Starting phenix.real_space_refine on Fri Mar 1 05:20:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phj_17667/03_2024/8phj_17667_updated.pdb" } resolution = 3.67 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4643 5.49 5 Mg 241 5.21 5 S 178 5.16 5 C 77500 2.51 5 N 28326 2.21 5 O 41628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152518 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "5" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 907 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "6" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 124} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "7" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p': 5, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 13, 'rna3p': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "8" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1642 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p': 5, 'rna3p_pur': 30, 'rna3p_pyr': 26} Link IDs: {'rna2p': 15, 'rna3p': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "9" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 32276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1503, 32276 Classifications: {'RNA': 1503} Modifications used: {'rna2p': 1, 'rna2p_pur': 119, 'rna2p_pyr': 80, 'rna3p': 10, 'rna3p_pur': 737, 'rna3p_pyr': 556} Link IDs: {'rna2p': 200, 'rna3p': 1302} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1185 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 146} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "W" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 402 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'TRANS': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2984 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 365} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "Y" Number of atoms: 2912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2912 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 357} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "a" Number of atoms: 61456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2862, 61456 Classifications: {'RNA': 2862} Modifications used: {'rna2p': 7, 'rna2p_pur': 274, 'rna2p_pyr': 143, 'rna3p': 16, 'rna3p_pur': 1369, 'rna3p_pyr': 1052} Link IDs: {'rna2p': 423, 'rna3p': 2438} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1301 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 165} 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: "h" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1079 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} 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: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "l" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 1 Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 491 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "y" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "Z" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Unusual residues: {' MG': 79} Classifications: {'undetermined': 79} Link IDs: {None: 78} Chain: "a" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 156 Unusual residues: {' MG': 156} Classifications: {'undetermined': 156} Link IDs: {None: 155} Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1383 SG CYS 3 11 180.421 105.496 131.340 1.00 31.15 S ATOM 1408 SG CYS 3 14 179.582 107.147 134.680 1.00 27.15 S ATOM 1511 SG CYS 3 27 181.474 109.075 131.957 1.00 30.93 S ATOM 1730 SG CYS 4 16 110.897 16.742 122.797 1.00 64.73 S ATOM 1742 SG CYS 4 18 113.287 13.847 121.980 1.00 64.59 S ATOM 1884 SG CYS 4 37 114.378 16.561 124.297 1.00 63.40 S ATOM 1905 SG CYS 4 40 113.891 17.375 120.611 1.00 64.70 S Time building chain proxies: 58.02, per 1000 atoms: 0.38 Number of scatterers: 152518 At special positions: 0 Unit cell: (243.04, 240.8, 276.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 178 16.00 P 4643 15.00 Mg 241 11.99 O 41628 8.00 N 28326 7.00 C 77500 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 56.56 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " Number of angles added : 9 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12432 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 221 helices and 80 sheets defined 41.9% alpha, 18.6% beta 1459 base pairs and 2677 stacking pairs defined. Time for finding SS restraints: 77.26 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 removed outlier: 3.714A pdb=" N SER 1 15 " --> pdb=" O LYS 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 17 through 24 removed outlier: 4.313A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 38 removed outlier: 3.591A pdb=" N VAL 1 30 " --> pdb=" O ASN 1 26 " (cutoff:3.500A) Processing helix chain '2' and resid 7 through 14 removed outlier: 3.718A pdb=" N LYS 2 12 " --> pdb=" O ARG 2 8 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 4.499A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 removed outlier: 3.556A pdb=" N LEU 2 44 " --> pdb=" O ARG 2 40 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG 2 45 " --> pdb=" O LYS 2 41 " (cutoff:3.500A) Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 52 through 63 removed outlier: 4.653A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 64 removed outlier: 3.940A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) Processing helix chain '5' and resid 4 through 22 Processing helix chain '5' and resid 34 through 49 Processing helix chain '5' and resid 56 through 65 removed outlier: 3.784A pdb=" N GLU 5 65 " --> pdb=" O ARG 5 61 " (cutoff:3.500A) Processing helix chain '5' and resid 69 through 74 removed outlier: 4.134A pdb=" N ASP 5 74 " --> pdb=" O GLU 5 70 " (cutoff:3.500A) Processing helix chain '5' and resid 90 through 103 removed outlier: 6.331A pdb=" N ARG 5 94 " --> pdb=" O GLY 5 90 " (cutoff:3.500A) Processing helix chain '5' and resid 123 through 129 Processing helix chain '6' and resid 24 through 32 removed outlier: 3.588A pdb=" N LEU 6 28 " --> pdb=" O VAL 6 24 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY 6 29 " --> pdb=" O GLY 6 25 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN 6 30 " --> pdb=" O PRO 6 26 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN 6 31 " --> pdb=" O ALA 6 27 " (cutoff:3.500A) Processing helix chain '6' and resid 34 through 47 removed outlier: 3.771A pdb=" N LYS 6 45 " --> pdb=" O ALA 6 41 