tppt) REVERT: A 866 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7563 (mm110) REVERT: A 1014 LYS cc_start: 0.8289 (ttmt) cc_final: 0.8019 (tppt) REVERT: A 1151 GLU cc_start: 0.8547 (mp0) cc_final: 0.7967 (tp30) REVERT: A 1242 LYS cc_start: 0.8892 (mttt) cc_final: 0.8430 (mmmt) REVERT: A 1276 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: A 1545 ASP cc_start: 0.8660 (m-30) cc_final: 0.8343 (m-30) REVERT: A 1618 ASN cc_start: 0.8126 (t0) cc_final: 0.7642 (t0) REVERT: A 1807 LYS cc_start: 0.8413 (pttm) cc_final: 0.8198 (ptpt) REVERT: A 2025 ILE cc_start: 0.2483 (OUTLIER) cc_final: 0.2176 (mt) REVERT: C 110 LYS cc_start: 0.8012 (mmtp) cc_final: 0.7479 (ttmm) REVERT: C 204 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7560 (mp0) REVERT: C 342 ASP cc_start: 0.8250 (m-30) cc_final: 0.7709 (t0) REVERT: C 362 LYS cc_start: 0.8437 (tttt) cc_final: 0.8147 (mtpp) REVERT: C 369 LYS cc_start: 0.6909 (ptmt) cc_final: 0.6539 (mtpt) REVERT: C 446 PHE cc_start: 0.9069 (m-10) cc_final: 0.8806 (m-10) REVERT: C 674 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7577 (mt) REVERT: C 766 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: C 804 LYS cc_start: 0.8090 (tttt) cc_final: 0.7632 (mtmt) REVERT: C 810 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8753 (mm-30) REVERT: C 818 TYR cc_start: 0.8174 (m-80) cc_final: 0.7569 (m-80) REVERT: C 822 SER cc_start: 0.7569 (t) cc_final: 0.7218 (p) REVERT: C 834 MET cc_start: 0.5471 (mmp) cc_final: 0.5022 (mmp) REVERT: C 859 GLU cc_start: 0.8662 (pt0) cc_final: 0.8402 (pt0) REVERT: C 878 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8363 (tp30) REVERT: C 943 ASP cc_start: 0.7396 (m-30) cc_final: 0.6462 (p0) REVERT: C 948 ASP cc_start: 0.9120 (m-30) cc_final: 0.8433 (t0) REVERT: C 972 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7357 (mtm-85) REVERT: Q 109 MET cc_start: 0.6916 (mmm) cc_final: 0.6661 (tpt) REVERT: R 120 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7379 (t80) REVERT: S 6 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6050 (mmt180) REVERT: S 167 GLN cc_start: 0.6240 (mt0) cc_final: 0.5972 (mt0) REVERT: T 136 LYS cc_start: 0.6497 (mmtm) cc_final: 0.6077 (mptt) REVERT: T 153 CYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8023 (m) REVERT: Z 67 LYS cc_start: 0.3463 (OUTLIER) cc_final: 0.2452 (mtmm) REVERT: c 216 ASP cc_start: 0.3590 (t0) cc_final: 0.3353 (t0) REVERT: H 3 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.5454 (mmt180) REVERT: H 37 ASN cc_start: 0.6790 (t0) cc_final: 0.6561 (t0) REVERT: n 58 ARG cc_start: 0.8720 (mtm110) cc_final: 0.8470 (tmm-80) REVERT: n 292 HIS cc_start: -0.0358 (OUTLIER) cc_final: -0.0979 (p90) REVERT: o 61 SER cc_start: 0.0660 (OUTLIER) cc_final: 0.0133 (t) REVERT: r 1 MET cc_start: 0.3355 (mtt) cc_final: 0.2639 (mpp) REVERT: r 27 LEU cc_start: 0.0234 (tp) cc_final: -0.1095 (tp) REVERT: k 37 PHE cc_start: 0.7102 (p90) cc_final: 0.6791 (p90) REVERT: k 49 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7027 (tp) REVERT: k 90 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7526 (tm-30) REVERT: k 91 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7541 (mm110) REVERT: i 16 CYS cc_start: 0.5389 (m) cc_final: 0.5149 (m) REVERT: i 91 THR cc_start: -0.0684 (OUTLIER) cc_final: -0.0928 (p) REVERT: h 31 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6516 (mt) REVERT: h 70 GLU cc_start: 0.4515 (tt0) cc_final: 0.3973 (tm-30) REVERT: j 12 ASP cc_start: 0.6769 (m-30) cc_final: 0.6257 (t0) REVERT: j 35 PHE cc_start: 0.7510 (m-80) cc_final: 0.7159 (t80) REVERT: j 54 ASN cc_start: 0.6481 (t0) cc_final: 0.6154 (t0) REVERT: j 59 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5439 (tp) REVERT: l 29 TYR cc_start: 0.7386 (m-80) cc_final: 0.6795 (m-80) REVERT: l 35 GLU cc_start: 0.8179 (tp30) cc_final: 0.7468 (tp30) REVERT: l 80 ASN cc_start: 0.9288 (t0) cc_final: 0.8783 (p0) REVERT: m 36 MET cc_start: 0.5793 (ttm) cc_final: 0.5586 (tmm) REVERT: m 47 LEU cc_start: 0.1591 (pt) cc_final: 0.1139 (tp) REVERT: s 35 MET cc_start: 0.3124 (mtt) cc_final: 0.1906 (tpp) REVERT: u 50 MET cc_start: 0.1614 (mmm) cc_final: 0.0853 (ttm) REVERT: y 59 MET cc_start: 0.2921 (ptp) cc_final: 0.1772 (ppp) REVERT: z 20 LYS cc_start: 0.0498 (OUTLIER) cc_final: -0.0464 (tptt) REVERT: e 67 MET cc_start: -0.0797 (tpp) cc_final: -0.1032 (mtt) REVERT: b 36 LEU cc_start: 0.4110 (tp) cc_final: 0.3150 (pp) outliers start: 262 outliers final: 183 residues processed: 1027 average time/residue: 0.6738 time to fit residues: 1222.2669 Evaluate side-chains 963 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 759 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ASN Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1444 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1619 VAL Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 2025 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 766 TRP Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 208 LEU Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 120 TYR Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 25 ILE Chi-restraints excluded: chain S residue 162 LYS Chi-restraints excluded: chain S residue 163 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 98 THR Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain T residue 122 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain T residue 153 CYS Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 199 GLU Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain Z residue 378 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 101 ARG Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 248 VAL 