Starting phenix.real_space_refine on Mon Sep 30 08:04:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/09_2024/5mq0_3541_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/09_2024/5mq0_3541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/09_2024/5mq0_3541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/09_2024/5mq0_3541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/09_2024/5mq0_3541_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/09_2024/5mq0_3541_neut.cif" } resolution = 4.17 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= 0.003 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 6 6.06 5 P 457 5.49 5 Mg 3 5.21 5 S 209 5.16 5 C 47117 2.51 5 N 13955 2.21 5 O 15692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 77441 Number of models: 1 Model: "" Number of chains: 53 Chain: "I" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 714 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna2p': 3, 'rna3p': 30} Chain breaks: 1 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 346 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 10} Chain: "2" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3271 Classifications: {'RNA': 155} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 10, 'rna3p_pur': 64, 'rna3p_pyr': 78} Link IDs: {'rna2p': 13, 'rna3p': 141} Chain breaks: 8 Chain: "6" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2108 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 12, 'rna3p_pur': 45, 'rna3p_pyr': 34} Link IDs: {'rna2p': 20, 'rna3p': 78} Chain breaks: 1 Chain: "5" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2999 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 61} Link IDs: {'rna2p': 20, 'rna3p': 120} Chain breaks: 2 Chain: "A" Number of atoms: 15199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1914, 15199 Classifications: {'peptide': 1914} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 2, 'PTRANS': 98, 'TRANS': 1813} Chain breaks: 3 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 28, 'PHE:plan': 1, 'GLU:plan': 69, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 459 Chain: "C" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6562 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 49, 'TRANS': 824} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 37, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 283 Chain: "H" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3261 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 394} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2690 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1458 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1162 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 76 Chain: "M" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2016 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 241} 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: "N" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1798 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1755 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 Chain: "P" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 2 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: "R" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 614 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 13, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 173 Chain: "S" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3229 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 8, 'TRANS': 459} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 853 Unresolved non-hydrogen angles: 1096 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 17, 'ASN:plan1': 5, 'TRP:plan': 8, 'ASP:plan': 12, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 513 Chain: "T" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 3064 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 567} Link IDs: {'PTRANS': 14, 'TRANS': 600} Chain breaks: 27 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2223 Unresolved non-hydrogen angles: 2859 Unresolved non-hydrogen dihedrals: 1910 Unresolved non-hydrogen chiralities: 178 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 8, 'TYR:plan': 33, 'ASN:plan1': 23, 'TRP:plan': 19, 'ASP:plan': 30, 'PHE:plan': 31, 'GLU:plan': 62, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 1302 Chain: "T" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "a" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1119 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 786 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 60 Chain: "o" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2425 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "X" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 338 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 66} Link IDs: {'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "y" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 679 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 Chain: "b" 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: "d" 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: {'PCIS': 1, 'PTRANS': 3, '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: "e" 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: "f" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} 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: "g" 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: "h" 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: "j" 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: "V" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 3189 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 569} Link IDs: {'PTRANS': 30, 'TRANS': 614} Chain breaks: 1 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 2019 Unresolved non-hydrogen angles: 2575 Unresolved non-hydrogen dihedrals: 1674 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 15, 'TYR:plan': 29, 'ASN:plan1': 25, 'TRP:plan': 2, 'ASP:plan': 35, 'PHE:plan': 25, 'GLU:plan': 40, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 1056 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: "l" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 618 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "n" 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: {'PCIS': 1, 'PTRANS': 3, '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: "r" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 526 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 816 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 694 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 14, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 8, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 294 Chain: "Y" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 416 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "p" 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: "q" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} 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: "3" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "s" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 548 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 237 Chain: "t" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 2171 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 395} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 5 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1372 Unresolved non-hydrogen angles: 1761 Unresolved non-hydrogen dihedrals: 1142 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 21, 'ASN:plan1': 25, 'TRP:plan': 6, 'ASP:plan': 35, 'PHE:plan': 12, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 708 Chain: "u" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 578 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 588 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "w" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 2156 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 392} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 5 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1365 Unresolved non-hydrogen angles: 1753 Unresolved non-hydrogen dihedrals: 1136 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 21, 'ASN:plan1': 25, 'TRP:plan': 6, 'ASP:plan': 35, 'PHE:plan': 12, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 700 Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 2, ' MG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39416 SG CYS L 104 174.825 184.199 99.661 1.00 75.41 S ATOM 39422 SG CYS L 105 171.484 184.196 102.152 1.00 94.62 S ATOM 39447 SG CYS L 108 174.592 181.531 101.558 1.00 75.02 S ATOM 39727 SG CYS L 148 172.421 182.236 98.785 1.00 84.39 S ATOM 39416 SG CYS L 104 174.825 184.199 99.661 1.00 75.41 S ATOM 39546 SG CYS L 122 177.833 181.020 99.531 1.00 79.14 S ATOM 39737 SG CYS L 150 176.230 182.600 96.606 1.00 83.92 S ATOM 39752 SG CYS L 153 177.808 184.783 98.534 1.00108.43 S ATOM 39447 SG CYS L 108 174.592 181.531 101.558 1.00 75.02 S ATOM 39532 SG CYS L 120 177.038 178.718 101.049 1.00 81.56 S ATOM 39546 SG CYS L 122 177.833 181.020 99.531 1.00 79.14 S ATOM 39704 SG CYS L 145 174.170 178.576 99.287 1.00 99.48 S ATOM 40337 SG CYS M 73 167.095 160.151 87.995 1.00 81.57 S ATOM 40399 SG CYS M 81 165.790 163.175 86.354 1.00 83.60 S ATOM 40439 SG CYS M 87 169.068 163.374 88.583 1.00106.84 S ATOM 42021 SG CYS N 34 170.190 146.082 113.528 1.00 79.22 S ATOM 42044 SG CYS N 37 170.308 144.168 116.076 1.00 94.61 S ATOM 42243 SG CYS N 61 173.325 145.867 116.331 1.00 90.51 S ATOM 42267 SG CYS N 64 173.135 143.053 114.643 1.00101.83 S ATOM 41863 SG CYS N 13 186.031 148.469 105.552 1.00136.95 S ATOM 41887 SG CYS N 16 183.206 150.992 104.415 1.00150.78 S ATOM 42321 SG CYS N 71 182.398 148.333 107.330 1.00119.28 S ATOM 42342 SG CYS N 74 183.285 148.546 103.872 1.00120.09 S Time building chain proxies: 33.44, per 1000 atoms: 0.43 Number of scatterers: 77441 At special positions: 0 Unit cell: (290.29, 286, 247.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 K 2 19.00 S 209 16.00 P 457 15.00 Mg 3 11.99 O 15692 8.00 N 13955 7.00 C 47117 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 Atom "ATOM 3992 O4' G 21149 .*. O " rejected from bonding due to valence issues. Atom "ATOM 3992 O4' G 21149 .*. O " rejected from bonding due to valence issues. Atom "ATOM 3992 O4' G 21149 .*. O " rejected from bonding due to valence issues. Atom "ATOM 3992 O4' G 21149 .*. O " rejected from bonding due to valence issues. Atom "ATOM 3989 O5' G 21149 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.28 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 148 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 105 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 150 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 153 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 145 " pdb=" ZN M1000 " pdb="ZN ZN M1000 " - pdb=" NE2 HIS M 91 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 73 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 87 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 81 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 34 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 64 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 61 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 71 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 16 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 74 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 13 " Number of angles added : 33 18814 Ramachandran restraints generated. 9407 Oldfield, 0 Emsley, 9407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18678 Finding SS restraints... Secondary structure from input PDB file: 344 helices and 75 sheets defined 47.5% alpha, 13.6% beta 140 base pairs and 235 stacking pairs defined. Time for finding SS restraints: 24.63 Creating SS restraints... Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.890A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.575A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'A' and resid 209 through 231 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.980A pdb=" N ASP A 278 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 removed outlier: 3.579A pdb=" N MET A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.609A pdb=" N TYR A 328 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.501A pdb=" N ASN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.882A pdb=" N SER A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.746A pdb=" N PHE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 535 Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.639A pdb=" N THR A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 587 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 618 through 641 Processing helix chain 'A' and resid 645 through 659 Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.059A pdb=" N TYR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 692 removed outlier: 4.107A pdb=" N GLN A 676 " --> pdb=" O LYS A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 735 Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 749 through 770 Processing helix chain 'A' and resid 775 through 796 removed outlier: 3.705A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 837 Processing helix chain 'A' and resid 841 through 870 Processing helix chain 'A' and resid 875 through 894 Processing helix chain 'A' and resid 907 through 926 removed outlier: 3.717A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 985 through 1007 removed outlier: 3.714A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1035 Processing helix chain 'A' and resid 1062 through 1074 Processing helix chain 'A' and resid 1075 through 1087 removed outlier: 3.510A pdb=" N ALA A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1136 removed outlier: 3.587A pdb=" N ILE A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLU A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A1130 " --> pdb=" O LEU A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1156 removed outlier: 3.746A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N HIS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 Processing helix chain 'A' and resid 1216 through 1234 Processing helix chain 'A' and resid 1242 through 1244 No H-bonds generated for 'chain 'A' and resid 1242 through 1244' Processing helix chain 'A' and resid 1305 through 1321 Processing helix chain 'A' and resid 1327 through 1346 Processing helix chain 'A' and resid 1347 through 1351 Processing helix chain 'A' and resid 1353 through 1375 Processing helix chain 'A' and resid 1385 through 1390 Processing helix chain 'A' and resid 1391 through 1395 removed outlier: 3.707A pdb=" N GLY A1395 " --> pdb=" O LYS A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1416 Processing helix chain 'A' and resid 1440 through 1444 Processing helix chain 'A' and resid 1446 through 1472 Processing helix chain 'A' and resid 1482 through 1486 removed outlier: 4.034A pdb=" N ASP A1485 " --> pdb=" O GLY A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1495 Processing helix chain 'A' and resid 1498 through 1503 Processing helix chain 'A' and resid 1507 through 1515 removed outlier: 3.739A pdb=" N ARG A1511 " --> pdb=" O GLY A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1534 Processing helix chain 'A' and resid 1539 through 1550 Processing helix chain 'A' and resid 1551 through 1560 removed outlier: 3.633A pdb=" N THR A1555 " --> pdb=" O GLY A1551 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A1560 " --> pdb=" O ILE A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1566 removed outlier: 3.513A pdb=" N THR A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1569 through 1574 removed outlier: 4.021A pdb=" N PHE A1574 " --> pdb=" O GLU A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1610 removed outlier: 3.786A pdb=" N ARG A1605 " --> pdb=" O ILE A1601 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A1606 " --> pdb=" O PRO A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1615 Processing helix chain 'A' and resid 1638 through 1649 Processing helix chain 'A' and resid 1652 through 1672 Processing helix chain 'A' and resid 1687 through 1692 Processing helix chain 'A' and resid 1748 through 1760 Processing helix chain 'A' and resid 1794 through 1808 Processing helix chain 'A' and resid 1809 through 1823 Processing helix chain 'A' and resid 1840 through 1844 removed outlier: 3.794A pdb=" N PHE A1844 " --> pdb=" O ALA A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1901 removed outlier: 3.829A pdb=" N GLY A1901 " --> pdb=" O SER A1897 " (cutoff:3.500A) Processing helix chain 'A' and resid 1904 through 1924 removed outlier: 3.668A pdb=" N LYS A1910 " --> pdb=" O SER A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1940 through 1948 removed outlier: 3.575A pdb=" N LEU A1944 " --> pdb=" O MET A1940 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A1946 " --> pdb=" O ASP A1942 " (cutoff:3.500A) 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 1966 through 1970 removed outlier: 3.539A pdb=" N MET A1969 " --> pdb=" O SER A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1981 Processing helix chain 'A' and resid 1993 through 1999 Processing helix chain 'A' and resid 2000 through 2018 Processing helix chain 'A' and resid 2018 through 2027 Processing helix chain 'A' and resid 2044 through 2067 Processing helix chain 'A' and resid 2074 through 2084 Processing helix chain 'A' and resid 2090 through 2100 removed outlier: 3.751A pdb=" N LYS A2094 " --> pdb=" O ALA A2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 145 through 158 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 221 through 232 Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 269 through 276 removed outlier: 4.090A pdb=" N LEU C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 340 through 349 removed outlier: 4.319A pdb=" N TRP C 349 " --> pdb=" O THR C 345 " (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 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.860A pdb=" N GLN C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 447 through 457 removed outlier: 4.071A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.958A pdb=" N GLU C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY C 466 " --> pdb=" O THR C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 466' Processing helix chain 'C' and resid 507 through 515 Processing helix chain 'C' and resid 567 through 571 Processing helix chain 'C' and resid 582 through 589 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: 3.668A pdb=" N LEU C 618 " --> pdb=" O GLU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 662 removed outlier: 3.511A pdb=" N MET C 652 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 725 removed outlier: 3.600A pdb=" N GLN C 721 " --> pdb=" O SER C 717 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 725 " --> pdb=" O GLN C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 756 Processing helix chain 'C' and resid 759 through 765 removed outlier: 3.545A pdb=" N VAL C 765 " --> pdb=" O ALA C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 805 Processing helix chain 'C' and resid 830 through 853 Proline residue: C 840 - end of helix Processing helix chain 'C' and resid 869 through 871 No H-bonds generated for 'chain 'C' and resid 869 through 871' Processing helix chain 'C' and resid 872 through 883 removed outlier: 3.802A pdb=" N VAL C 876 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 922 Processing helix chain 'C' and resid 961 through 975 Processing helix chain 'C' and resid 990 through 997 Processing helix chain 'H' and resid 12 through 32 Proline residue: H 27 - end of helix removed outlier: 3.826A pdb=" N SER H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 36 through 47 removed outlier: 3.752A pdb=" N SER H 40 " --> pdb=" O ASN H 36 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL H 47 " --> pdb=" O ASP H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 66 Processing helix chain 'H' and resid 71 through 87 Processing helix chain 'H' and resid 87 through 108 removed outlier: 3.996A pdb=" N GLY H 91 " --> pdb=" O ILE H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 127 Processing helix chain 'H' and resid 133 through 145 removed outlier: 4.065A pdb=" N LYS H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 165 removed outlier: 3.698A pdb=" N MET H 155 " --> pdb=" O VAL H 151 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TRP H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 183 Processing helix chain 'H' and resid 187 through 204 removed outlier: 3.681A pdb=" N LYS H 203 " --> pdb=" O GLU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 262 removed outlier: 4.277A pdb=" N LEU H 251 " --> pdb=" O ASN H 247 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR H 252 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 254 " --> pdb=" O GLU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 302 removed outlier: 3.609A pdb=" N SER H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 315 removed outlier: 3.501A pdb=" N ALA H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 336 Processing helix chain 'H' and resid 340 through 354 removed outlier: 3.740A pdb=" N HIS H 354 " --> pdb=" O MET H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 371 Processing helix chain 'H' and resid 372 through 376 Processing helix chain 'H' and resid 377 through 393 Processing helix chain 'H' and resid 415 through 431 Processing helix chain 'H' and resid 432 through 443 Processing helix chain 'H' and resid 457 through 468 removed outlier: 3.745A pdb=" N SER H 461 " --> pdb=" O HIS H 457 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 468 " --> pdb=" O PHE H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 481 Processing helix chain 'J' and resid 111 through 121 Processing helix chain 'K' and resid 39 through 43 Processing helix chain 'K' and resid 59 through 85 Processing helix chain 'K' and resid 87 through 94 removed outlier: 3.868A pdb=" N ARG K 92 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR K 93 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL K 94 " --> pdb=" O SER K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 164 Proline residue: K 160 - end of helix Processing helix chain 'K' and resid 181 through 186 Processing helix chain 'K' and resid 200 through 225 Processing helix chain 'L' and resid 15 through 34 removed outlier: 4.310A pdb=" N ILE L 19 " --> pdb=" O GLY L 15 " (cutoff:3.500A) Proline residue: L 21 - end of helix removed outlier: 3.549A pdb=" N PHE L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 68 Processing helix chain 'L' and resid 74 through 85 Processing helix chain 'L' and resid 88 through 97 Processing helix chain 'L' and resid 105 through 110 removed outlier: 3.848A pdb=" N GLN L 110 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 124 Processing helix chain 'L' and resid 125 through 137 Processing helix chain 'M' and resid 54 through 59 Processing helix chain 'M' and resid 63 through 68 Processing helix chain 'M' and resid 73 through 78 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.564A pdb=" N CYS M 87 " --> pdb=" O GLY M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 103 Processing helix chain 'M' and resid 104 through 108 removed outlier: 3.783A pdb=" N GLU M 107 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 146 Processing helix chain 'M' and resid 152 through 166 removed outlier: 3.655A pdb=" N ARG M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 199 Processing helix chain 'M' and resid 231 through 254 removed outlier: 4.182A pdb=" N ARG M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE M 254 " --> pdb=" O MET M 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 18 removed outlier: 3.903A pdb=" N LEU N 17 " --> pdb=" O CYS N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 69 Processing helix chain 'N' and resid 83 through 94 Processing helix chain 'N' and resid 106 through 116 removed outlier: 4.013A pdb=" N ARG N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 128 removed outlier: 4.417A pdb=" N ASP N 128 " --> pdb=" O GLN N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 144 Processing helix chain 'N' and resid 215 through 226 Processing helix chain 'N' and resid 255 through 266 Processing helix chain 'N' and resid 307 through 324 Processing helix chain 'O' and resid 14 through 29 Processing helix chain 'O' and resid 32 through 40 removed outlier: 3.568A pdb=" N VAL O 36 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 66 through 80 Processing helix chain 'O' and resid 83 through 92 Processing helix chain 'O' and resid 94 through 107 Processing helix chain 'O' and resid 145 through 160 Processing helix chain 'O' and resid 164 through 195 Processing helix chain 'O' and resid 230 through 251 Processing helix chain 'P' and resid 14 through 20 Processing helix chain 'P' and resid 163 through 173 Processing helix chain 'R' and resid 10 through 15 removed outlier: 4.528A pdb=" N SER R 14 " --> pdb=" O SER R 10 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 10 through 15' Processing helix chain 'R' and resid 25 through 31 Processing helix chain 'R' and resid 36 through 47 removed outlier: 4.001A pdb=" N GLN R 40 " --> pdb=" O GLN R 36 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN R 43 " --> pdb=" O ARG R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 87 Processing helix chain 'R' and resid 91 through 116 removed outlier: 4.007A pdb=" N ILE R 95 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 61 Processing helix chain 'S' and resid 64 through 79 Processing helix chain 'S' and resid 80 through 95 removed outlier: 3.628A pdb=" N ALA S 84 " --> pdb=" O ASP S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 112 removed outlier: 3.845A pdb=" N TRP S 102 " --> pdb=" O PHE S 98 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 129 Processing helix chain 'S' and resid 132 through 147 removed outlier: 4.468A pdb=" N TRP S 136 " --> pdb=" O VAL S 132 " (cutoff:3.500A) Processing helix chain 'S' and resid 148 through 162 Processing helix chain 'S' and resid 165 through 179 removed outlier: 3.605A pdb=" N TRP S 169 " --> pdb=" O GLY S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 196 Processing helix chain 'S' and resid 198 through 212 Processing helix chain 'S' and resid 214 through 232 removed outlier: 4.083A pdb=" N THR S 218 " --> pdb=" O ASN S 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 257 removed outlier: 3.776A pdb=" N VAL S 243 " --> pdb=" O SER S 239 " (cutoff:3.500A) Processing helix chain 'S' and resid 259 through 274 removed outlier: 3.751A pdb=" N SER S 263 " --> pdb=" O GLU S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 291 Processing helix chain 'S' and resid 296 through 315 Processing helix chain 'S' and resid 321 through 332 Processing helix chain 'S' and resid 335 through 349 Processing helix chain 'S' and resid 357 through 377 Processing helix chain 'S' and resid 382 through 395 Processing helix chain 'S' and resid 404 through 416 Processing helix chain 'S' and resid 420 through 432 removed outlier: 3.562A pdb=" N LYS S 425 " --> pdb=" O PRO S 421 " (cutoff:3.500A) Processing helix chain 'S' and resid 440 through 450 Processing helix chain 'S' and resid 453 through 467 Processing helix chain 'S' and resid 471 through 483 Processing helix chain 'S' and resid 486 through 500 Processing helix chain 'S' and resid 508 through 521 Processing helix chain 'S' and resid 531 through 541 removed outlier: 3.703A pdb=" N ASN S 541 " --> pdb=" O TYR S 537 " (cutoff:3.500A) Processing helix chain 'S' and resid 546 through 556 Processing helix chain 'T' and resid 22 through 33 removed outlier: 3.805A pdb=" N THR T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.645A pdb=" N LYS T 41 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP T 47 " --> pdb=" O TYR T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 68 Processing helix chain 'T' and resid 71 through 83 Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 107 through 121 removed outlier: 3.553A pdb=" N ILE T 111 " --> pdb=" O ASP T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 139 Processing helix chain 'T' and resid 144 through 159 removed outlier: 3.671A pdb=" N TRP T 148 " --> pdb=" O HIS T 144 " (cutoff:3.500A) Proline residue: T 150 - end of helix Processing helix chain 'T' and resid 175 through 191 Processing helix chain 'T' and resid 210 through 218 Processing helix chain 'T' and resid 225 through 238 Processing helix chain 'T' and resid 241 through 251 Processing helix chain 'T' and resid 271 through 282 Processing helix chain 'T' and resid 285 through 296 Processing helix chain 'T' and resid 300 through 314 Processing helix chain 'T' and resid 318 through 332 Processing helix chain 'T' and resid 340 through 365 removed outlier: 3.565A pdb=" N LYS T 362 " --> pdb=" O LEU T 358 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU T 363 " --> pdb=" O GLY T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 374 through 391 Processing helix chain 'T' and resid 391 through 403 Processing helix chain 'T' and resid 408 through 419 removed outlier: 3.878A pdb=" N LYS T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) Processing helix chain 'T' and resid 424 through 435 removed outlier: 4.428A pdb=" N ILE T 435 " --> pdb=" O ALA T 431 " (cutoff:3.500A) Processing helix chain 'T' and resid 449 through 461 Processing helix chain 'T' and resid 462 through 475 Processing helix chain 'T' and resid 484 through 497 removed outlier: 3.518A pdb=" N ARG T 494 " --> pdb=" O ASN T 490 " (cutoff:3.500A) Processing helix chain 'T' and resid 502 through 523 Proline residue: T 515 - end of helix Proline residue: T 518 - end of helix Processing helix chain 'T' and resid 542 through 555 Processing helix chain 'T' and resid 567 through 581 Processing helix chain 'T' and resid 586 through 597 Processing helix chain 'T' and resid 602 through 612 Processing helix chain 'T' and resid 618 through 634 removed outlier: 3.678A pdb=" N GLU T 622 " --> pdb=" O GLU T 618 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS T 634 " --> pdb=" O VAL T 630 " (cutoff:3.500A) Processing helix chain 'T' and resid 642 through 655 Processing helix chain 'T' and resid 661 through 677 Processing helix chain 'T' and resid 681 through 693 Processing helix chain 'T' and resid 703 through 719 Processing helix chain 