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 85 Processing helix chain '6' and resid 102 through 117 removed outlier: 4.188A pdb=" N ALA 6 115 " --> pdb=" O GLN 6 111 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP 6 116 " --> pdb=" O THR 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 137 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 32 removed outlier: 4.339A pdb=" N LYS B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Proline residue: B 29 - end of helix removed outlier: 5.882A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 32' Processing helix chain 'B' and resid 42 through 64 removed outlier: 3.660A pdb=" N THR B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Proline residue: B 48 - end of helix removed outlier: 3.909A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.154A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.535A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 5.934A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.936A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.140A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 removed outlier: 3.503A pdb=" N ALA C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.543A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.875A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.248A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.692A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 4.006A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.594A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 4.103A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.749A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.918A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 4.016A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 removed outlier: 4.133A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.516A pdb=" N MET E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 15 through 33 Proline residue: F 19 - end of helix removed outlier: 3.617A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 removed outlier: 4.131A pdb=" N GLY G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.814A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 149 Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 40 removed outlier: 4.858A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 removed outlier: 3.663A pdb=" N GLU I 92 " --> pdb=" O MET I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.535A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.093A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 4.114A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 76 removed outlier: 5.370A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.690A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.892A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.993A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 4.092A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.507A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.774A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.584A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.431A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 74 removed outlier: 3.863A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 removed outlier: 3.534A pdb=" N GLN O 80 " --> pdb=" O ALA O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 Processing helix chain 'R' and resid 11 through 17 Processing helix chain 'R' and resid 25 through 34 removed outlier: 3.969A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.638A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 removed outlier: 3.535A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.675A pdb=" N THR T 80 " --> pdb=" O LYS T 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.738A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 4.794A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 76 Processing helix chain 'W' and resid 79 through 90 removed outlier: 3.709A pdb=" N ALA W 90 " --> pdb=" O LEU W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 114 removed outlier: 3.853A pdb=" N LEU W 106 " --> pdb=" O ASP W 102 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA W 109 " --> pdb=" O ALA W 105 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA W 113 " --> pdb=" O ALA W 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY W 114 " --> pdb=" O LEU W 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 15 removed outlier: 4.297A pdb=" N LYS X 14 " --> pdb=" O THR X 10 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LYS X 15 " --> pdb=" O ALA X 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 10 through 15' Processing helix chain 'X' and resid 24 through 32 removed outlier: 4.065A pdb=" N GLY X 32 " --> pdb=" O VAL X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 46 removed outlier: 3.546A pdb=" N ALA X 37 " --> pdb=" O GLY X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 Processing helix chain 'X' and resid 61 through 71 removed outlier: 3.543A pdb=" N HIS X 65 " --> pdb=" O SER X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 104 Proline residue: X 104 - end of helix Processing helix chain 'X' and resid 120 through 144 removed outlier: 5.270A pdb=" N VAL X 129 " --> pdb=" O ARG X 125 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU X 130 " --> pdb=" O THR X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 171 removed outlier: 3.931A pdb=" N VAL X 160 " --> pdb=" O PHE X 156 " (cutoff:3.500A) Proline residue: X 161 - end of helix Processing helix chain 'X' and resid 195 through 203 removed outlier: 3.551A pdb=" N LEU X 199 " --> pdb=" O ALA X 195 " (cutoff:3.500A) Proline residue: X 201 - end of helix Processing helix chain 'X' and resid 204 through 212 Processing helix chain 'X' and resid 216 through 225 Proline residue: X 225 - end of helix Processing helix chain 'X' and resid 226 through 238 removed outlier: 3.534A pdb=" N ARG X 230 " --> pdb=" O SER X 226 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER X 235 " --> pdb=" O GLU X 231 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU X 236 " --> pdb=" O ILE X 232 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE X 237 " --> pdb=" O LEU X 233 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU X 238 " --> pdb=" O ASP X 234 " (cutoff:3.500A) Processing helix chain 'X' and resid 248 through 259 Processing