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 77 GLU Chi-restraints excluded: chain d residue 228 THR Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain v residue 580 LEU 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 722 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain n residue 61 LYS Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 292 HIS 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 35 THR Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO 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 109 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 40 HIS Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 54 ASN Chi-restraints excluded: chain h residue 75 CYS Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 59 LEU Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 72 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain u residue 80 ILE Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain b residue 44 PRO Chi-restraints excluded: chain b residue 148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 773 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 457 optimal weight: 9.9990 chunk 585 optimal weight: 5.9990 chunk 453 optimal weight: 6.9990 chunk 675 optimal weight: 4.9990 chunk 447 optimal weight: 6.9990 chunk 799 optimal weight: 0.3980 chunk 500 optimal weight: 3.9990 chunk 487 optimal weight: 0.7980 chunk 368 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1369 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN C 929 GLN O 121 GLN ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 GLN ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 GLN R 252 HIS d 210 ASN F 65 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 33 GLN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 77229 Z= 0.254 Angle : 0.626 12.540 106267 Z= 0.320 Chirality : 0.042 0.293 12649 Planarity : 0.005 0.097 12082 Dihedral : 16.131 178.504 15660 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.97 % Favored : 93.64 % Rotamer: Outliers : 3.20 % Allowed : 18.12 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 1.17 % Twisted General : 0.09 % 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: -0.22 (0.10), residues: 7812 helix: 1.48 (0.09), residues: 3165 sheet: -0.62 (0.15), residues: 1151 loop : -1.55 (0.10), residues: 3496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 217 HIS 0.019 0.001 HIS A1431 PHE 0.053 0.002 PHE C 364 TYR 0.021 0.002 TYR v 669 ARG 0.017 0.001 ARG k 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 804 time to evaluate : 5.623 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 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 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 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 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: b residue: PRO 44 >>> skipping REVERT: A 249 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7520 (pt) REVERT: A 272 ASP cc_start: 0.8061 (m-30) cc_final: 0.7660 (t0) REVERT: A 397 SER cc_start: 0.9206 (m) cc_final: 0.8924 (p) REVERT: A 495 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7906 (mtp85) REVERT: A 612 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7201 (tmtp) REVERT: A 618 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7542 (p) REVERT: A 768 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6390 (mm-30) REVERT: A 800 ASP cc_start: 0.8504 (m-30) cc_final: 0.8303 (t70) REVERT: A 832 GLU cc_start: 0.8921 (tp30) cc_final: 0.8417 (mm-30) REVERT: A 841 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6545 (mp0) REVERT: A 842 LYS cc_start: 0.8714 (tptm) cc_final: 0.8065 (tppt) REVERT: A 908 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: A 937 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8621 (mm) REVERT: A 1151 GLU cc_start: 0.8609 (mp0) cc_final: 0.8024 (tp30) REVERT: A 1242 LYS cc_start: 0.8777 (mttt) cc_final: 0.8267 (mmmt) REVERT: A 1306 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8619 (tp30) REVERT: A 1325 SER cc_start: 0.5610 (t) cc_final: 0.5405 (p) REVERT: A 1545 ASP cc_start: 0.8682 (m-30) cc_final: 0.8349 (m-30) REVERT: A 1618 ASN cc_start: 0.8112 (t0) cc_final: 0.7654 (t0) REVERT: A 1807 LYS cc_start: 0.8373 (pttm) cc_final: 0.8141 (ptpt) REVERT: A 1986 MET cc_start: 0.4733 (ttm) cc_final: 0.3013 (tpp) REVERT: C 110 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7516 (ttmm) REVERT: C 204 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7446 (mp0) REVERT: C 342 ASP cc_start: 0.8241 (m-30) cc_final: 0.7693 (t0) REVERT: C 362 LYS cc_start: 0.8444 (tttt) cc_final: 0.8126 (mtpp) REVERT: C 369 LYS cc_start: 0.6763 (ptmt) cc_final: 0.6477 (mtpt) REVERT: C 384 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7383 (tp) REVERT: C 441 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8403 (mtm-85) REVERT: C 766 TRP cc_start: 0.7847 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: C 804 LYS cc_start: 0.8231 (tttt) cc_final: 0.7766 (mtmt) REVERT: C 810 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8863 (mm-30) REVERT: C 818 TYR cc_start: 0.8213 (m-80) cc_final: 0.7663 (m-80) REVERT: C 822 SER cc_start: 0.7725 (t) cc_final: 0.7389 (p) REVERT: C 834 MET cc_start: 0.5497 (mmp) cc_final: 0.5051 (mmp) REVERT: C 878 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8411 (tp30) REVERT: C 943 ASP cc_start: 0.7339 (m-30) cc_final: 0.6521 (p0) REVERT: C 945 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 948 ASP cc_start: 0.9100 (m-30) cc_final: 0.8406 (t0) REVERT: Q 109 MET cc_start: 0.7081 (mmm) cc_final: 0.6715 (tpt) REVERT: R 53 