'T' and resid 724 through 735 Processing helix chain 'T' and resid 740 through 755 Processing helix chain 'T' and resid 759 through 771 Processing helix chain 'T' and resid 778 through 790 Processing helix chain 'T' and resid 1001 through 1017 Processing helix chain 'a' and resid 77 through 89 Processing helix chain 'a' and resid 107 through 127 removed outlier: 4.035A pdb=" N SER a 127 " --> pdb=" O ARG a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 151 removed outlier: 4.052A pdb=" N ASP a 138 " --> pdb=" O GLU a 134 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS a 141 " --> pdb=" O LEU a 137 " (cutoff:3.500A) Proline residue: a 145 - end of helix Processing helix chain 'a' and resid 156 through 172 removed outlier: 3.559A pdb=" N SER a 162 " --> pdb=" O ASP a 158 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN a 172 " --> pdb=" O TYR a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 188 Processing helix chain 'a' and resid 224 through 246 removed outlier: 4.043A pdb=" N LEU a 228 " --> pdb=" O GLU a 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 167 through 172 Processing helix chain 'c' and resid 179 through 196 removed outlier: 3.588A pdb=" N ASP c 192 " --> pdb=" O LYS c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 217 through 224 Processing helix chain 'c' and resid 294 through 313 removed outlier: 3.922A pdb=" N LYS c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 324 through 329 Processing helix chain 'c' and resid 334 through 348 removed outlier: 4.133A pdb=" N TYR c 338 " --> pdb=" O THR c 334 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG c 343 " --> pdb=" O LEU c 339 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 60 removed outlier: 3.536A pdb=" N LEU o 56 " --> pdb=" O THR o 52 " (cutoff:3.500A) Processing helix chain 'o' and resid 276 through 283 Processing helix chain 'X' and resid 6 through 15 removed outlier: 4.060A pdb=" N UNK X 10 " --> pdb=" O UNK X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 26 Processing helix chain 'X' and resid 92 through 129 removed outlier: 4.649A pdb=" N UNK X 107 " --> pdb=" O UNK X 103 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N UNK X 108 " --> pdb=" O UNK X 104 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N UNK X 117 " --> pdb=" O UNK X 113 " (cutoff:3.500A) Processing helix chain 'y' and resid 96 through 114 Processing helix chain 'y' and resid 157 through 184 Processing helix chain 'y' and resid 197 through 209 removed outlier: 3.509A pdb=" N GLN y 202 " --> pdb=" O ASP y 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 16 Processing helix chain 'd' and resid 5 through 14 Processing helix chain 'e' and resid 12 through 24 Processing helix chain 'e' and resid 84 through 87 Processing helix chain 'f' and resid 14 through 22 removed outlier: 3.509A pdb=" N PHE f 18 " --> pdb=" O ASN f 14 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 10 removed outlier: 4.111A pdb=" N PHE h 6 " --> pdb=" O LYS h 2 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 108 removed outlier: 3.875A pdb=" N LEU h 106 " --> pdb=" O ASN h 102 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL h 108 " --> pdb=" O ASP h 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 29 Processing helix chain 'j' and resid 31 through 41 Processing helix chain 'V' and resid 477 through 481 Processing helix chain 'V' and resid 482 through 487 removed outlier: 6.102A pdb=" N VAL V 485 " --> pdb=" O THR V 482 " (cutoff:3.500A) Processing helix chain 'V' and resid 488 through 499 Processing helix chain 'V' and resid 511 through 525 removed outlier: 4.541A pdb=" N THR V 517 " --> pdb=" O THR V 513 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN V 518 " --> pdb=" O THR V 514 " (cutoff:3.500A) Processing helix chain 'V' and resid 537 through 553 Processing helix chain 'V' and resid 581 through 591 removed outlier: 3.571A pdb=" N LEU V 590 " --> pdb=" O ARG V 586 " (cutoff:3.500A) Processing helix chain 'V' and resid 604 through 608 Processing helix chain 'V' and resid 609 through 626 removed outlier: 3.601A pdb=" N LYS V 621 " --> pdb=" O ALA V 617 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE V 624 " --> pdb=" O LYS V 620 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS V 625 " --> pdb=" O LYS V 621 " (cutoff:3.500A) Processing helix chain 'V' and resid 640 through 647 Processing helix chain 'V' and resid 673 through 689 removed outlier: 3.662A pdb=" N ALA V 677 " --> pdb=" O ASP V 673 " (cutoff:3.500A) Processing helix chain 'V' and resid 700 through 718 Processing helix chain 'V' and resid 735 through 740 Processing helix chain 'V' and resid 741 through 744 Processing helix chain 'V' and resid 758 through 763 removed outlier: 4.341A pdb=" N THR V 762 " --> pdb=" O ASN V 758 " (cutoff:3.500A) Processing helix chain 'V' and resid 798 through 808 Processing helix chain 'V' and resid 809 through 811 No H-bonds generated for 'chain 'V' and resid 809 through 811' Processing helix chain 'V' and resid 822 through 829 Processing helix chain 'V' and resid 836 through 841 removed outlier: 3.940A pdb=" N GLN V 841 " --> pdb=" O ILE V 838 " (cutoff:3.500A) Processing helix chain 'V' and resid 843 through 853 Processing helix chain 'V' and resid 868 through 882 removed outlier: 3.621A pdb=" N MET V 872 " --> pdb=" O PRO V 868 " (cutoff:3.500A) Processing helix chain 'V' and resid 892 through 901 removed outlier: 3.622A pdb=" N LEU V 900 " --> pdb=" O LYS V 896 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE V 901 " --> pdb=" O GLU V 897 " (cutoff:3.500A) Processing helix chain 'V' and resid 904 through 913 Processing helix chain 'V' and resid 914 through 916 No H-bonds generated for 'chain 'V' and resid 914 through 916' Processing helix chain 'V' and resid 919 through 931 Processing helix chain 'V' and resid 942 through 952 removed outlier: 3.523A pdb=" N LYS V 952 " --> pdb=" O SER V 948 " (cutoff:3.500A) Processing helix chain 'V' and resid 958 through 971 Processing helix chain 'V' and resid 978 through 983 Processing helix chain 'V' and resid 986 through 1008 Processing helix chain 'V' and resid 1017 through 1030 removed outlier: 4.199A pdb=" N ILE V1021 " --> pdb=" O ASP V1017 " (cutoff:3.500A) Processing helix chain 'V' and resid 1087 through 1095 removed outlier: 3.570A pdb=" N LEU V1091 " --> pdb=" O GLU V1087 " (cutoff:3.500A) Processing helix chain 'V' and resid 1100 through 1104 Processing helix chain 'V' and resid 1108 through 1120 Proline residue: V1116 - end of helix Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.573A pdb=" N LEU l 7 " --> pdb=" O LEU l 3 " (cutoff:3.500A) Processing helix chain 'm' and resid 17 through 21 Processing helix chain 'm' and resid 24 through 29 removed outlier: 3.624A pdb=" N HIS m 28 " --> pdb=" O PHE m 24 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 40 Processing helix chain 'n' and resid 5 through 14 Processing helix chain 'W' and resid 4 through 11 Processing helix chain 'W' and resid 42 through 46 removed outlier: 3.600A pdb=" N SER W 45 " --> pdb=" O SER W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 111 through 116 removed outlier: 4.187A pdb=" N ARG W 116 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 124 removed outlier: 3.676A pdb=" N THR W 123 " --> pdb=" O ARG W 119 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 119 through 124' Processing helix chain 'W' and resid 132 through 137 Processing helix chain 'W' and resid 139 through 148 Processing helix chain 'W' and resid 160 through 167 Processing helix chain 'Y' and resid 40 through 53 Processing helix chain 'Y' and resid 78 through 89 Processing helix chain 'p' and resid 12 through 24 removed outlier: 3.586A pdb=" N ILE p 17 " --> pdb=" O PRO p 13 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE p 18 " --> pdb=" O ILE p 14 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 22 Processing helix chain 's' and resid 15 through 31 Processing helix chain 's' and resid 86 through 91 Processing helix chain 's' and resid 92 through 94 No H-bonds generated for 'chain 's' and resid 92 through 94' Processing helix chain 's' and resid 113 through 118 Processing helix chain 's' and resid 120 through 131 Processing helix chain 's' and resid 137 through 174 removed outlier: 3.690A pdb=" N ASN s 143 " --> pdb=" O GLN s 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR s 146 " --> pdb=" O ILE s 142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE s 153 " --> pdb=" O GLN s 149 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL s 154 " --> pdb=" O THR s 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU s 155 " --> pdb=" O CYS s 151 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG s 174 " --> pdb=" O ILE s 170 " (cutoff:3.500A) Processing helix chain 't' and resid 25 through 35 Processing helix chain 't' and resid 79 through 143 removed outlier: 3.563A pdb=" N ALA t 90 " --> pdb=" O ASN t 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS t 108 " --> pdb=" O SER t 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL t 122 " --> pdb=" O ALA t 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) Proline residue: t 138 - end of helix removed outlier: 3.644A pdb=" N GLN t 143 " --> pdb=" O LYS t 139 " (cutoff:3.500A) Processing helix chain 'u' and resid 25 through 35 Processing helix chain 'u' and resid 77 through 137 removed outlier: 3.711A pdb=" N THR u 82 " --> pdb=" O PRO u 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU u 93 " --> pdb=" O ASP u 89 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU u 98 " --> pdb=" O GLU u 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR u 101 " --> pdb=" O LYS u 97 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU u 102 " --> pdb=" O LEU u 98 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR u 106 " --> pdb=" O LEU u 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS u 107 " --> pdb=" O ASP u 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL u 112 " --> pdb=" O LYS u 108 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU u 121 " --> pdb=" O ASP u 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA u 124 " --> pdb=" O LYS u 120 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN u 125 " --> pdb=" O LEU u 121 " (cutoff:3.500A) Processing helix chain 'v' and resid 25 through 35 removed outlier: 3.578A pdb=" N LYS v 33 " --> pdb=" O GLU v 29 " (cutoff:3.500A) Processing helix chain 'v' and resid 77 through 81 Processing helix chain 'v' and resid 81 through 141 removed outlier: 3.502A pdb=" N LEU v 105 " --> pdb=" O THR v 101 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER v 110 " --> pdb=" O THR v 106 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR v 111 " --> pdb=" O LYS v 107 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN v 131 " --> pdb=" O LEU v 127 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU v 132 " --> pdb=" O MET v 128 " (cutoff:3.500A) Proline residue: v 138 - end of helix removed outlier: 3.525A pdb=" N SER v 141 " --> pdb=" O LEU v 137 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 35 removed outlier: 3.562A pdb=" N GLN w 30 " --> pdb=" O SER w 26 " (cutoff:3.500A) Processing helix chain 'w' and resid 78 through 106 removed outlier: 3.815A pdb=" N LEU w 93 " --> pdb=" O ASP w 89 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU w 98 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR w 101 " --> pdb=" O LYS w 97 " (cutoff:3.500A) Processing helix chain 'w' and resid 106 through 137 removed outlier: 3.780A pdb=" N THR w 111 " --> pdb=" O LYS w 107 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL w 112 " --> pdb=" O LYS w 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU w 121 " --> pdb=" O ASP w 117 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL w 122 " --> pdb=" O ALA w 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN w 131 " --> pdb=" O LEU w 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 194 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 593 Processing sheet with id=AA5, first strand: chain 'A' and resid 968 through 972 Processing sheet with id=AA6, first strand: chain 'A' and resid 1158 through 1160 removed outlier: 6.237A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1258 through 1262 Processing sheet with id=AA8, first strand: chain 'A' and resid 1406 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 1678 through 1683 removed outlier: 8.031A pdb=" N VAL A1773 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N TRP A1733 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A1775 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP A1735 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE A1777 " --> pdb=" O ASP A1735 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1955 through 1958 removed outlier: 3.520A pdb=" N LEU A1850 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A1985 " --> pdb=" O ILE A1893 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1955 through 1958 removed outlier: 3.520A pdb=" N LEU A1850 " --> pdb=" O GLN A1932 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1859 through 1864 removed outlier: 4.561A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 79 through 81 removed outlier: 6.038A pdb=" N GLU C 79 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU J 131 " --> pdb=" O LYS J 427 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS J 427 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.670A pdb=" N ILE C 134 " --> pdb=" O ASN C 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 240 removed outlier: 6.070A pdb=" N ILE C 239 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 537 through 538 removed outlier: 4.356A pdb=" N LEU C 468 " --> pdb=" O SER C 579 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRP C 469 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU C 485 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR C 475 " --> pdb=" O TRP C 483 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP C 483 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 492 through 494 Processing sheet with id=AC2, first strand: chain 'C' and resid 642 through 646 Processing sheet with id=AC3, first strand: chain 'C' and resid 678 through 681 Processing sheet with id=AC4, first strand: chain 'C' and resid 709 through 714 removed outlier: 6.395A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 775 " --> pdb=" O TYR C 818 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 820 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASP C 777 " --> pdb=" O LEU C 820 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N SER C 822 " --> pdb=" O ASP C 777 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 887 through 890 removed outlier: 3.556A pdb=" N TYR C 889 " --> pdb=" O ARG C 903 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ARG C 903 " --> pdb=" O TYR C 889 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 144 through 147 removed outlier: 6.461A pdb=" N ASP J 168 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 174 " --> pdb=" O ASP J 168 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 185 through 190 removed outlier: 6.489A pdb=" N CYS J 208 " --> pdb=" O ILE J 217 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 227 through 232 removed outlier: 3.786A pdb=" N ILE J 248 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP J 252 " --> pdb=" O PRO J 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 271 through 274 removed outlier: 4.668A pdb=" N VAL J 281 " --> pdb=" O TRP J 293 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL J 290 " --> pdb=" O VAL J 303 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL J 303 " --> pdb=" O VAL J 290 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU J 292 " --> pdb=" O MET J 301 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 314 through 316 removed outlier: 4.791A pdb=" N GLY J 335 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU J 341 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 365 through 367 removed outlier: 3.959A pdb=" N ALA J 366 " --> pdb=" O SER J 374 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 111 through 115 removed outlier: 7.953A pdb=" N HIS K 111 " --> pdb=" O ILE N 23 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N MET N 25 " --> pdb=" O HIS K 111 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU K 113 " --> pdb=" O MET N 25 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS N 27 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL K 115 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ARG N 24 " --> pdb=" O LYS N 47 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS N 47 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 30 Processing sheet with id=AD5, first strand: chain 'M' and resid 170 through 173 removed outlier: 6.673A pdb=" N LYS M 185 " --> pdb=" O ASP M 171 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE M 173 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE M 183 " --> pdb=" O ILE M 173 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'o' and resid 156 through 158 removed outlier: 4.242A pdb=" N LYS o 450 " --> pdb=" O GLY o 446 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'o' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'o' and resid 209 through 214 removed outlier: 6.376A pdb=" N SER o 224 " --> pdb=" O LYS o 210 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU o 212 " --> pdb=" O LEU o 222 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU o 222 " --> pdb=" O LEU o 212 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N PHE o 214 " --> pdb=" O SER o 220 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER o 220 " --> pdb=" O PHE o 214 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'o' and resid 252 through 255 removed outlier: 3.638A pdb=" N ASP o 252 " --> pdb=" O GLY o 266 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'o' and resid 300 through 301 Processing sheet with id=AE2, first strand: chain 'o' and resid 339 through 342 removed outlier: 3.503A pdb=" N MET o 339 " --> pdb=" O GLN o 354 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'o' and resid 386 through 388 Processing sheet with id=AE4, first strand: chain 'y' and resid 144 through 146 Processing sheet with id=AE5, first strand: chain 'e' and resid 27 through 30 removed outlier: 3.604A pdb=" N ASP e 55 " --> pdb=" O LYS e 42 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL e 52 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU e 82 " --> pdb=" O VAL e 52 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS f 30 " --> pdb=" O LEU f 79 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE f 81 " --> pdb=" O GLY f 28 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY f 28 " --> pdb=" O ILE f 81 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN f 52 " --> pdb=" O ILE f 71 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE f 71 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN f 54 " --> pdb=" O GLY f 69 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY f 69 " --> pdb=" O ASN f 54 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA f 56 " --> pdb=" O THR f 67 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR f 67 " --> pdb=" O ALA f 56 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU f 58 " --> pdb=" O HIS f 65 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU f 70 " --> pdb=" O LYS j 106 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS j 106 " --> pdb=" O GLU f 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL j 103 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS j 53 " --> pdb=" O GLU j 74 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU j 74 " --> pdb=" O LYS j 53 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE j 55 " --> pdb=" O VAL j 72 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL j 72 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N SER j 92 " --> pdb=" O ASN j 71 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS j 73 " --> pdb=" O PHE j 90 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE j 90 " --> pdb=" O LYS j 73 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU j 75 " --> pdb=" O GLU j 88 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU j 88 " --> pdb=" O LEU j 75 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR j 77 " --> pdb=" O ASN j 86 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN j 86 " --> pdb=" O THR j 77 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU h 18 " --> pdb=" O ARG h 93 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE h 95 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR h 16 " --> pdb=" O ILE h 95 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR h 28 " --> pdb=" O ASP h 42 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP h 42 " --> pdb=" O THR h 28 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN h 30 " --> pdb=" O LEU h 40 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU h 40 " --> pdb=" O GLN h 30 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL h 32 " --> pdb=" O ALA h 38 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA h 38 " --> pdb=" O VAL h 32 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR h 84 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL b 97 " --> pdb=" O TYR h 84 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER b 94 " --> pdb=" O LEU b 23 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS b 19 " --> pdb=" O GLU b 98 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL b 29 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU b 50 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE b 31 " --> pdb=" O CYS b 48 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N CYS b 48 " --> pdb=" O ILE b 31 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN b 33 " --> pdb=" O ASN b 46 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL b 44 " --> pdb=" O MET b 35 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU b 47 " --> pdb=" O GLY b 83 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY b 83 " --> pdb=" O GLU b 47 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE b 49 " --> pdb=" O VAL b 81 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL b 81 " --> pdb=" O ILE b 49 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU d 22 " --> pdb=" O LYS d 70 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE d 72 " --> pdb=" O SER d 20 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER d 20 " --> pdb=" O ILE d 72 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR d 28 " --> pdb=" O ALA d 49 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA d 49 " --> pdb=" O THR d 28 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG d 30 " --> pdb=" O VAL d 47 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL d 47 " --> pdb=" O ARG d 30 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN d 43 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLN d 61 " --> pdb=" O ALA g 73 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA g 73 " --> pdb=" O GLN d 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN g 18 " --> pdb=" O ILE g 69 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU g 71 " --> pdb=" O LEU g 16 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU g 16 " --> pdb=" O LEU g 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 59 through 61 removed outlier: 3.604A pdb=" N ASP e 55 " --> pdb=" O LYS e 42 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL e 52 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU e 82 " --> pdb=" O VAL e 52 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS f 30 " --> pdb=" O LEU f 79 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE f 81 " --> pdb=" O GLY f 28 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY f 28 " --> pdb=" O ILE f 81 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN f 52 " --> pdb=" O ILE f 71 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE f 71 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN f 54 " --> pdb=" O GLY f 69 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY f 69 " --> pdb=" O ASN f 54 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA f 56 " --> pdb=" O THR f 67 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR f 67 " --> pdb=" O ALA f 56 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU f 58 " --> pdb=" O HIS f 65 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU f 70 " --> pdb=" O LYS j 106 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS j 106 " --> pdb=" O GLU f 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL j 103 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS j 53 " --> pdb=" O GLU j 74 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU j 74 " --> pdb=" O LYS j 53 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE j 55 " --> pdb=" O VAL j 72 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL j 72 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N SER j 92 " --> pdb=" O ASN j 71 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS j 73 " --> pdb=" O PHE j 90 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE j 90 " --> pdb=" O LYS j 73 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU j 75 " --> pdb=" O GLU j 88 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU j 88 " --> pdb=" O LEU j 75 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR j 77 " --> pdb=" O ASN j 86 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN j 86 " --> pdb=" O THR j 77 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU h 18 " --> pdb=" O ARG h 93 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE h 95 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR h 16 " --> pdb=" O ILE h 95 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR h 28 " --> pdb=" O ASP h 42 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP h 42 " --> pdb=" O THR h 28 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN h 30 " --> pdb=" O LEU h 40 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU h 40 " --> pdb=" O GLN h 30 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL h 32 " --> pdb=" O ALA h 38 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA h 38 " --> pdb=" O VAL h 32 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'g' and resid 29 through 31 removed outlier: 6.686A pdb=" N VAL g 39 " --> pdb=" O ARG g 30 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 44 through 45 Processing sheet with id=AE9, first strand: chain 'V' and resid 567 through 569 removed outlier: 6.417A pdb=" N GLY V 561 " --> pdb=" O TYR V 578 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR V 580 " --> pdb=" O GLY V 561 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR V 563 " --> pdb=" O THR V 580 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE V 531 " --> pdb=" O LYS V 577 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N MET V 579 " --> pdb=" O ILE V 531 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N CYS V 533 " --> pdb=" O MET V 579 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET V 530 " --> pdb=" O VAL V 599 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N MET V 601 " --> pdb=" O MET V 530 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY V 532 " --> pdb=" O MET V 601 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 662 through 666 removed outlier: 6.503A pdb=" N GLU V 663 " --> pdb=" O CYS V 817 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG V 819 " --> pdb=" O GLU V 663 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU V 665 " --> pdb=" O ARG V 819 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR V 770 " --> pdb=" O LYS V 816 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR V 818 " --> pdb=" O TYR V 770 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL V 772 " --> pdb=" O TYR V 818 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ASP V 693 " --> pdb=" O ILE V 769 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE V 694 " --> pdb=" O VAL V 754 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA V 756 " --> pdb=" O ILE V 694 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL V 696 " --> pdb=" O ALA V 756 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU V 726 " --> pdb=" O VAL V 753 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE V 755 " --> pdb=" O LEU V 726 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU V 728 " --> pdb=" O PHE V 755 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 777 through 784 Processing sheet with id=AF3, first strand: chain 'V' and resid 1033 through 1037 removed outlier: 7.297A pdb=" N GLU V1050 " --> pdb=" O GLU V1078 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET V1080 " --> pdb=" O GLU V1050 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY V1052 " --> pdb=" O MET V1080 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLN V1082 " --> pdb=" O GLY V1052 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL V1083 " --> pdb=" O TYR V1069 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR V1069 " --> pdb=" O VAL V1083 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER V1085 " --> pdb=" O VAL V1067 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL V1067 " --> pdb=" O SER V1085 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'k' and resid 29 through 33 removed outlier: 7.406A pdb=" N LYS k 19 " --> pdb=" O GLU k 98 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU k 23 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER k 94 " --> pdb=" O LEU k 23 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'k' and resid 85 through 87 removed outlier: 4.129A pdb=" N SER n 20 " --> pdb=" O VAL n 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY n 31 " --> pdb=" O VAL n 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR n 28 " --> pdb=" O THR n 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG n 30 " --> pdb=" O ILE n 48 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS n 32 " --> pdb=" O ASP n 46 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP n 46 " --> pdb=" O LYS n 32 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'k' and resid 85 through 87 removed outlier: 4.129A pdb=" N SER n 20 " --> pdb=" O VAL n 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY n 31 " --> pdb=" O VAL n 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR n 28 " --> pdb=" O THR n 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG n 30 " --> pdb=" O ILE n 48 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS n 32 " --> pdb=" O ASP n 46 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP n 46 " --> pdb=" O LYS n 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL n 42 " --> pdb=" O VAL n 64 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN n 61 " --> pdb=" O ALA r 73 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA r 73 " --> pdb=" O GLN n 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU r 71 " --> pdb=" O PHE n 63 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER r 70 " --> pdb=" O ASN r 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU r 40 " --> pdb=" O THR r 61 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'l' and resid 14 through 15 Processing sheet with id=AF8, first strand: chain 'm' and resid 43 through 47 removed outlier: 4.677A pdb=" N ARG m 57 " --> pdb=" O ASN m 71 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASN m 71 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS m 59 " --> pdb=" O LEU m 69 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU m 69 " --> pdb=" O LYS m 59 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'm' and resid 103 through 105 removed outlier: 6.802A pdb=" N HIS q 65 " --> pdb=" O PHE q 59 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N PHE q 59 " --> pdb=" O HIS q 65 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR q 67 " --> pdb=" O GLU q 57 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU q 57 " --> pdb=" O THR q 67 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY q 69 " --> pdb=" O GLU q 55 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA q 56 " --> pdb=" O ARG q 39 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG q 39 " --> pdb=" O ALA q 56 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU q 58 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU q 37 " --> pdb=" O GLU q 58 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY q 28 " --> pdb=" O ILE q 81 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE q 81 " --> pdb=" O GLY q 28 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS q 30 " --> pdb=" O LEU q 79 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU p 82 " --> pdb=" O VAL p 52 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL p 52 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU p 56 " --> pdb=" O LYS p 42 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS p 42 " --> pdb=" O GLU p 56 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'r' and resid 44 through 45 Processing sheet with id=AG2, first strand: chain 'W' and resid 153 through 154 removed outlier: 3.563A pdb=" N GLN W 157 " --> pdb=" O LEU W 154 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 30 through 32 removed outlier: 3.846A pdb=" N ALA Y 72 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 't' and resid 13 through 15 Processing sheet with id=AG5, first strand: chain 't' and resid 179 through 187 removed outlier: 6.470A pdb=" N ILE t 498 " --> pdb=" O LEU t 183 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA t 185 " --> pdb=" O PHE t 496 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE t 496 " --> pdb=" O ALA t 185 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE t 486 " --> pdb=" O LEU t 501 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY t 482 " --> pdb=" O GLY t 485 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 't' and resid 193 through 194 removed outlier: 6.351A pdb=" N LYS t 193 " --> pdb=" O ILE t 249 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ARG t 251 " --> pdb=" O LYS t 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE t 248 " --> pdb=" O LEU t 260 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP t 270 " --> pdb=" O VAL t 276 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL t 276 " --> pdb=" O ASP t 270 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 't' and resid 197 through 200 Processing sheet with id=AG8, first strand: chain 't' and resid 288 through 292 removed outlier: 6.514A pdb=" N ALA t 305 " --> pdb=" O ILE t 289 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET t 291 " --> pdb=" O ILE t 303 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE t 303 " --> pdb=" O MET t 291 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE t 311 " --> pdb=" O VAL t 324 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 't' and resid 335 through 338 Processing sheet with id=AH1, first strand: chain 't' and resid 377 through 382 Processing sheet with id=AH2, first strand: chain 't' and resid 424 through 428 removed outlier: 6.236A pdb=" N LYS t 449 " --> pdb=" O LYS t 459 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS t 459 " --> pdb=" O LYS t 449 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'u' and resid 13 through 16 removed outlier: 4.064A pdb=" N THR u 21 " --> pdb=" O SER u 16 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'v' and resid 13 through 15 Processing sheet with id=AH5, first strand: chain 'w' and resid 13 through 15 Processing sheet with id=AH6, first strand: chain 'w' and resid 179 through 187 removed outlier: 6.472A pdb=" N ILE w 498 " --> pdb=" O LEU w 183 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA w 185 " --> pdb=" O PHE w 496 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE w 496 " --> pdb=" O ALA w 185 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE w 486 " --> pdb=" O LEU w 501 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY w 482 " --> pdb=" O GLY w 485 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'w' and resid 193 through 194 removed outlier: 6.350A pdb=" N LYS w 193 " --> pdb=" O ILE w 249 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ARG w 251 " --> pdb=" O LYS w 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE w 248 " --> pdb=" O LEU w 260 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP w 270 " --> pdb=" O VAL w 276 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL w 276 " --> pdb=" O ASP w 270 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'w' and resid 197 through 200 Processing sheet with id=AH9, first strand: chain 'w' and resid 288 through 292 removed outlier: 6.515A pdb=" N ALA w 305 " --> pdb=" O ILE w 289 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET w 291 " --> pdb=" O ILE w 303 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE w 303 " --> pdb=" O MET w 291 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE w 311 " --> pdb=" O VAL w 324 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'w' and resid 335 through 338 Processing sheet with id=AI2, first strand: chain 'w' and resid 377 through 382 Processing sheet with id=AI3, first strand: chain 'w' and resid 424 through 428 removed outlier: 6.236A pdb=" N LYS w 449 " --> pdb=" O LYS w 459 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS w 459 " --> pdb=" O LYS w 449 " (cutoff:3.500A) 3763 hydrogen bonds defined for protein. 10860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 606 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 235 stacking parallelities Total time for adding SS restraints: 61.64 Time building geometry restraints manager: 18.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 31466 1.40 - 1.64: 47730 1.64 - 1.88: 345 1.88 - 2.12: 0 2.12 - 2.35: 2 Bond restraints: 79543 Sorted by residual: bond pdb=" C MET V 903 " pdb=" N ASP V 904 " ideal model delta sigma weight residual 1.328 2.352 -1.024 1.44e-02 4.82e+03 5.06e+03 bond pdb=" C ASP T 300 " pdb=" N LYS T 301 " ideal model delta sigma weight residual 1.332 2.163 -0.830 1.40e-02 5.10e+03 3.52e+03 bond pdb=" C LEU V1009 " pdb=" N LYS V1010 " ideal model delta sigma weight residual 1.331 1.503 -0.172 1.37e-02 5.33e+03 1.58e+02 bond pdb=" C THR V 834 " pdb=" N VAL V 835 " ideal model delta sigma weight residual 1.329 1.215 0.115 1.13e-02 7.83e+03 1.03e+02 bond pdb=" C LEU v 109 " pdb=" N SER v 110 " ideal model delta sigma weight residual 1.335 1.440 -0.105 1.31e-02 5.83e+03 6.46e+01 ... (remaining 79538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 23.40: 110377 23.40 - 46.81: 6 46.81 - 70.21: 1 70.21 - 93.62: 1 93.62 - 117.02: 1 Bond angle restraints: 110386 Sorted by residual: angle pdb=" C THR V 834 " pdb=" N VAL V 835 " pdb=" CA VAL V 835 " ideal model delta sigma weight residual 122.13 5.11 117.02 1.85e+00 2.92e-01 4.00e+03 angle pdb=" CA THR V 834 " pdb=" C THR V 834 " pdb=" N VAL V 835 " ideal model delta sigma weight residual 116.84 31.91 84.93 1.71e+00 3.42e-01 2.47e+03 angle pdb=" CA LEU V1009 " pdb=" C LEU V1009 " pdb=" N LYS V1010 " ideal model delta sigma weight residual 116.39 67.67 48.72 1.26e+00 6.30e-01 1.49e+03 angle pdb=" O LEU V1009 " pdb=" C LEU V1009 " pdb=" N LYS V1010 " ideal model delta sigma weight residual 123.13 166.52 -43.39 1.15e+00 7.56e-01 1.42e+03 angle pdb=" C LEU V1009 " pdb=" N LYS V1010 " pdb=" CA LYS V1010 " ideal model delta sigma weight residual 120.95 74.32 46.63 1.40e+00 5.10e-01 1.11e+03 ... (remaining 110381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 46414 35.47 - 70.94: 1704 70.94 - 106.40: 162 106.40 - 141.87: 13 141.87 - 177.34: 7 Dihedral angle restraints: 48300 sinusoidal: 19775 harmonic: 28525 Sorted by residual: dihedral pdb=" CA LEU s 132 " pdb=" C LEU s 132 " pdb=" N PRO s 133 " pdb=" CA PRO s 133 " ideal model delta harmonic sigma weight residual 180.00 -129.71 -50.29 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA THR V 834 " pdb=" C THR V 834 " pdb=" N VAL V 835 " pdb=" CA VAL V 835 " ideal model delta harmonic sigma weight residual -180.00 -134.69 -45.31 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" O4' C 5 79 " pdb=" C1' C 5 79 " pdb=" N1 C 5 79 " pdb=" C2 C 5 79 " ideal model delta sinusoidal sigma weight residual 200.00 68.39 131.61 1 1.50e+01 4.44e-03 7.10e+01 ... (remaining 48297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 13540 0.990 - 1.980: 0 1.980 - 2.970: 0 2.970 - 3.960: 0 3.960 - 4.950: 2 Chirality restraints: 13542 Sorted by residual: chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.43 -4.95 2.00e-01 2.50e+01 6.12e+02 chirality pdb=" C3 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" O13 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.34 2.45 -4.79 2.00e-01 2.50e+01 5.74e+02 chirality pdb=" C3' C 6 92 " pdb=" C4' C 6 92 " pdb=" O3' C 6 92 " pdb=" C2' C 6 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.01 -0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 13539 not shown) Planarity restraints: 12622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR V 659 " -0.141 2.00e-02 2.50e+03 2.46e-01 6.07e+02 pdb=" C THR V 659 " 0.421 2.00e-02 2.50e+03 pdb=" O THR V 659 " -0.198 2.00e-02 2.50e+03 pdb=" N PHE V 660 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP T 300 " -0.129 2.00e-02 2.50e+03 1.94e-01 3.75e+02 pdb=" C ASP T 300 " 0.332 2.00e-02 2.50e+03 pdb=" O ASP T 300 " -0.139 2.00e-02 2.50e+03 pdb=" N LYS T 301 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR V 834 " -0.219 2.00e-02 2.50e+03 1.78e-01 3.17e+02 pdb=" C THR V 834 " 0.129 2.00e-02 2.50e+03 pdb=" O THR V 834 " -0.125 2.00e-02 2.50e+03 pdb=" N VAL V 835 " 0.215 2.00e-02 2.50e+03 ... (remaining 12619 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.57: 34 1.57 - 2.46: 207 2.46 - 3.36: 100806 3.36 - 4.25: 228973 4.25 - 5.14: 409423 Warning: very small nonbonded interaction distances. Nonbonded interactions: 739443 Sorted by model distance: nonbonded pdb=" C4' G 21149 " pdb=" NH1 ARG k 52 " model vdw 0.679 3.550 nonbonded pdb=" CB TYR T 274 " pdb=" CB MET T 294 " model vdw 0.680 3.840 nonbonded pdb=" O4' G 21149 " pdb=" CZ ARG k 52 " model vdw 0.683 3.270 nonbonded pdb=" O2' C 21093 " pdb=" C GLY n 54 " model vdw 0.834 3.270 nonbonded pdb=" C LEU k 102 " pdb=" C TYR W 14 " model vdw 0.937 3.500 ... (remaining 739438 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 'b' selection = chain 'k' } ncs_group { reference = chain 'd' selection = chain 'n' } ncs_group { reference = chain 'e' selection = chain 'p' } ncs_group { reference = chain 'f' selection = chain 'q' } ncs_group { reference = (chain 'g' and (resid 2 through 40 or (resid 41 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 76)) selection = chain 'r' } ncs_group { reference = (chain 'h' and (resid 1 through 98 or (resid 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 106)) selection = chain 'l' } ncs_group { reference = (chain 'j' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 108)) selection = chain 'm' } ncs_group { reference = (chain 't' and (resid 1 through 139 or resid 171 through 503)) selection = (chain 'w' and (resid 1 through 51 or resid 78 through 503)) } ncs_group { reference = (chain 'u' and (resid 1 through 51 or resid 76 through 139)) selection = (chain 'v' and resid 1 through 139) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.480 Check model and map are aligned: 0.450 Set scattering table: 0.580 Process input model: 198.370 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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 : 0.010 1.024 79543 Z= 0.649 Angle : 1.544 117.021 110386 Z= 1.081 Chirality : 0.107 4.950 13542 Planarity : 0.008 0.246 12622 Dihedral : 17.517 177.338 29622 Min Nonbonded Distance : 0.679 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.71 % Favored : 91.40 % Rotamer: Outliers : 2.73 % Allowed : 7.86 % Favored : 89.41 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.08), residues: 9407 helix: 0.16 (0.07), residues: 4061 sheet: -2.22 (0.13), residues: 1232 loop : -2.62 (0.09), residues: 4114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 711 HIS 0.014 0.002 HIS A 138 PHE 0.039 0.003 PHE J 198 TYR 0.030 0.003 TYR J 378 ARG 0.010 0.001 ARG C 973 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18814 Ramachandran restraints generated. 9407 Oldfield, 0 Emsley, 9407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18814 Ramachandran restraints generated. 9407 Oldfield, 0 Emsley, 9407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 978 time to evaluate : 6.