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8222 (pt) REVERT: R 120 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7379 (t80) REVERT: S 6 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6002 (mmt180) REVERT: S 162 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6924 (mtmm) REVERT: S 167 GLN cc_start: 0.6204 (mt0) cc_final: 0.5983 (mt0) REVERT: T 136 LYS cc_start: 0.6557 (mmtm) cc_final: 0.6091 (mptt) REVERT: T 153 CYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8003 (m) REVERT: Z 67 LYS cc_start: 0.3436 (OUTLIER) cc_final: 0.2483 (mtmm) REVERT: c 216 ASP cc_start: 0.3377 (t0) cc_final: 0.3086 (t0) REVERT: d 210 ASN cc_start: 0.5817 (m-40) cc_final: 0.5602 (m110) REVERT: d 228 THR cc_start: 0.6742 (m) cc_final: 0.6337 (m) REVERT: H 3 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.5285 (mmt180) REVERT: H 37 ASN cc_start: 0.6818 (t0) cc_final: 0.6577 (t0) REVERT: o 61 SER cc_start: 0.0759 (OUTLIER) cc_final: 0.0212 (t) REVERT: r 1 MET cc_start: 0.3260 (mtt) cc_final: 0.2325 (mpp) REVERT: k 49 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7078 (tp) REVERT: k 90 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7654 (tm-30) REVERT: k 91 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7190 (mm-40) REVERT: i 91 THR cc_start: -0.1041 (OUTLIER) cc_final: -0.1300 (p) REVERT: h 70 GLU cc_start: 0.4482 (tt0) cc_final: 0.3928 (tm-30) REVERT: j 12 ASP cc_start: 0.6380 (m-30) cc_final: 0.5970 (t0) REVERT: j 35 PHE cc_start: 0.7616 (m-80) cc_final: 0.7124 (t80) REVERT: j 59 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5522 (tp) REVERT: l 35 GLU cc_start: 0.8078 (tp30) cc_final: 0.7386 (tp30) REVERT: m 36 MET cc_start: 0.5893 (ttm) cc_final: 0.5670 (tmm) REVERT: m 47 LEU cc_start: 0.1777 (pt) cc_final: 0.1352 (tp) REVERT: g 73 LYS cc_start: 0.5582 (tppt) cc_final: 0.5269 (tppt) REVERT: s 35 MET cc_start: 0.3132 (mtt) cc_final: 0.1896 (tpp) REVERT: u 50 MET cc_start: 0.0653 (mmm) cc_final: 0.0036 (ttm) REVERT: y 59 MET cc_start: 0.3099 (ptp) cc_final: 0.1893 (ppp) REVERT: z 20 LYS cc_start: 0.0374 (OUTLIER) cc_final: -0.0478 (tptt) REVERT: e 67 MET cc_start: 0.0411 (tpp) cc_final: 0.0040 (mtm) REVERT: b 36 LEU cc_start: 0.3739 (tp) cc_final: 0.2795 (pp) outliers start: 240 outliers final: 178 residues processed: 996 average time/residue: 0.6650 time to fit residues: 1165.3618 Evaluate side-chains 955 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 756 time to evaluate : 5.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ASN Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1369 ASN Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1444 ILE Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 766 TRP Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 208 LEU Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 257 GLU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 120 TYR Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 25 ILE Chi-restraints excluded: chain S residue 162 LYS Chi-restraints excluded: chain S residue 163 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 98 THR Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain T residue 122 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain T residue 153 CYS Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 193 SER Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 248 VAL 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 77 GLU Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain v residue 580 LEU 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 722 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain n residue 61 LYS Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 257 PRO 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 35 THR Chi-restraints excluded: chain o residue 44 PRO 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 44 PRO Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO 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 109 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 40 HIS Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain h residue 54 ASN Chi-restraints excluded: chain h residue 75 CYS Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 59 LEU Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 72 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain u residue 80 ILE Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 41 THR Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain b residue 44 PRO Chi-restraints excluded: chain b residue 148 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 494 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 477 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 507 optimal weight: 0.7980 chunk 544 optimal weight: 40.0000 chunk 395 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 628 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 541 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 ASN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1548 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 GLN R 44 ASN R 252 HIS T 56 HIS ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN y 61 GLN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 77229 Z= 0.237 Angle : 0.623 18.483 106267 Z= 0.317 Chirality : 0.041 0.291 12649 Planarity : 0.004 0.097 12082 Dihedral : 16.082 178.709 15655 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.04 % Favored : 93.56 % Rotamer: Outliers : 3.23 % Allowed : 18.51 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 1.17 % Twisted General : 0.09 % 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: -0.14 (0.10), residues: 7812 helix: 1.55 (0.09), residues: 