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8697 (tt0) cc_final: 0.8488 (tt0) REVERT: A 777 LYS cc_start: 0.7806 (mppt) cc_final: 0.7475 (pttt) REVERT: A 788 GLU cc_start: 0.9244 (tt0) cc_final: 0.8808 (tp30) REVERT: A 841 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8204 (mm-30) REVERT: A 842 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8744 (mttm) REVERT: A 958 LEU cc_start: 0.9153 (mt) cc_final: 0.8884 (tt) REVERT: A 1007 LYS cc_start: 0.8937 (mmtm) cc_final: 0.8574 (ttpt) REVERT: A 1049 LEU cc_start: 0.8445 (tp) cc_final: 0.8109 (tt) REVERT: A 1086 ASN cc_start: 0.9133 (m-40) cc_final: 0.8921 (t0) REVERT: A 1103 LEU cc_start: 0.8903 (tt) cc_final: 0.8684 (tt) REVERT: A 1171 LEU cc_start: 0.8673 (tp) cc_final: 0.8425 (tp) REVERT: A 1212 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7878 (ptt180) REVERT: A 1304 VAL cc_start: 0.9019 (t) cc_final: 0.8509 (p) REVERT: A 1308 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8845 (mm-30) REVERT: A 1309 ILE cc_start: 0.9699 (mt) cc_final: 0.9481 (tt) REVERT: A 1321 MET cc_start: 0.8074 (ptp) cc_final: 0.7865 (ppp) REVERT: A 1414 TRP cc_start: 0.9113 (m-90) cc_final: 0.8877 (m-90) REVERT: A 1627 LEU cc_start: 0.8626 (mt) cc_final: 0.8332 (mt) REVERT: A 1783 MET cc_start: 0.8162 (mtt) cc_final: 0.7903 (tpt) REVERT: A 2005 PHE cc_start: 0.9312 (t80) cc_final: 0.9100 (t80) REVERT: C 123 MET cc_start: 0.9144 (ttp) cc_final: 0.8918 (mtp) REVERT: C 163 ASP cc_start: 0.8486 (m-30) cc_final: 0.8017 (t0) REVERT: C 209 MET cc_start: 0.8556 (ppp) cc_final: 0.8219 (ppp) REVERT: C 658 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.7979 (t70) REVERT: C 774 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.2517 (mm) REVERT: C 920 LEU cc_start: 0.9052 (mt) cc_final: 0.8807 (mt) REVERT: C 968 MET cc_start: 0.8800 (mmm) cc_final: 0.8310 (mmm) REVERT: H 20 MET cc_start: 0.6402 (ptm) cc_final: 0.6180 (ppp) REVERT: H 169 THR cc_start: 0.8976 (m) cc_final: 0.8390 (t) REVERT: J 399 GLU cc_start: 0.8982 (tt0) cc_final: 0.8445 (tt0) REVERT: K 37 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8125 (t0) REVERT: L 55 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8337 (tt) REVERT: M 31 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8059 (t0) REVERT: M 98 ASP cc_start: 0.8776 (m-30) cc_final: 0.8536 (m-30) REVERT: N 106 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7072 (t0) REVERT: N 130 SER cc_start: 0.9508 (m) cc_final: 0.9243 (p) REVERT: N 207 LEU cc_start: 0.8308 (mp) cc_final: 0.8044 (tp) REVERT: O 204 LYS cc_start: 0.6836 (mttt) cc_final: 0.6073 (tppt) REVERT: O 234 ASP cc_start: 0.8616 (m-30) cc_final: 0.8326 (m-30) REVERT: P 161 THR cc_start: 0.8304 (p) cc_final: 0.7814 (m) REVERT: P 162 LYS cc_start: 0.9206 (mttt) cc_final: 0.8979 (mmtt) REVERT: P 164 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7783 (tp30) REVERT: P 167 GLN cc_start: 0.9019 (mt0) cc_final: 0.8434 (mm-40) REVERT: R 17 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9098 (t) REVERT: S 128 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8402 (p) REVERT: S 141 ILE cc_start: 0.9548 (pt) cc_final: 0.9242 (mm) REVERT: S 163 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7141 (tm-30) REVERT: S 180 LYS cc_start: 0.9254 (mtmm) cc_final: 0.9047 (mmmt) REVERT: S 199 MET cc_start: 0.9024 (tpp) cc_final: 0.7688 (mmm) REVERT: a 177 ASN cc_start: 0.9042 (t0) cc_final: 0.8798 (m-40) REVERT: a 183 TYR cc_start: 0.8908 (t80) cc_final: 0.8684 (t80) REVERT: b 5 GLN cc_start: 0.8620 (mt0) cc_final: 0.8230 (pp30) REVERT: d 60 ASP cc_start: 0.9200 (m-30) cc_final: 0.8856 (p0) REVERT: d 76 ASP cc_start: 0.8555 (m-30) cc_final: 0.8090 (p0) REVERT: f 55 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9244 (tm-30) REVERT: f 57 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8929 (mm-30) REVERT: g 8 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7605 (tptp) REVERT: g 17 LEU cc_start: 0.8213 (mp) cc_final: 0.7951 (tp) REVERT: j 31 MET cc_start: 0.8542 (mmm) cc_final: 0.8086 (mpp) REVERT: l 30 GLN cc_start: 0.6119 (mt0) cc_final: 0.5909 (mt0) REVERT: l 31 SER cc_start: 0.3134 (p) cc_final: 0.2906 (t) REVERT: l 36 MET cc_start: 0.6122 (ttm) cc_final: 0.5610 (mpp) REVERT: l 43 VAL cc_start: 0.0103 (OUTLIER) cc_final: -0.0171 (p) REVERT: l 92 ILE cc_start: 0.4570 (mm) cc_final: 0.4224 (pt) REVERT: m 41 ARG cc_start: 0.5533 (OUTLIER) cc_final: 0.5245 (ptp-170) REVERT: m 84 VAL cc_start: 0.2930 (t) cc_final: 0.2699 (m) REVERT: n 18 ILE cc_start: 0.4076 (mm) cc_final: 0.3819 (tt) REVERT: n 20 SER cc_start: 0.5311 (OUTLIER) cc_final: 0.4771 (m) REVERT: p 42 LYS cc_start: 0.7966 (mttt) cc_final: 0.7685 (ttpp) outliers start: 153 outliers final: 29 residues processed: 1109 average time/residue: 0.8581 time to fit residues: 1653.3745 Evaluate side-chains 545 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 504 time to evaluate : 6.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 843 optimal weight: 7.9990 chunk 757 optimal weight: 40.0000 chunk 420 optimal weight: 0.8980 chunk 258 optimal weight: 0.9990 chunk 510 optimal weight: 8.9990 chunk 404 optimal weight: 1.9990 chunk 783 optimal weight: 8.9990 chunk 303 optimal weight: 0.9990 chunk 476 optimal weight: 0.9980 chunk 582 optimal weight: 20.0000 chunk 907 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 344 ASN A 542 HIS A 760 ASN A 848 ASN A 868 GLN A1369 ASN A1471 GLN A1532 HIS A1856 ASN A2047 GLN C 143 HIS C 158 HIS C 211 ASN C 289 ASN C 358 ASN C 403 ASN C 423 HIS C 431 GLN C 683 ASN C 764 ASN C 776 ASN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 271 GLN ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 HIS ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 ASN K 86 ASN K 171 ASN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 147 ASN ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 HIS R 21 GLN S 73 GLN S 79 HIS S 117 HIS S 248 ASN S 277 ASN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 246 ASN ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 332 ASN y 144 GLN ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 ASN g 66 ASN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 GLN ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN r 53 ASN q 24 ASN q 77 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5674 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 79543 Z= 0.232 Angle : 0.717 19.760 110386 Z= 0.373 Chirality : 0.045 0.536 13542 Planarity : 0.005 0.115 12622 Dihedral : 17.633 177.103 17101 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.96 % Favored : 94.93 % Rotamer: Outliers : 0.25 % Allowed : 3.43 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.04 % 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: -0.47 (0.09), residues: 9411 helix: 1.80 (0.08), residues: 4139 sheet: -1.90 (0.13), residues: 1383 loop : -2.12 (0.09), residues: 3889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1012 HIS 0.008 0.001 HIS A 785 PHE 0.035 0.002 PHE e 18 TYR 0.023 0.002 TYR a 183 ARG 0.018 0.001 ARG k 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 658 time to evaluate : 6.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: A 172 ILE cc_start: 0.9638 (mt) cc_final: 0.9384 (mm) REVERT: A 179 MET cc_start: 0.8352 (tpp) cc_final: 0.8061 (tpt) REVERT: A 224 MET cc_start: 0.9196 (mtp) cc_final: 0.8950 (mtp) REVERT: A 312 TYR cc_start: 0.8359 (t80) cc_final: 0.8078 (t80) REVERT: A 565 VAL cc_start: 0.9115 (t) cc_final: 0.8645 (t) REVERT: A 578 MET cc_start: 0.8500 (mtp) cc_final: 0.8261 (mtp) REVERT: A 579 LEU cc_start: 0.9519 (mt) cc_final: 0.9258 (mt) REVERT: A 774 ILE cc_start: 0.8049 (pt) cc_final: 0.7654 (pt) REVERT: A 775 ARG cc_start: 0.8365 (mmp-170) cc_final: 0.6848 (ptm160) REVERT: A 777 LYS cc_start: 0.7658 (mppt) cc_final: 0.7137 (tttt) REVERT: A 841 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8077 (mp0) REVERT: A 912 LEU cc_start: 0.9471 (tt) cc_final: 0.9181 (tt) REVERT: A 914 LEU cc_start: 0.8877 (mp) cc_final: 0.8420 (tp) REVERT: A 951 LEU cc_start: 0.9688 (mt) cc_final: 0.9428 (mt) REVERT: A 1007 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8628 (tptp) REVERT: A 1213 MET cc_start: 0.8001 (ttt) cc_final: 0.7634 (mmm) REVERT: A 1379 MET cc_start: 0.5863 (ttt) cc_final: 0.5349 (tpt) REVERT: A 1627 LEU cc_start: 0.8605 (mt) cc_final: 0.8217 (mt) REVERT: A 1783 MET cc_start: 0.8306 (mtt) cc_final: 0.7989 (tpt) REVERT: A 1819 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9261 (pt) REVERT: A 1945 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8579 (tp30) REVERT: A 2005 PHE cc_start: 0.9051 (t80) cc_final: 0.8817 (t80) REVERT: C 123 MET cc_start: 0.9199 (ttp) cc_final: 0.8942 (ttp) REVERT: C 163 ASP cc_start: 0.8501 (m-30) cc_final: 0.8250 (t0) REVERT: C 229 LEU cc_start: 0.9373 (mt) cc_final: 0.9164 (tp) REVERT: C 880 MET cc_start: 0.8953 (tpt) cc_final: 0.8203 (mmm) REVERT: C 920 LEU cc_start: 0.9144 (mt) cc_final: 0.8909 (mt) REVERT: C 968 MET cc_start: 0.8883 (mmm) cc_final: 0.8307 (mmm) REVERT: H 34 MET cc_start: 0.4468 (mpp) cc_final: 0.3328 (tmm) REVERT: H 155 MET cc_start: 0.8488 (mpp) cc_final: 0.8015 (mpp) REVERT: J 392 MET cc_start: 0.8533 (tpp) cc_final: 0.8317 (tpp) REVERT: J 399 GLU cc_start: 0.9084 (tt0) cc_final: 0.8557 (tt0) REVERT: K 107 ASN cc_start: 0.9191 (p0) cc_final: 0.8808 (m-40) REVERT: K 149 MET cc_start: 0.8097 (tmm) cc_final: 0.7396 (ppp) REVERT: L 110 GLN cc_start: 0.8782 (mt0) cc_final: 0.8343 (tp-100) REVERT: M 98 ASP cc_start: 0.9056 (m-30) cc_final: 0.8264 (p0) REVERT: M 156 ILE cc_start: 0.9069 (mt) cc_final: 0.8702 (mm) REVERT: N 75 MET cc_start: 0.6765 (mmp) cc_final: 0.6462 (mmp) REVERT: O 204 LYS cc_start: 0.7183 (mttt) cc_final: 0.6581 (tppt) REVERT: O 234 ASP cc_start: 0.8642 (m-30) cc_final: 0.8154 (m-30) REVERT: P 161 THR cc_start: 0.8392 (p) cc_final: 0.7414 (m) REVERT: P 162 LYS cc_start: 0.9084 (mttt) cc_final: 0.8708 (mmtt) REVERT: P 164 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8030 (tp30) REVERT: P 167 GLN cc_start: 0.8978 (mt0) cc_final: 0.8720 (tp40) REVERT: S 163 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7353 (tm-30) REVERT: S 180 LYS cc_start: 0.9211 (mtmm) cc_final: 0.9005 (mmmt) REVERT: S 199 MET cc_start: 0.9058 (tpp) cc_final: 0.8550 (mmt) REVERT: b 5 GLN cc_start: 0.8651 (mt0) cc_final: 0.8290 (pp30) REVERT: b 95 THR cc_start: 0.9521 (p) cc_final: 0.9284 (p) REVERT: d 76 ASP cc_start: 0.8548 (m-30) cc_final: 0.8120 (p0) REVERT: e 18 PHE cc_start: 0.9008 (m-80) cc_final: 0.8794 (m-10) REVERT: f 65 HIS cc_start: 0.6979 (t-90) cc_final: 0.6700 (m170) REVERT: l 36 MET cc_start: 0.5919 (ttm) cc_final: 0.5565 (mpp) REVERT: l 92 ILE cc_start: 0.4651 (mm) cc_final: 0.4304 (pt) REVERT: m 31 MET cc_start: 0.3360 (mtt) cc_final: 0.2622 (mpp) REVERT: m 38 MET cc_start: -0.0056 (ttt) cc_final: -0.0314 (ttt) REVERT: m 58 VAL cc_start: 0.3898 (t) cc_final: 0.3215 (t) REVERT: p 42 LYS cc_start: 0.7928 (mttt) cc_final: 0.7703 (ttpp) outliers start: 14 outliers final: 5 residues processed: 668 average time/residue: 0.7403 time to fit residues: 869.2435 Evaluate side-chains 446 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 440 time to evaluate : 6.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 504 optimal weight: 7.9990 chunk 281 optimal weight: 0.7980 chunk 755 optimal weight: 30.0000 chunk 617 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 908 optimal weight: 50.0000 chunk 981 optimal weight: 50.0000 chunk 809 optimal weight: 0.7980 chunk 901 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 729 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 509 HIS A 748 GLN A 784 GLN A 848 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 GLN A1091 ASN A1115 GLN A1190 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 GLN A2047 GLN C 158 HIS ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS C 934 HIS H 59 ASN ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 GLN H 437 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN M 252 HIS ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 GLN S 67 GLN S 78 GLN S 117 HIS S 233 GLN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 181 GLN a 247 HIS ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN o 261 HIS ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 ASN ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** l 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 28 HIS n 43 GLN r 18 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 79543 Z= 0.283 Angle : 0.680 19.573 110386 Z= 0.351 Chirality : 0.043 0.350 13542 Planarity : 0.005 0.068 12622 Dihedral : 17.471 175.524 17101 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 0.20 % Allowed : 5.00 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.06 (0.09), residues: 9411 helix: 2.03 (0.08), residues: 4155 sheet: -1.52 (0.13), residues: 1362 loop : -1.85 (0.10), residues: 3894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 564 HIS 0.016 0.002 HIS J 382 PHE 0.064 0.002 PHE O 241 TYR 0.063 0.002 TYR A 154 ARG 0.026 0.001 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 528 time to evaluate : 6.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.9707 (mt) cc_final: 0.9454 (tt) REVERT: A 224 MET cc_start: 0.9254 (mtp) cc_final: 0.8962 (mtp) REVERT: A 914 LEU cc_start: 0.9012 (mp) cc_final: 0.8800 (tp) REVERT: A 1057 MET cc_start: 0.8620 (tmm) cc_final: 0.8395 (tmm) REVERT: A 1213 MET cc_start: 0.8557 (ttt) cc_final: 0.8209 (tmm) REVERT: A 1379 MET cc_start: 0.6908 (ttt) cc_final: 0.6573 (tpp) REVERT: A 1519 LEU cc_start: 0.9256 (tp) cc_final: 0.8815 (tp) REVERT: A 1627 LEU cc_start: 0.8913 (mt) cc_final: 0.8502 (mt) REVERT: A 1783 MET cc_start: 0.7866 (mtt) cc_final: 0.7635 (mtp) REVERT: A 1819 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9224 (pt) REVERT: A 1840 TYR cc_start: 0.8843 (t80) cc_final: 0.8504 (t80) REVERT: A 2005 PHE cc_start: 0.9080 (t80) cc_final: 0.8854 (t80) REVERT: C 209 MET cc_start: 0.8405 (ppp) cc_final: 0.8186 (ppp) REVERT: C 255 GLN cc_start: 0.8444 (tp40) cc_final: 0.8232 (tp40) REVERT: C 263 MET cc_start: 0.9062 (ptt) cc_final: 0.8697 (ptp) REVERT: C 834 MET cc_start: 0.5554 (ppp) cc_final: 0.5174 (ppp) REVERT: C 880 MET cc_start: 0.9019 (tpt) cc_final: 0.8598 (mmm) REVERT: C 968 MET cc_start: 0.8666 (mmm) cc_final: 0.8322 (mmm) REVERT: H 155 MET cc_start: 0.8526 (mpp) cc_final: 0.8222 (mpp) REVERT: J 392 MET cc_start: 0.8732 (tpp) cc_final: 0.8524 (tpp) REVERT: J 399 GLU cc_start: 0.9061 (tt0) cc_final: 0.8554 (tt0) REVERT: K 107 ASN cc_start: 0.9169 (p0) cc_final: 0.8469 (m-40) REVERT: M 98 ASP cc_start: 0.9085 (m-30) cc_final: 0.8224 (p0) REVERT: N 75 MET cc_start: 0.7222 (mmp) cc_final: 0.6905 (mmp) REVERT: N 124 GLN cc_start: 0.9047 (pm20) cc_final: 0.8689 (pm20) REVERT: O 204 LYS cc_start: 0.7281 (mttt) cc_final: 0.6799 (tppt) REVERT: O 234 ASP cc_start: 0.8775 (m-30) cc_final: 0.8389 (m-30) REVERT: P 161 THR cc_start: 0.8074 (p) cc_final: 0.7375 (p) REVERT: P 162 LYS cc_start: 0.9097 (mttt) cc_final: 0.8880 (mmtt) REVERT: P 164 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7871 (tp30) REVERT: S 163 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7847 (tm-30) REVERT: S 180 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8797 (mmmt) REVERT: c 181 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8761 (pm20) REVERT: o 444 CYS cc_start: 0.7074 (t) cc_final: 0.6813 (t) REVERT: y 168 LEU cc_start: 0.9747 (mt) cc_final: 0.9455 (mt) REVERT: y 171 GLU cc_start: 0.8933 (pt0) cc_final: 0.8521 (tp30) REVERT: b 5 GLN cc_start: 0.8746 (mt0) cc_final: 0.8373 (pp30) REVERT: d 76 ASP cc_start: 0.8779 (m-30) cc_final: 0.8354 (p0) REVERT: j 31 MET cc_start: 0.8657 (mpp) cc_final: 0.8251 (mpp) REVERT: k 28 ARG cc_start: 0.4128 (mtt90) cc_final: 0.3877 (mmt90) REVERT: l 36 MET cc_start: 0.5903 (ttm) cc_final: 0.5665 (mpp) REVERT: l 92 ILE cc_start: 0.5091 (mm) cc_final: 0.4699 (pt) REVERT: m 31 MET cc_start: 0.2399 (mtt) cc_final: 0.1737 (mpp) REVERT: p 42 LYS cc_start: 0.7822 (mttt) cc_final: 0.7582 (ttpp) outliers start: 11 outliers final: 1 residues processed: 539 average time/residue: 0.7190 time to fit residues: 693.6028 Evaluate side-chains 409 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 407 time to evaluate : 6.