3168 sheet: -0.57 (0.15), residues: 1165 loop : -1.52 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1335 HIS 0.019 0.001 HIS A1431 PHE 0.049 0.002 PHE C 364 TYR 0.022 0.002 TYR v 608 ARG 0.008 0.001 ARG A1370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 795 time to evaluate : 5.673 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 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 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 722 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> 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 133 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: b residue: PRO 44 >>> skipping REVERT: A 249 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7468 (pt) REVERT: A 272 ASP cc_start: 0.8070 (m-30) cc_final: 0.7665 (t0) REVERT: A 495 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7944 (mtp85) REVERT: A 612 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7196 (tmtp) REVERT: A 618 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7416 (p) REVERT: A 800 ASP cc_start: 0.8466 (m-30) cc_final: 0.8233 (t70) REVERT: A 832 GLU cc_start: 0.8900 (tp30) cc_final: 0.8395 (mm-30) REVERT: A 841 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6575 (mp0) REVERT: A 842 LYS cc_start: 0.8522 (tptm) cc_final: 0.7940 (tppt) REVERT: A 908 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: A 916 LEU cc_start: 0.9295 (mm) cc_final: 0.9022 (mm) REVERT: A 937 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 1086 ASN cc_start: 0.9051 (m-40) cc_final: 0.8814 (m-40) REVERT: A 1151 GLU cc_start: 0.8684 (mp0) cc_final: 0.8166 (tp30) REVERT: A 1242 LYS cc_start: 0.8669 (mttt) cc_final: 0.8272 (mmmt) REVERT: A 1306 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8615 (tp30) REVERT: A 1369 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8629 (t0) REVERT: A 1379 MET cc_start: 0.6556 (mtp) cc_final: 0.6354 (mtp) REVERT: A 1545 ASP cc_start: 0.8661 (m-30) cc_final: 0.8328 (m-30) REVERT: A 1618 ASN cc_start: 0.8134 (t0) cc_final: 0.7666 (t0) REVERT: A 1807 LYS cc_start: 0.8431 (pttm) cc_final: 0.8177 (ptpt) REVERT: A 1969 MET cc_start: 0.2655 (mtm) cc_final: 0.0798 (tmm) REVERT: A 1986 MET cc_start: 0.4704 (ttm) cc_final: 0.2997 (tpp) REVERT: C 110 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7544 (ttmm) REVERT: C 126 MET cc_start: 0.7608 (tpp) cc_final: 0.7312 (tpp) REVERT: C 204 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7404 (mp0) REVERT: C 342 ASP cc_start: 0.8243 (m-30) cc_final: 0.7707 (t0) REVERT: C 362 LYS cc_start: 0.8405 (tttt) cc_final: 0.8044 (ttmm) REVERT: C 369 LYS cc_start: 0.6801 (ptmt) cc_final: 0.6553 (mtpt) REVERT: C 441 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8398 (mtm-85) REVERT: C 641 GLU cc_start: 0.8144 (pt0) cc_final: 0.7943 (pm20) REVERT: C 716 ASP cc_start: 0.6535 (t0) cc_final: 0.6127 (t70) REVERT: C 766 TRP cc_start: 0.7850 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: C 804 LYS cc_start: 0.8267 (tttt) cc_final: 0.7770 (mtmt) REVERT: C 810 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8873 (mm-30) REVERT: C 818 TYR cc_start: 0.8309 (m-80) cc_final: 0.7751 (m-80) REVERT: C 822 SER cc_start: 0.7768 (t) cc_final: 0.7464 (p) REVERT: C 834 MET cc_start: 0.5827 (mmp) cc_final: 0.5377 (mmp) REVERT: C 878 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8424 (tp30) REVERT: C 943 ASP cc_start: 0.7544 (m-30) cc_final: 0.6622 (p0) REVERT: C 945 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 948 ASP cc_start: 0.9098 (m-30) cc_final: 0.8383 (t0) REVERT: O 253 MET cc_start: 0.7943 (ttm) cc_final: 0.7510 (ttm) REVERT: Q 109 MET cc_start: 0.7125 (mmm) cc_final: 0.6863 (tpt) REVERT: Q 217 TRP cc_start: 0.7091 (p90) cc_final: 0.6619 (p90) REVERT: R 53 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8188 (pt) REVERT: R 120 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7388 (t80) REVERT: R 124 MET cc_start: 0.7750 (mpp) cc_final: 0.7542 (mpp) REVERT: S 6 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.5987 (mmt180) REVERT: S 162 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7089 (mtmm) REVERT: T 136 LYS cc_start: 0.6604 (mmtm) cc_final: 0.6190 (mptt) REVERT: T 153 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7908 (m) REVERT: Z 67 LYS cc_start: 0.3713 (OUTLIER) cc_final: 0.2752 (mtmm) REVERT: c 216 ASP cc_start: 0.3342 (t0) cc_final: 0.3102 (t0) REVERT: d 60 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7769 (mtm180) REVERT: d 81 MET cc_start: 0.7593 (mmm) cc_final: 0.7386 (tpp) REVERT: d 210 ASN cc_start: 0.5805 (m-40) cc_final: 0.5568 (m110) REVERT: d 228 THR cc_start: 0.6925 (OUTLIER) cc_final: 0.6552 (m) REVERT: H 3 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.5610 (mmt180) REVERT: n 296 ILE cc_start: 0.1929 (mt) cc_final: 0.1581 (mp) REVERT: o 61 SER cc_start: 0.0668 (OUTLIER) cc_final: 0.0107 (t) REVERT: r 1 MET cc_start: 0.2868 (mtt) cc_final: 0.1809 (mpp) REVERT: k 21 ARG cc_start: 0.2944 (OUTLIER) cc_final: 0.2000 (mtp-110) REVERT: k 39 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7259 (tmtt) REVERT: k 80 ARG cc_start: 0.7622 (ttm170) cc_final: 0.7318 (ttp80) REVERT: k 90 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7657 (tm-30) REVERT: k 91 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7014 (mm-40) REVERT: i 91 THR cc_start: -0.1315 (OUTLIER) cc_final: -0.1607 (p) REVERT: h 70 GLU cc_start: 0.4510 (tt0) cc_final: 0.3986 (tm-30) REVERT: j 12 ASP cc_start: 0.6285 (m-30) cc_final: 0.5833 (t0) REVERT: j 35 PHE cc_start: 0.7623 (m-80) cc_final: 0.7214 (t80) REVERT: j 59 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5550 (tp) REVERT: l 35 GLU cc_start: 0.8063 (tp30) cc_final: 0.7375 (tp30) REVERT: l 65 ARG cc_start: 0.7149 (ttt180) cc_final: 0.6851 (ttm-80) REVERT: s 8 HIS cc_start: 0.2030 (OUTLIER) cc_final: 0.1546 (t-90) REVERT: s 35 MET cc_start: 0.3122 (mtt) cc_final: 0.1891 (tpp) REVERT: u 50 MET cc_start: 0.0674 (mmm) cc_final: 0.0033 (ttm) REVERT: y 59 MET cc_start: 0.3098 (ptp) cc_final: 0.1912 (ppp) REVERT: z 20 LYS cc_start: 0.0373 (OUTLIER) cc_final: -0.0523 (tptt) REVERT: e 67 MET cc_start: 0.0154 (tpp) cc_final: -0.0162 (mtm) outliers start: 241 outliers final: 182 residues processed: 982 average time/residue: 0.7156 time to fit residues: 1237.7887 Evaluate side-chains 949 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 743 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ASN Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1369 ASN Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1444 ILE Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1619 VAL Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 766 TRP Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 208 LEU Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 257 GLU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 120 TYR Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 25 ILE Chi-restraints excluded: chain S residue 162 LYS Chi-restraints excluded: chain S residue 163 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 98 THR Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain T residue 122 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain T residue 153 CYS Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 193 SER Chi-restraints excluded: chain Z residue 205 TYR Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain Z residue 378 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 101 ARG Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 248 VAL 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 60 ARG Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 228 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain v residue 580 LEU Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 722 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain n residue 61 LYS Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 257 PRO 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 35 THR Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO 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 109 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 21 ARG Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain h residue 54 ASN Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 59 LEU Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 72 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain s residue 8 HIS Chi-restraints excluded: chain u residue 80 ILE Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 41 THR Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain b residue 44 PRO Chi-restraints excluded: chain b residue 148 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 726 optimal weight: 30.0000 chunk 765 optimal weight: 20.0000 chunk 698 optimal weight: 10.0000 chunk 744 optimal weight: 20.0000 chunk 448 optimal weight: 0.3980 chunk 324 optimal weight: 1.9990 chunk 584 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 672 optimal weight: 6.9990 chunk 704 optimal weight: 5.9990 chunk 741 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- 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 839 HIS ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 HIS C 776 ASN ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 HIS ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 GLN c 53 ASN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** g 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 20 ASN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 77229 Z= 0.376 Angle : 0.703 17.114 106267 Z= 0.358 Chirality : 0.044 0.311 12649 Planarity : 0.005 0.103 12082 Dihedral : 16.168 179.221 15649 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.77 % Favored : 92.82 % Rotamer: Outliers : 3.14 % Allowed : 18.99 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 1.17 % Twisted General : 0.09 % 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: -0.39 (0.09), residues: 7812 helix: 1.32 (0.09), residues: 3181 sheet: -0.63 (0.15), residues: 1096 loop : -1.64 (0.10), residues: 3535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1414 HIS 0.022 0.002 HIS A1431 PHE 0.048 0.002 PHE C 364 TYR 0.024 0.002 TYR A 128 ARG 0.006 0.001 ARG C 919 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 761 time to evaluate : 5.663 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 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 Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping revert: symmetry clash Corrupt residue: chain: n residue: PRO 162 >>> 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 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: 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: b residue: PRO 44 >>> skipping REVERT: A 249 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7485 (pt) REVERT: A 272 ASP cc_start: 0.8107 (m-30) cc_final: 0.7754 (t0) REVERT: A 495 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7860 (mtp85) REVERT: A 612 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7262 (tmtp) REVERT: A 618 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 800 ASP cc_start: 0.8512 (m-30) cc_final: 0.8305 (t70) REVERT: A 832 GLU cc_start: 0.8880 (tp30) cc_final: 0.8414 (mm-30) REVERT: A 841 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6673 (mp0) REVERT: A 908 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8224 (m-30) REVERT: A 916 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9104 (mm) REVERT: A 937 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 1151 GLU cc_start: 0.8858 (mp0) cc_final: 0.8404 (tp30) REVERT: A 1218 GLN cc_start: 0.7789 (pm20) cc_final: 0.7479 (tp40) REVERT: A 1242 LYS cc_start: 0.8708 (mttt) cc_final: 0.8302 (mmmt) REVERT: A 1276 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8541 (pp20) REVERT: A 1618 ASN cc_start: 0.8145 (t0) cc_final: 0.7652 (t0) REVERT: A 1807 LYS cc_start: 0.8491 (pttm) cc_final: 0.8195 (ptpt) REVERT: A 1969 MET cc_start: 0.2166 (mtm) cc_final: 0.0592 (tmm) REVERT: A 2025 ILE cc_start: 0.1661 (OUTLIER) cc_final: 0.1441 (mt) REVERT: C 204 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7427 (mp0) REVERT: C 342 ASP cc_start: 0.8222 (m-30) cc_final: 0.7924 (t0) REVERT: C 362 LYS cc_start: 0.8333 (tttt) cc_final: 0.8002 (ttmm) REVERT: C 369 LYS cc_start: 0.6893 (ptmt) cc_final: 0.6662 (mtpt) REVERT: C 441 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.7994 (mtm-85) REVERT: C 716 ASP cc_start: 0.6624 (t0) cc_final: 0.6263 (t70) REVERT: C 766 TRP cc_start: 0.7776 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: C 804 LYS cc_start: 0.8360 (tttt) cc_final: 0.7654 (mtmt) REVERT: C 810 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9037 (mm-30) REVERT: C 818 TYR cc_start: 0.8253 (m-80) cc_final: 0.7792 (m-80) REVERT: C 822 SER cc_start: 0.7779 (t) cc_final: 0.7494 (p) REVERT: C 834 MET cc_start: 0.5970 (mmp) cc_final: 0.5544 (mmp) REVERT: C 878 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8462 (tp30) REVERT: C 943 ASP cc_start: 0.7587 (m-30) cc_final: 0.6856 (p0) REVERT: O 253 MET cc_start: 0.7923 (ttm) cc_final: 0.7562 (ttm) REVERT: Q 217 TRP cc_start: 0.7171 (p90) cc_final: 0.6827 (p90) REVERT: R 53 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8315 (pt) REVERT: R 120 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7653 (t80) REVERT: S 6 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6071 (mmt180) REVERT: T 136 LYS cc_start: 0.6591 (mmtm) cc_final: 0.6266 (mptt) REVERT: T 153 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8083 (m) REVERT: Z 67 LYS cc_start: 0.3829 (OUTLIER) cc_final: 0.2910 (mtmm) REVERT: d 210 ASN cc_start: 0.6071 (m-40) cc_final: 0.5763 (m110) REVERT: d 228 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6896 (m) REVERT: H 3 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.5292 (mmt180) REVERT: n 296 ILE cc_start: 0.2521 (mt) cc_final: 0.1993 (mp) REVERT: r 1 MET cc_start: 0.2827 (mtt) cc_final: 0.1725 (mpp) REVERT: k 21 ARG cc_start: 0.2951 (OUTLIER) cc_final: 0.1968 (mtp-110) REVERT: k 39 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7350 (tmtt) REVERT: i 91 THR cc_start: -0.1121 (OUTLIER) cc_final: -0.1422 (p) REVERT: h 70 GLU cc_start: 0.4547 (tt0) cc_final: 0.3981 (tm-30) REVERT: j 12 ASP cc_start: 0.6650 (m-30) cc_final: 0.6037 (t0) REVERT: j 35 PHE cc_start: 0.7626 (m-80) cc_final: 0.7287 (t80) REVERT: j 59 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5584 (tp) REVERT: j 71 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7124 (pp) REVERT: l 35 GLU cc_start: 0.8050 (tp30) cc_final: 0.7343 (tp30) REVERT: m 36 MET cc_start: 0.5999 (ttp) cc_final: 0.5681 (tpt) REVERT: g 38 MET cc_start: 0.5871 (tpt) cc_final: 0.4809 (ttp) REVERT: s 8 HIS cc_start: 0.1904 (OUTLIER) cc_final: 0.1412 (t-90) REVERT: s 35 MET cc_start: 0.2697 (mtt) cc_final: 0.1411 (tpp) REVERT: u 50 MET cc_start: 0.0102 (mmm) cc_final: -0.0302 (mtm) REVERT: y 59 MET cc_start: 0.3139 (ptp) cc_final: 0.2048 (ppp) REVERT: z 20 LYS cc_start: -0.0355 (OUTLIER) cc_final: -0.0830 (tptt) REVERT: e 67 MET cc_start: -0.0312 (tpp) cc_final: -0.0583 (mtm) outliers start: 231 outliers final: 178 residues processed: 935 average time/residue: 0.6801 time to fit residues: 1116.8249 Evaluate side-chains 927 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 726 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ASN Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1444 ILE Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1619 VAL Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 2025 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 766 TRP Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 110 HIS Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 208 LEU Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 257 GLU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 120 TYR Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 25 ILE Chi-restraints excluded: chain S residue 163 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 98 THR Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain T residue 122 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain T residue 153 CYS Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 193 SER Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain Z residue 378 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 101 ARG Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 248 VAL 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 77 GLU Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 228 THR Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain v residue 580 LEU Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain n residue 61 LYS Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 257 PRO 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 436 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 35 THR 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 109 