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 897 optimal weight: 30.0000 chunk 683 optimal weight: 1.9990 chunk 471 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 433 optimal weight: 8.9990 chunk 610 optimal weight: 8.9990 chunk 912 optimal weight: 50.0000 chunk 965 optimal weight: 30.0000 chunk 476 optimal weight: 0.9980 chunk 864 optimal weight: 20.0000 chunk 260 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 636 HIS A 784 GLN A 830 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 310 ASN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 HIS ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 HIS J 354 ASN L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN O 197 ASN ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 HIS P 167 GLN P 171 HIS S 117 HIS S 233 GLN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN o 283 GLN ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 61 GLN j 83 ASN ** l 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 79543 Z= 0.235 Angle : 0.624 18.258 110386 Z= 0.322 Chirality : 0.042 0.294 13542 Planarity : 0.004 0.092 12622 Dihedral : 17.382 175.584 17101 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.12 % Rotamer: Outliers : 0.12 % Allowed : 3.43 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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 (0.09), residues: 9411 helix: 2.10 (0.08), residues: 4179 sheet: -1.36 (0.13), residues: 1393 loop : -1.68 (0.10), residues: 3839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 18 HIS 0.008 0.001 HIS o 161 PHE 0.038 0.002 PHE e 18 TYR 0.022 0.002 TYR a 183 ARG 0.008 0.001 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 499 time to evaluate : 6.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.9723 (mt) cc_final: 0.9521 (tt) REVERT: A 224 MET cc_start: 0.9254 (mtp) cc_final: 0.9044 (mtp) REVERT: A 578 MET cc_start: 0.8622 (mtp) cc_final: 0.8398 (mtp) REVERT: A 636 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.7012 (m-70) REVERT: A 763 MET cc_start: 0.9302 (tmm) cc_final: 0.8922 (tmm) REVERT: A 766 ILE cc_start: 0.8801 (mm) cc_final: 0.8488 (pt) REVERT: A 770 MET cc_start: 0.9187 (tpp) cc_final: 0.8845 (tpp) REVERT: A 914 LEU cc_start: 0.8998 (mp) cc_final: 0.8784 (tp) REVERT: A 942 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9027 (pp20) REVERT: A 1057 MET cc_start: 0.8615 (tmm) cc_final: 0.8336 (tmm) REVERT: A 1213 MET cc_start: 0.8476 (ttt) cc_final: 0.8159 (tpp) REVERT: A 1519 LEU cc_start: 0.9278 (tp) cc_final: 0.8837 (tp) REVERT: A 1732 MET cc_start: 0.7960 (tpp) cc_final: 0.7655 (tpp) REVERT: A 1783 MET cc_start: 0.8147 (mtt) cc_final: 0.7893 (mtp) REVERT: A 1840 TYR cc_start: 0.8878 (t80) cc_final: 0.8452 (t80) REVERT: A 2005 PHE cc_start: 0.9134 (t80) cc_final: 0.8701 (t80) REVERT: C 150 MET cc_start: 0.9219 (mtp) cc_final: 0.8981 (mtp) REVERT: C 209 MET cc_start: 0.8324 (ppp) cc_final: 0.8031 (ppp) REVERT: C 263 MET cc_start: 0.9207 (ptt) cc_final: 0.8800 (ptp) REVERT: C 495 ARG cc_start: 0.8732 (tmm160) cc_final: 0.8101 (pmt170) REVERT: C 880 MET cc_start: 0.9020 (mmm) cc_final: 0.8754 (mmm) REVERT: C 968 MET cc_start: 0.8742 (mmm) cc_final: 0.8516 (mmm) REVERT: H 155 MET cc_start: 0.8337 (mpp) cc_final: 0.7960 (mpp) REVERT: J 399 GLU cc_start: 0.8959 (tt0) cc_final: 0.8501 (tt0) REVERT: L 36 ASP cc_start: 0.8701 (m-30) cc_final: 0.7653 (t0) REVERT: M 98 ASP cc_start: 0.9255 (m-30) cc_final: 0.8335 (p0) REVERT: N 107 ASP cc_start: 0.8975 (m-30) cc_final: 0.8406 (p0) REVERT: N 124 GLN cc_start: 0.8885 (pm20) cc_final: 0.8523 (pm20) REVERT: N 139 LEU cc_start: 0.9195 (tp) cc_final: 0.8966 (tp) REVERT: O 161 ASN cc_start: 0.9375 (t0) cc_final: 0.8689 (p0) REVERT: O 204 LYS cc_start: 0.7323 (mttt) cc_final: 0.6880 (tppt) REVERT: O 234 ASP cc_start: 0.8817 (m-30) cc_final: 0.8448 (m-30) REVERT: P 41 LYS cc_start: 0.9211 (tmtt) cc_final: 0.8831 (pttm) REVERT: P 161 THR cc_start: 0.7986 (p) cc_final: 0.7276 (p) REVERT: P 164 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7717 (tp30) REVERT: S 163 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7906 (tm-30) REVERT: S 174 ASP cc_start: 0.9001 (m-30) cc_final: 0.8607 (t70) REVERT: S 180 LYS cc_start: 0.9402 (mppt) cc_final: 0.9198 (mmmt) REVERT: c 181 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8855 (pm20) REVERT: o 69 TRP cc_start: 0.7392 (t-100) cc_final: 0.5796 (t-100) REVERT: o 444 CYS cc_start: 0.7113 (t) cc_final: 0.6868 (t) REVERT: b 5 GLN cc_start: 0.8836 (mt0) cc_final: 0.8474 (pp30) REVERT: d 38 ASP cc_start: 0.9200 (t0) cc_final: 0.8982 (t0) REVERT: d 40 MET cc_start: 0.8082 (mpp) cc_final: 0.7597 (mpp) REVERT: d 76 ASP cc_start: 0.8852 (m-30) cc_final: 0.8411 (p0) REVERT: e 82 LEU cc_start: 0.8230 (tt) cc_final: 0.8000 (mp) REVERT: g 44 MET cc_start: 0.6567 (mmm) cc_final: 0.6366 (tpp) REVERT: j 31 MET cc_start: 0.8687 (mpp) cc_final: 0.8261 (mpp) REVERT: k 28 ARG cc_start: 0.4120 (mtt90) cc_final: 0.3866 (mmt90) REVERT: m 31 MET cc_start: 0.2575 (mtt) cc_final: 0.1951 (mpp) REVERT: p 42 LYS cc_start: 0.7726 (mttt) cc_final: 0.7470 (ttpp) outliers start: 7 outliers final: 0 residues processed: 506 average time/residue: 0.7021 time to fit residues: 637.3044 Evaluate side-chains 391 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 6.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 804 optimal weight: 9.9990 chunk 548 optimal weight: 7.9990 chunk 14 optimal weight: 50.0000 chunk 718 optimal weight: 9.9990 chunk 398 optimal weight: 0.7980 chunk 824 optimal weight: 6.9990 chunk 667 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 493 optimal weight: 3.9990 chunk 866 optimal weight: 6.9990 chunk 243 optimal weight: 0.0030 overall best weight: 3.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A1404 HIS ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN ** A1508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN C 194 ASN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 HIS ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 905 GLN C 934 HIS J 136 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN K 111 HIS L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 ASN ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS S 170 ASN S 214 ASN S 268 GLN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 177 ASN a 247 HIS o 247 ASN o 292 HIS ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN f 50 ASN g 55 HIS ** l 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 79543 Z= 0.292 Angle : 0.661 18.188 110386 Z= 0.338 Chirality : 0.042 0.260 13542 Planarity : 0.005 0.073 12622 Dihedral : 17.366 172.003 17101 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.11 (0.09), residues: 9411 helix: 1.96 (0.08), residues: 4196 sheet: -1.23 (0.14), residues: 1382 loop : -1.62 (0.10), residues: 3833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 933 HIS 0.012 0.002 HIS A 636 PHE 0.021 0.002 PHE A 239 TYR 0.048 0.002 TYR S 105 ARG 0.020 0.001 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 470 time to evaluate : 6.483 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: A 224 MET cc_start: 0.9285 (mtp) cc_final: 0.8958 (mtp) REVERT: A 583 ILE cc_start: 0.9504 (pt) cc_final: 0.9141 (mm) REVERT: A 763 MET cc_start: 0.9378 (tmm) cc_final: 0.8932 (tmm) REVERT: A 766 ILE cc_start: 0.8794 (mm) cc_final: 0.8461 (pt) REVERT: A 914 LEU cc_start: 0.8976 (mp) cc_final: 0.8617 (tp) REVERT: A 942 GLU cc_start: 0.9328 (mm-30) cc_final: 0.9037 (tm-30) REVERT: A 1057 MET cc_start: 0.8686 (tmm) cc_final: 0.8325 (tmm) REVERT: A 1213 MET cc_start: 0.8529 (ttt) cc_final: 0.8003 (tpp) REVERT: A 1519 LEU cc_start: 0.9300 (tp) cc_final: 0.8880 (tp) REVERT: A 1732 MET cc_start: 0.8207 (tpp) cc_final: 0.7619 (tpt) REVERT: A 1783 MET cc_start: 0.8522 (mtt) cc_final: 0.8228 (mtp) REVERT: A 1840 TYR cc_start: 0.8920 (t80) cc_final: 0.8419 (t80) REVERT: A 1986 MET cc_start: 0.8549 (tpt) cc_final: 0.7792 (tpt) REVERT: A 2005 PHE cc_start: 0.9098 (t80) cc_final: 0.8679 (t80) REVERT: C 126 MET cc_start: 0.8763 (tpp) cc_final: 0.8508 (tpp) REVERT: C 209 MET cc_start: 0.8487 (ppp) cc_final: 0.8280 (ppp) REVERT: C 263 MET cc_start: 0.9201 (ptt) cc_final: 0.8681 (ptp) REVERT: C 495 ARG cc_start: 0.8702 (tmm160) cc_final: 0.8116 (pmt170) REVERT: H 108 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7915 (tmt-80) REVERT: H 350 MET cc_start: 0.9159 (mmm) cc_final: 0.8603 (mmm) REVERT: J 266 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8468 (mmtt) REVERT: J 399 GLU cc_start: 0.9027 (tt0) cc_final: 0.8736 (tt0) REVERT: L 86 TYR cc_start: 0.7163 (m-80) cc_final: 0.6957 (m-10) REVERT: N 107 ASP cc_start: 0.8950 (m-30) cc_final: 0.8508 (t70) REVERT: N 124 GLN cc_start: 0.9029 (pm20) cc_final: 0.8512 (pm20) REVERT: O 18 ASP cc_start: 0.8530 (m-30) cc_final: 0.8274 (m-30) REVERT: O 204 LYS cc_start: 0.7562 (mttt) cc_final: 0.7201 (tppt) REVERT: P 164 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7853 (tp30) REVERT: S 163 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8199 (tm-30) REVERT: S 174 ASP cc_start: 0.9024 (m-30) cc_final: 0.8715 (t70) REVERT: a 138 ASP cc_start: 0.8871 (m-30) cc_final: 0.8265 (p0) REVERT: c 181 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8897 (pm20) REVERT: o 69 TRP cc_start: 0.7555 (t-100) cc_final: 0.6057 (t-100) REVERT: o 444 CYS cc_start: 0.7017 (t) cc_final: 0.6786 (t) REVERT: b 5 GLN cc_start: 0.8811 (mt0) cc_final: 0.8327 (pp30) REVERT: d 76 ASP cc_start: 0.8828 (m-30) cc_final: 0.8405 (p0) REVERT: j 31 MET cc_start: 0.8526 (mpp) cc_final: 0.8108 (mpp) REVERT: k 28 ARG cc_start: 0.4406 (mtt90) cc_final: 0.4059 (mmt90) REVERT: l 104 ASP cc_start: 0.2680 (p0) cc_final: 0.2181 (t0) REVERT: m 31 MET cc_start: 0.2206 (mtt) cc_final: 0.1617 (mpp) REVERT: p 42 LYS cc_start: 0.7404 (mttt) cc_final: 0.7094 (ttpp) outliers start: 1 outliers final: 0 residues processed: 471 average time/residue: 0.6965 time to fit residues: 589.6882 Evaluate side-chains 372 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 6.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 324 optimal weight: 8.9990 chunk 869 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 566 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 966 optimal weight: 10.0000 chunk 802 optimal weight: 0.9990 chunk 447 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 507 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 HIS ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 236 GLN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 309 HIS c 326 GLN o 247 ASN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN f 77 ASN ** j 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 35 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 79543 Z= 0.337 Angle : 0.688 19.128 110386 Z= 0.354 Chirality : 0.043 0.286 13542 Planarity : 0.005 0.106 12622 Dihedral : 17.435 167.869 17101 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.02 (0.09), residues: 9411 helix: 1.79 (0.08), residues: 4192 sheet: -1.21 (0.14), residues: 1374 loop : -1.62 (0.10), residues: 3845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP H 174 HIS 0.011 0.002 HIS C 218 PHE 0.052 0.002 PHE e 18 TYR 0.028 0.002 TYR S 105 ARG 0.022 0.001 ARG A1442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 6.581 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: A 224 MET cc_start: 0.9379 (mtp) cc_final: 0.9080 (mtp) REVERT: A 237 MET cc_start: 0.8318 (mmm) cc_final: 0.8038 (mmm) REVERT: A 578 MET cc_start: 0.8698 (mtp) cc_final: 0.8372 (mtp) REVERT: A 583 ILE cc_start: 0.9528 (pt) cc_final: 0.9172 (mm) REVERT: A 763 MET cc_start: 0.9352 (tmm) cc_final: 0.8897 (tmm) REVERT: A 914 LEU cc_start: 0.9097 (mp) cc_final: 0.8808 (tp) REVERT: A 942 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9044 (pp20) REVERT: A 1057 MET cc_start: 0.8590 (tmm) cc_final: 0.8322 (tmm) REVERT: A 1213 MET cc_start: 0.8656 (ttt) cc_final: 0.8406 (tmm) REVERT: A 1519 LEU cc_start: 0.9283 (tp) cc_final: 0.8885 (tp) REVERT: A 1641 LEU cc_start: 0.9375 (tp) cc_final: 0.9165 (tp) REVERT: A 1694 MET cc_start: 0.8751 (tpp) cc_final: 0.8394 (tpp) REVERT: A 1732 MET cc_start: 0.8123 (tpp) cc_final: 0.7728 (tpt) REVERT: A 1766 MET cc_start: 0.9318 (ppp) cc_final: 0.9090 (ppp) REVERT: A 1783 MET cc_start: 0.8364 (mtt) cc_final: 0.7996 (mtp) REVERT: A 1840 TYR cc_start: 0.8952 (t80) cc_final: 0.8460 (t80) REVERT: A 1986 MET cc_start: 0.8223 (tpt) cc_final: 0.7981 (tpt) REVERT: A 2005 PHE cc_start: 0.9255 (t80) cc_final: 0.8660 (t80) REVERT: C 126 MET cc_start: 0.8779 (tpp) cc_final: 0.8506 (tpp) REVERT: C 209 MET cc_start: 0.8691 (ppp) cc_final: 0.8375 (ppp) REVERT: C 263 MET cc_start: 0.9192 (ptt) cc_final: 0.8868 (ptp) REVERT: C 495 ARG cc_start: 0.8518 (tmm160) cc_final: 0.8055 (pmt170) REVERT: C 652 MET cc_start: 0.7988 (tpp) cc_final: 0.7550 (tpp) REVERT: C 968 MET cc_start: 0.8755 (mmp) cc_final: 0.8549 (mmm) REVERT: J 399 GLU cc_start: 0.9010 (tt0) cc_final: 0.8782 (tt0) REVERT: L 86 TYR cc_start: 0.7328 (m-80) cc_final: 0.7065 (m-10) REVERT: N 107 ASP cc_start: 0.8885 (m-30) cc_final: 0.8364 (t70) REVERT: O 204 LYS cc_start: 0.7805 (mttt) cc_final: 0.7600 (tppt) REVERT: P 164 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7890 (tp30) REVERT: S 163 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8318 (tm-30) REVERT: a 184 MET cc_start: 0.8638 (ttp) cc_final: 0.8397 (ttp) REVERT: o 444 CYS cc_start: 0.6829 (t) cc_final: 0.6604 (t) REVERT: b 5 GLN cc_start: 0.8811 (mt0) cc_final: 0.8248 (pp30) REVERT: b 41 MET cc_start: 0.9426 (tpp) cc_final: 0.9207 (tpp) REVERT: b 43 LEU cc_start: 0.9549 (mt) cc_final: 0.9168 (mt) REVERT: d 76 ASP cc_start: 0.8840 (m-30) cc_final: 0.8476 (p0) REVERT: j 31 MET cc_start: 0.8587 (mpp) cc_final: 0.8188 (mpp) REVERT: j 38 MET cc_start: 0.7942 (ptp) cc_final: 0.7730 (ptp) REVERT: l 104 ASP cc_start: 0.2593 (p0) cc_final: 0.2094 (t0) REVERT: m 31 MET cc_start: 0.2092 (mtt) cc_final: 0.1544 (mpp) REVERT: p 42 LYS cc_start: 0.7504 (mttt) cc_final: 0.7200 (ttpp) outliers start: 1 outliers final: 0 residues processed: 452 average time/residue: 0.7147 time to fit residues: 580.5089 Evaluate side-chains 357 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 6.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 931 optimal weight: 30.0000 chunk 108 optimal weight: 0.9980 chunk 550 optimal weight: 10.0000 chunk 705 optimal weight: 6.9990 chunk 546 optimal weight: 0.3980 chunk 813 optimal weight: 2.9990 chunk 539 optimal weight: 10.0000 chunk 962 optimal weight: 50.0000 chunk 602 optimal weight: 20.0000 chunk 587 optimal weight: 20.0000 chunk 444 optimal weight: 9.