LEU Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO 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 109 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 21 ARG Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 16 CYS Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain h residue 54 ASN Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 59 LEU Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 72 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain g residue 24 PHE Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain s residue 8 HIS Chi-restraints excluded: chain u residue 80 ILE Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain y residue 20 SER Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 41 THR Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain b residue 44 PRO Chi-restraints excluded: chain b residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 488 optimal weight: 1.9990 chunk 787 optimal weight: 20.0000 chunk 480 optimal weight: 1.9990 chunk 373 optimal weight: 0.3980 chunk 547 optimal weight: 30.0000 chunk 825 optimal weight: 20.0000 chunk 760 optimal weight: 20.0000 chunk 657 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 507 optimal weight: 0.5980 chunk 403 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN A1369 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 GLN F 65 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN g 35 ASN z 30 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 77229 Z= 0.180 Angle : 0.620 12.078 106267 Z= 0.315 Chirality : 0.041 0.298 12649 Planarity : 0.004 0.104 12082 Dihedral : 16.094 178.782 15645 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.40 % Favored : 94.23 % Rotamer: Outliers : 2.20 % Allowed : 20.08 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 0.88 % Twisted General : 0.08 % 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: -0.09 (0.10), residues: 7812 helix: 1.57 (0.09), residues: 3177 sheet: -0.52 (0.15), residues: 1147 loop : -1.49 (0.10), residues: 3488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1570 HIS 0.018 0.001 HIS A1431 PHE 0.046 0.001 PHE C 364 TYR 0.019 0.001 TYR v 608 ARG 0.007 0.000 ARG H 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 784 time to evaluate : 5.753 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 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 Corrupt residue: chain: v residue: PRO 616 >>> skipping Corrupt residue: chain: v residue: PRO 617 >>> skipping revert: symmetry clash Corrupt residue: chain: n residue: PRO 162 >>> 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 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: 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: b residue: PRO 44 >>> skipping REVERT: A 249 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7372 (pt) REVERT: A 272 ASP cc_start: 0.8198 (m-30) cc_final: 0.7851 (t0) REVERT: A 495 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7914 (mtp85) REVERT: A 612 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7183 (tmtp) REVERT: A 618 SER cc_start: 0.7745 (OUTLIER) cc_final: 0.7379 (p) REVERT: A 800 ASP cc_start: 0.8351 (m-30) cc_final: 0.8068 (t70) REVERT: A 832 GLU cc_start: 0.8961 (tp30) cc_final: 0.8473 (mm-30) REVERT: A 841 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6566 (mp0) REVERT: A 842 LYS cc_start: 0.8698 (tptp) cc_final: 0.7944 (ttpt) REVERT: A 908 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: A 937 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 972 MET cc_start: 0.8619 (ptm) cc_final: 0.8380 (ptm) REVERT: A 1151 GLU cc_start: 0.8829 (mp0) cc_final: 0.8396 (tp30) REVERT: A 1242 LYS cc_start: 0.8667 (mttt) cc_final: 0.8270 (mmmt) REVERT: A 1276 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8628 (pp20) REVERT: A 1306 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8574 (tp30) REVERT: A 1379 MET cc_start: 0.6666 (mtp) cc_final: 0.6456 (mtp) REVERT: A 1545 ASP cc_start: 0.8743 (m-30) cc_final: 0.8379 (m-30) REVERT: A 1618 ASN cc_start: 0.8116 (t0) cc_final: 0.7679 (t0) REVERT: A 1807 LYS cc_start: 0.8415 (pttm) cc_final: 0.8106 (ptpt) REVERT: A 1948 MET cc_start: 0.4412 (mmm) cc_final: 0.4168 (mmm) REVERT: A 1969 MET cc_start: 0.2233 (mtm) cc_final: 0.0672 (tmm) REVERT: A 1986 MET cc_start: 0.4333 (ttm) cc_final: 0.3859 (ttp) REVERT: C 110 LYS cc_start: 0.7990 (mmtp) cc_final: 0.7455 (ttmm) REVERT: C 204 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7476 (mp0) REVERT: C 342 ASP cc_start: 0.8208 (m-30) cc_final: 0.7743 (t0) REVERT: C 362 LYS cc_start: 0.8395 (tttt) cc_final: 0.8064 (ttmm) REVERT: C 369 LYS cc_start: 0.7155 (ptmt) cc_final: 0.6114 (mtpt) REVERT: C 441 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8280 (mtm-85) REVERT: C 716 ASP cc_start: 0.6566 (t0) cc_final: 0.6187 (t70) REVERT: C 766 TRP cc_start: 0.7811 (OUTLIER) cc_final: 0.7564 (m-10) REVERT: C 804 LYS cc_start: 0.8318 (tttt) cc_final: 0.7623 (mtmt) REVERT: C 810 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8951 (mm-30) REVERT: C 818 TYR cc_start: 0.8312 (m-80) cc_final: 0.7876 (m-80) REVERT: C 822 SER cc_start: 0.7786 (t) cc_final: 0.7548 (p) REVERT: C 878 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8476 (tp30) REVERT: C 943 ASP cc_start: 0.7544 (m-30) cc_final: 0.6773 (p0) REVERT: P 201 PHE cc_start: 0.5921 (m-10) cc_final: 0.5718 (m-10) REVERT: Q 103 GLU cc_start: 0.6899 (tt0) cc_final: 0.6509 (tt0) REVERT: Q 217 TRP cc_start: 0.7050 (p90) cc_final: 0.6734 (p90) REVERT: R 53 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8308 (pt) REVERT: R 120 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7325 (t80) REVERT: S 6 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6396 (mmt180) REVERT: T 136 LYS cc_start: 0.6504 (mmtm) cc_final: 0.6138 (mptt) REVERT: T 153 CYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7742 (m) REVERT: Z 67 LYS cc_start: 0.3890 (OUTLIER) cc_final: 0.2964 (mtmm) REVERT: c 216 ASP cc_start: 0.3377 (t0) cc_final: 0.3067 (t0) REVERT: d 81 MET cc_start: 0.7382 (tpp) cc_final: 0.7117 (mmm) REVERT: d 210 ASN cc_start: 0.6145 (m-40) cc_final: 0.5943 (m110) REVERT: d 228 THR cc_start: 0.7244 (m) cc_final: 0.6909 (m) REVERT: F 44 MET cc_start: 0.6527 (mtt) cc_final: 0.6280 (ptp) REVERT: H 3 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.5123 (mmt180) REVERT: r 1 MET cc_start: 0.2900 (mtt) cc_final: 0.1839 (mpp) REVERT: k 39 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7329 (tmtt) REVERT: h 55 GLU cc_start: 0.5032 (mt-10) cc_final: 0.4712 (pp20) REVERT: h 70 GLU cc_start: 0.4494 (tt0) cc_final: 0.3965 (tm-30) REVERT: j 12 ASP cc_start: 0.6287 (m-30) cc_final: 0.5796 (t0) REVERT: j 35 PHE cc_start: 0.7775 (m-80) cc_final: 0.7294 (t80) REVERT: j 71 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7083 (pp) REVERT: l 35 GLU cc_start: 0.8173 (tp30) cc_final: 0.7597 (tp30) REVERT: m 36 MET cc_start: 0.5670 (ttp) cc_final: 0.5431 (tpt) REVERT: g 38 MET cc_start: 0.6193 (tpt) cc_final: 0.4978 (ttp) REVERT: s 8 HIS cc_start: 0.2005 (OUTLIER) cc_final: 0.1540 (t-90) REVERT: s 35 MET cc_start: 0.3012 (mtt) cc_final: 0.1704 (tpp) REVERT: u 50 MET cc_start: 0.0584 (mmm) cc_final: 0.0125 (mtm) REVERT: y 59 MET cc_start: 0.3269 (ptp) cc_final: 0.2183 (ppp) outliers start: 172 outliers final: 135 residues processed: 922 average time/residue: 0.6878 time to fit residues: 1115.1922 Evaluate side-chains 885 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 734 time to evaluate : 5.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ASN Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1369 ASN Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 766 TRP Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain Q residue 34 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 245 LYS Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 120 TYR Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 25 ILE Chi-restraints excluded: chain T residue 98 THR Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain T residue 122 CYS Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 148 CYS Chi-restraints excluded: chain T residue 153 CYS Chi-restraints excluded: chain Z residue 67 LYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 193 SER Chi-restraints excluded: chain Z residue 320 ASN Chi-restraints excluded: chain Z residue 337 SER Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 101 ARG Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 248 VAL 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 94 VAL Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 3 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain v residue 616 PRO Chi-restraints excluded: chain v residue 617 PRO Chi-restraints excluded: chain v residue 725 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain n residue 61 LYS Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 257 PRO 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 436 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 35 THR 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 109 LEU Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 21 THR Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO 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 109 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 49 ILE Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain i residue 16 CYS Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain h residue 54 ASN Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain s residue 8 HIS Chi-restraints excluded: chain u residue 80 ILE Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain b residue 44 PRO Chi-restraints excluded: chain b residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 829 random chunks: chunk 522 optimal weight: 5.9990 chunk 700 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 606 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 658 optimal weight: 50.0000 chunk 275 optimal weight: 2.9990 chunk 676 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 GLN ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 ASN c 53 ASN F 65 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN j 18 ASN w 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.192879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140494 restraints weight = 148500.034| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.20 r_work: 0.3333 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 77229 Z= 0.258 Angle : 0.643 15.043 106267 Z= 0.327 Chirality : 0.042 0.305 12649 Planarity : 0.005 0.105 12082 Dihedral : 16.069 179.224 15645 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.22 % Favored : 93.42 % Rotamer: Outliers : 2.10 % Allowed : 20.24 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 0.88 % Twisted General : 0.08 % 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: -0.12 (0.10), residues: 7812 helix: 1.54 (0.09), residues: 3181 sheet: -0.49 (0.15), residues: 1119 loop : -1.50 (0.10), residues: 3512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1570 HIS 0.019 0.001 HIS A1431 PHE 0.042 0.002 PHE C 364 TYR 0.023 0.002 TYR A1813 ARG 0.022 0.001 ARG A1370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22497.31 seconds wall clock time: 386 minutes 36.95 seconds (23196.95 seconds total)