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN A 784 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 HIS A1424 HIS ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 HIS ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 94 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 79543 Z= 0.302 Angle : 0.669 19.138 110386 Z= 0.343 Chirality : 0.043 0.368 13542 Planarity : 0.005 0.124 12622 Dihedral : 17.388 167.513 17101 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.02 (0.09), residues: 9411 helix: 1.80 (0.08), residues: 4195 sheet: -1.14 (0.14), residues: 1365 loop : -1.61 (0.10), residues: 3851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1012 HIS 0.010 0.002 HIS S 117 PHE 0.026 0.002 PHE H 353 TYR 0.048 0.002 TYR C 382 ARG 0.014 0.001 ARG y 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 6.442 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: A 134 MET cc_start: 0.8019 (pmm) cc_final: 0.7788 (pmm) REVERT: A 224 MET cc_start: 0.9398 (mtp) cc_final: 0.8900 (mtm) REVERT: A 237 MET cc_start: 0.8559 (mmm) cc_final: 0.8348 (mmm) REVERT: A 490 LYS cc_start: 0.9364 (pptt) cc_final: 0.9130 (pttm) REVERT: A 578 MET cc_start: 0.8597 (mtp) cc_final: 0.8288 (mtp) REVERT: A 763 MET cc_start: 0.9367 (tmm) cc_final: 0.9107 (tmm) REVERT: A 914 LEU cc_start: 0.9060 (mp) cc_final: 0.8704 (tp) REVERT: A 942 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9027 (tm-30) REVERT: A 1057 MET cc_start: 0.8699 (tmm) cc_final: 0.8383 (tmm) REVERT: A 1213 MET cc_start: 0.8671 (ttt) cc_final: 0.8348 (tmm) REVERT: A 1429 MET cc_start: 0.8376 (tpt) cc_final: 0.7736 (ttt) REVERT: A 1519 LEU cc_start: 0.9213 (tp) cc_final: 0.8826 (tp) REVERT: A 1694 MET cc_start: 0.8529 (tpp) cc_final: 0.8180 (tpp) REVERT: A 1783 MET cc_start: 0.8299 (mtt) cc_final: 0.7809 (mtp) REVERT: A 1840 TYR cc_start: 0.8907 (t80) cc_final: 0.7663 (t80) REVERT: A 2005 PHE cc_start: 0.9322 (t80) cc_final: 0.8387 (t80) REVERT: C 209 MET cc_start: 0.8705 (ppp) cc_final: 0.8379 (ppp) REVERT: C 263 MET cc_start: 0.9136 (ptt) cc_final: 0.8926 (ptp) REVERT: C 485 LEU cc_start: 0.9102 (tp) cc_final: 0.8807 (tt) REVERT: C 652 MET cc_start: 0.7985 (tpp) cc_final: 0.7570 (tpp) REVERT: C 834 MET cc_start: 0.6023 (ppp) cc_final: 0.5748 (tmm) REVERT: C 968 MET cc_start: 0.8722 (mmp) cc_final: 0.8495 (mmm) REVERT: H 147 SER cc_start: 0.8419 (t) cc_final: 0.8111 (m) REVERT: J 399 GLU cc_start: 0.8962 (tt0) cc_final: 0.8615 (tt0) REVERT: N 107 ASP cc_start: 0.9002 (m-30) cc_final: 0.8448 (t70) REVERT: P 164 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8035 (tp30) REVERT: S 163 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8236 (tm-30) REVERT: o 444 CYS cc_start: 0.6866 (t) cc_final: 0.6651 (t) REVERT: b 5 GLN cc_start: 0.8860 (mt0) cc_final: 0.8287 (pp30) REVERT: b 41 MET cc_start: 0.9474 (tpp) cc_final: 0.9199 (tpp) REVERT: b 43 LEU cc_start: 0.9609 (mt) cc_final: 0.9149 (mt) REVERT: d 76 ASP cc_start: 0.8753 (m-30) cc_final: 0.8437 (p0) REVERT: j 31 MET cc_start: 0.8544 (mpp) cc_final: 0.8122 (mpp) REVERT: l 104 ASP cc_start: 0.2768 (p0) cc_final: 0.2235 (t0) REVERT: m 31 MET cc_start: 0.2423 (mtt) cc_final: 0.1912 (mpp) REVERT: m 38 MET cc_start: 0.0550 (ttt) cc_final: -0.0076 (tpp) REVERT: m 61 PHE cc_start: 0.0561 (t80) cc_final: 0.0260 (t80) REVERT: p 42 LYS cc_start: 0.7136 (mttt) cc_final: 0.6829 (ttpp) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.6652 time to fit residues: 535.4152 Evaluate side-chains 358 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 595 optimal weight: 20.0000 chunk 384 optimal weight: 8.9990 chunk 575 optimal weight: 0.0020 chunk 290 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 612 optimal weight: 2.9990 chunk 656 optimal weight: 5.9990 chunk 476 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 756 optimal weight: 50.0000 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 HIS N 95 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 158 ASN R 21 GLN S 67 GLN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 171 GLN c 309 HIS o 247 ASN o 283 GLN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 184 GLN ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 204 ASN b 8 HIS b 33 GLN j 52 HIS l 94 GLN n 61 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 79543 Z= 0.165 Angle : 0.604 17.624 110386 Z= 0.305 Chirality : 0.041 0.281 13542 Planarity : 0.004 0.095 12622 Dihedral : 17.198 168.523 17101 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 0.04 % Allowed : 1.48 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.35 (0.09), residues: 9411 helix: 2.15 (0.08), residues: 4182 sheet: -1.07 (0.14), residues: 1401 loop : -1.47 (0.10), residues: 3828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP S 238 HIS 0.021 0.001 HIS C 554 PHE 0.026 0.001 PHE A1388 TYR 0.031 0.002 TYR S 105 ARG 0.015 0.001 ARG k 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 463 time to evaluate : 6.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8294 (mmm) cc_final: 0.8079 (mmm) REVERT: A 224 MET cc_start: 0.9326 (mtp) cc_final: 0.8776 (mtm) REVERT: A 508 GLN cc_start: 0.9236 (pt0) cc_final: 0.8903 (pp30) REVERT: A 722 LEU cc_start: 0.8819 (mm) cc_final: 0.8585 (mm) REVERT: A 763 MET cc_start: 0.9349 (tmm) cc_final: 0.9086 (tmm) REVERT: A 886 MET cc_start: 0.8839 (tpp) cc_final: 0.8521 (tpp) REVERT: A 914 LEU cc_start: 0.8984 (mp) cc_final: 0.8646 (tp) REVERT: A 1213 MET cc_start: 0.8560 (ttt) cc_final: 0.8269 (tmm) REVERT: A 1519 LEU cc_start: 0.9319 (tp) cc_final: 0.9028 (tp) REVERT: A 1694 MET cc_start: 0.8318 (tpp) cc_final: 0.7962 (tpp) REVERT: A 1783 MET cc_start: 0.8442 (mtt) cc_final: 0.7980 (mtp) REVERT: A 1840 TYR cc_start: 0.8791 (t80) cc_final: 0.8313 (t80) REVERT: A 2005 PHE cc_start: 0.9152 (t80) cc_final: 0.8492 (t80) REVERT: C 209 MET cc_start: 0.8372 (ppp) cc_final: 0.8066 (ppp) REVERT: C 485 LEU cc_start: 0.9016 (tp) cc_final: 0.8781 (tt) REVERT: C 652 MET cc_start: 0.7798 (tpp) cc_final: 0.7303 (tpp) REVERT: C 834 MET cc_start: 0.6030 (ppp) cc_final: 0.5754 (tmm) REVERT: H 147 SER cc_start: 0.8348 (t) cc_final: 0.8002 (m) REVERT: H 155 MET cc_start: 0.8699 (mpp) cc_final: 0.8290 (mpp) REVERT: H 204 ASP cc_start: 0.6105 (t0) cc_final: 0.5683 (m-30) REVERT: J 399 GLU cc_start: 0.8976 (tt0) cc_final: 0.8572 (tt0) REVERT: L 36 ASP cc_start: 0.8918 (m-30) cc_final: 0.7800 (t0) REVERT: L 121 ILE cc_start: 0.8456 (mp) cc_final: 0.8123 (mp) REVERT: N 107 ASP cc_start: 0.8920 (m-30) cc_final: 0.8415 (t70) REVERT: P 164 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7987 (tp30) REVERT: S 163 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8163 (tm-30) REVERT: o 444 CYS cc_start: 0.6924 (t) cc_final: 0.6708 (t) REVERT: b 5 GLN cc_start: 0.8822 (mt0) cc_final: 0.8213 (pp30) REVERT: b 41 MET cc_start: 0.9471 (tpp) cc_final: 0.9148 (tpp) REVERT: b 43 LEU cc_start: 0.9617 (mt) cc_final: 0.9169 (mt) REVERT: d 76 ASP cc_start: 0.8743 (m-30) cc_final: 0.8400 (p0) REVERT: j 31 MET cc_start: 0.8727 (mpp) cc_final: 0.8285 (mpp) REVERT: l 104 ASP cc_start: 0.2896 (p0) cc_final: 0.2319 (t0) REVERT: m 31 MET cc_start: 0.2103 (mtt) cc_final: 0.1435 (mpp) REVERT: m 61 PHE cc_start: 0.1326 (t80) cc_final: 0.0528 (t80) REVERT: p 42 LYS cc_start: 0.7165 (mttt) cc_final: 0.6860 (ttpp) outliers start: 2 outliers final: 0 residues processed: 465 average time/residue: 0.6954 time to fit residues: 584.8481 Evaluate side-chains 364 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 6.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 875 optimal weight: 30.0000 chunk 922 optimal weight: 0.0270 chunk 841 optimal weight: 8.9990 chunk 897 optimal weight: 50.0000 chunk 540 optimal weight: 40.0000 chunk 390 optimal weight: 10.0000 chunk 704 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 810 optimal weight: 3.9990 chunk 848 optimal weight: 20.0000 chunk 894 optimal weight: 3.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN ** A1508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1947 HIS ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 GLN S 210 ASN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN o 354 GLN o 413 ASN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN h 30 GLN ** l 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 79543 Z= 0.336 Angle : 0.690 19.858 110386 Z= 0.352 Chirality : 0.043 0.607 13542 Planarity : 0.005 0.062 12622 Dihedral : 17.264 168.021 17101 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.09), residues: 9411 helix: 1.94 (0.08), residues: 4179 sheet: -0.98 (0.14), residues: 1343 loop : -1.53 (0.10), residues: 3889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1012 HIS 0.010 0.002 HIS o 161 PHE 0.032 0.002 PHE e 18 TYR 0.041 0.002 TYR S 156 ARG 0.009 0.001 ARG y 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 6.557 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: A 224 MET cc_start: 0.9408 (mtp) cc_final: 0.9114 (mtp) REVERT: A 578 MET cc_start: 0.8620 (mtp) cc_final: 0.8176 (mtp) REVERT: A 634 ASP cc_start: 0.9021 (m-30) cc_final: 0.8526 (t0) REVERT: A 722 LEU cc_start: 0.8916 (mm) cc_final: 0.8685 (mm) REVERT: A 763 MET cc_start: 0.9173 (tmm) cc_final: 0.8642 (tmm) REVERT: A 914 LEU cc_start: 0.9121 (mp) cc_final: 0.8858 (tp) REVERT: A 1057 MET cc_start: 0.8783 (tmm) cc_final: 0.8479 (tmm) REVERT: A 1213 MET cc_start: 0.8652 (ttt) cc_final: 0.8338 (tmm) REVERT: A 1519 LEU cc_start: 0.9427 (tp) cc_final: 0.9160 (tp) REVERT: A 1694 MET cc_start: 0.8518 (tpp) cc_final: 0.8254 (tpp) REVERT: A 1783 MET cc_start: 0.8117 (mtt) cc_final: 0.7610 (mtp) REVERT: A 1840 TYR cc_start: 0.8936 (t80) cc_final: 0.8016 (t80) REVERT: A 1945 GLU cc_start: 0.9565 (mt-10) cc_final: 0.9351 (mt-10) REVERT: A 2005 PHE cc_start: 0.9132 (t80) cc_final: 0.8311 (t80) REVERT: C 391 MET cc_start: 0.8146 (ptm) cc_final: 0.7613 (ptm) REVERT: C 485 LEU cc_start: 0.9066 (tp) cc_final: 0.8758 (tt) REVERT: C 494 LYS cc_start: 0.9190 (mttt) cc_final: 0.8578 (tptt) REVERT: C 652 MET cc_start: 0.8038 (tpp) cc_final: 0.7686 (tpp) REVERT: C 834 MET cc_start: 0.6264 (ppp) cc_final: 0.6001 (tmm) REVERT: C 968 MET cc_start: 0.8848 (mmp) cc_final: 0.8642 (mmm) REVERT: H 147 SER cc_start: 0.8460 (t) cc_final: 0.8159 (m) REVERT: H 204 ASP cc_start: 0.6020 (t0) cc_final: 0.5670 (m-30) REVERT: J 399 GLU cc_start: 0.8916 (tt0) cc_final: 0.8665 (tt0) REVERT: N 107 ASP cc_start: 0.8993 (m-30) cc_final: 0.8414 (t70) REVERT: P 164 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8017 (tp30) REVERT: S 163 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8254 (tm-30) REVERT: o 444 CYS cc_start: 0.6463 (t) cc_final: 0.6250 (t) REVERT: b 5 GLN cc_start: 0.8973 (mt0) cc_final: 0.8311 (pp30) REVERT: b 41 MET cc_start: 0.9514 (tpp) cc_final: 0.9171 (tpp) REVERT: b 43 LEU cc_start: 0.9626 (mt) cc_final: 0.9155 (mt) REVERT: d 76 ASP cc_start: 0.8748 (m-30) cc_final: 0.8502 (p0) REVERT: h 1 MET cc_start: 0.5068 (mtp) cc_final: 0.4668 (mmt) REVERT: j 31 MET cc_start: 0.8517 (mpp) cc_final: 0.8147 (mpp) REVERT: l 104 ASP cc_start: 0.2955 (p0) cc_final: 0.2309 (t0) REVERT: m 31 MET cc_start: 0.2124 (mtt) cc_final: 0.1471 (mpp) REVERT: m 61 PHE cc_start: 0.0570 (t80) cc_final: 0.0106 (t80) REVERT: p 42 LYS cc_start: 0.7186 (mttt) cc_final: 0.6859 (ttpp) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.6878 time to fit residues: 523.6447 Evaluate side-chains 350 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 6.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 589 optimal weight: 40.0000 chunk 948 optimal weight: 9.9990 chunk 579 optimal weight: 4.9990 chunk 450 optimal weight: 7.9990 chunk 659 optimal weight: 10.0000 chunk 995 optimal weight: 20.0000 chunk 916 optimal weight: 50.0000 chunk 792 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 612 optimal weight: 8.9990 chunk 485 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 HIS H 437 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 HIS ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 233 GLN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN o 354 GLN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 HIS g 66 ASN h 30 GLN ** j 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 8 HIS ** l 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 79543 Z= 0.409 Angle : 0.772 19.610 110386 Z= 0.397 Chirality : 0.045 0.377 13542 Planarity : 0.005 0.066 12622 Dihedral : 17.549 177.769 17101 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.97 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.02 % 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: 9411 helix: 1.42 (0.08), residues: 4187 sheet: -1.13 (0.14), residues: 1328 loop : -1.67 (0.10), residues: 3896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP C 933 HIS 0.013 0.002 HIS A 636 PHE 0.033 0.003 PHE S 250 TYR 0.043 0.003 TYR S 156 ARG 0.011 0.001 ARG y 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 6.577 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: A 224 MET cc_start: 0.9383 (mtp) cc_final: 0.9176 (mtp) REVERT: A 578 MET cc_start: 0.8650 (mtp) cc_final: 0.8241 (mtp) REVERT: A 763 MET cc_start: 0.9142 (tmm) cc_final: 0.8797 (tmm) REVERT: A 914 LEU cc_start: 0.9155 (mp) cc_final: 0.8855 (tp) REVERT: A 1213 MET cc_start: 0.8654 (ttt) cc_final: 0.8406 (tpp) REVERT: A 1379 MET cc_start: 0.8115 (mmp) cc_final: 0.7520 (mmm) REVERT: A 1519 LEU cc_start: 0.9448 (tp) cc_final: 0.9236 (tp) REVERT: A 1694 MET cc_start: 0.8725 (tpp) cc_final: 0.8316 (tpp) REVERT: A 1840 TYR cc_start: 0.9032 (t80) cc_final: 0.8288 (t80) REVERT: A 2005 PHE cc_start: 0.9144 (t80) cc_final: 0.8547 (t80) REVERT: C 391 MET cc_start: 0.8073 (ptm) cc_final: 0.7446 (ptm) REVERT: C 485 LEU cc_start: 0.9156 (tp) cc_final: 0.8820 (tt) REVERT: H 204 ASP cc_start: 0.5967 (t0) cc_final: 0.5639 (m-30) REVERT: L 86 TYR cc_start: 0.7559 (m-80) cc_final: 0.7329 (m-80) REVERT: N 107 ASP cc_start: 0.9197 (m-30) cc_final: 0.8655 (t70) REVERT: P 164 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8182 (tp30) REVERT: a 184 MET cc_start: 0.8795 (ttp) cc_final: 0.8542 (ttp) REVERT: o 163 GLU cc_start: 0.7930 (pt0) cc_final: 0.7410 (pm20) REVERT: o 444 CYS cc_start: 0.6549 (t) cc_final: 0.6346 (t) REVERT: b 5 GLN cc_start: 0.9018 (mt0) cc_final: 0.8352 (pp30) REVERT: b 41 MET cc_start: 0.9522 (tpp) cc_final: 0.9164 (tpp) REVERT: b 43 LEU cc_start: 0.9642 (mt) cc_final: 0.9091 (mt) REVERT: d 76 ASP cc_start: 0.8892 (m-30) cc_final: 0.8538 (p0) REVERT: j 31 MET cc_start: 0.8678 (mpp) cc_final: 0.8288 (mpp) REVERT: m 31 MET cc_start: 0.1372 (mtt) cc_final: 0.0871 (mpp) REVERT: m 38 MET cc_start: 0.0927 (ttt) cc_final: 0.0681 (tpp) REVERT: p 42 LYS cc_start: 0.7055 (mttt) cc_final: 0.6764 (ttpp) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.6744 time to fit residues: 504.7695 Evaluate side-chains 332 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 6.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 629 optimal weight: 4.9990 chunk 844 optimal weight: 50.0000 chunk 242 optimal weight: 0.7980 chunk 730 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 793 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 chunk 815 optimal weight: 30.0000 chunk 100 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 HIS ** J 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 HIS ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.079820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.062290 restraints weight = 673237.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.060904 restraints weight = 526357.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.061233 restraints weight = 425785.442| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 79543 Z= 0.236 Angle : 0.647 18.977 110386 Z= 0.330 Chirality : 0.042 0.381 13542 Planarity : 0.004 0.062 12622 Dihedral : 17.391 177.712 17101 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.01 % 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: 0.02 (0.09), residues: 9411 helix: 1.75 (0.08), residues: 4195 sheet: -1.10 (0.14), residues: 1334 loop : -1.55 (0.10), residues: 3882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 933 HIS 0.008 0.001 HIS J 382 PHE 0.033 0.002 PHE e 18 TYR 0.044 0.002 TYR S 105 ARG 0.025 0.001 ARG k 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14209.31 seconds wall clock time: 249 minutes 10.27 seconds (14950.27 seconds total)