helix chain 'X' and resid 269 through 281 removed outlier: 4.531A pdb=" N ALA X 281 " --> pdb=" O LEU X 277 " (cutoff:3.500A) Processing helix chain 'X' and resid 285 through 298 Proline residue: X 298 - end of helix Processing helix chain 'X' and resid 299 through 305 removed outlier: 3.528A pdb=" N LYS X 305 " --> pdb=" O LEU X 301 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 356 removed outlier: 3.657A pdb=" N ASP X 347 " --> pdb=" O ALA X 343 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP X 348 " --> pdb=" O ASP X 344 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 367 removed outlier: 4.163A pdb=" N ARG X 361 " --> pdb=" O ASP X 357 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG X 366 " --> pdb=" O VAL X 362 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ARG X 367 " --> pdb=" O VAL X 363 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 32 removed outlier: 3.601A pdb=" N GLY Y 32 " --> pdb=" O VAL Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 46 removed outlier: 3.700A pdb=" N LYS Y 39 " --> pdb=" O GLU Y 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL Y 40 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR Y 44 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE Y 45 " --> pdb=" O ILE Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 58 Processing helix chain 'Y' and resid 61 through 71 Processing helix chain 'Y' and resid 85 through 104 removed outlier: 3.541A pdb=" N CYS Y 91 " --> pdb=" O ASP Y 87 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG Y 97 " --> pdb=" O TRP Y 93 " (cutoff:3.500A) Proline residue: Y 104 - end of helix Processing helix chain 'Y' and resid 120 through 144 removed outlier: 3.737A pdb=" N PHE Y 124 " --> pdb=" O ASP Y 120 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU Y 130 " --> pdb=" O THR Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 171 removed outlier: 4.448A pdb=" N VAL Y 160 " --> pdb=" O PHE Y 156 " (cutoff:3.500A) Proline residue: Y 161 - end of helix removed outlier: 3.966A pdb=" N ILE Y 166 " --> pdb=" O TYR Y 162 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 204 Proline residue: Y 201 - end of helix Proline residue: Y 204 - end of helix Processing helix chain 'Y' and resid 205 through 212 removed outlier: 3.734A pdb=" N ILE Y 209 " --> pdb=" O LEU Y 205 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 224 Processing helix chain 'Y' and resid 230 through 238 removed outlier: 4.698A pdb=" N ASP Y 234 " --> pdb=" O ARG Y 230 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER Y 235 " --> pdb=" O GLU Y 231 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU Y 236 " --> pdb=" O ILE Y 232 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE Y 237 " --> pdb=" O LEU Y 233 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLU Y 238 " --> pdb=" O ASP Y 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 230 through 238' Processing helix chain 'Y' and resid 248 through 260 removed outlier: 3.507A pdb=" N LEU Y 253 " --> pdb=" O PRO Y 249 " (cutoff:3.500A) Processing helix chain 'Y' and resid 269 through 283 removed outlier: 3.540A pdb=" N LEU Y 277 " --> pdb=" O LEU Y 273 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS Y 278 " --> pdb=" O ASP Y 274 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA Y 281 " --> pdb=" O LEU Y 277 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR Y 282 " --> pdb=" O LYS Y 278 " (cutoff:3.500A) Processing helix chain 'Y' and resid 285 through 298 removed outlier: 3.677A pdb=" N ASP Y 289 " --> pdb=" O THR Y 285 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) Proline residue: Y 298 - end of helix Processing helix chain 'Y' and resid 299 through 305 removed outlier: 3.817A pdb=" N LYS Y 305 " --> pdb=" O LEU Y 301 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 356 removed outlier: 4.379A pdb=" N LYS Y 355 " --> pdb=" O THR Y 351 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR Y 356 " --> pdb=" O GLN Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 367 removed outlier: 5.384A pdb=" N ARG Y 361 " --> pdb=" O ASP Y 357 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL Y 362 " --> pdb=" O ALA Y 358 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU Y 365 " --> pdb=" O ARG Y 361 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG Y 366 " --> pdb=" O VAL Y 362 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ARG Y 367 " --> pdb=" O VAL Y 363 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 4.890A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.693A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 4.028A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG c 212 " --> pdb=" O ALA c 208 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.926A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 3.671A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 260 through 268' Processing helix chain 'c' and resid 197 through 202 removed outlier: 3.992A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.859A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.403A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.664A pdb=" N ALA e 39 " --> pdb=" O TYR e 35 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.733A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.603A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.588A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 4.154A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.544A pdb=" N TRP f 97 " --> pdb=" O GLY f 93 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.682A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.684A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.477A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 3.695A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.605A pdb=" N GLN h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 29 through 34' Processing helix chain 'h' and resid 40 through 51 removed outlier: 4.558A pdb=" N ILE h 44 " --> pdb=" O THR h 40 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU h 45 " --> pdb=" O LYS h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 52 through 76 removed outlier: 4.356A pdb=" N ALA h 56 " --> pdb=" O ALA h 52 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS h 57 " --> pdb=" O GLU h 53 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 107 Processing helix chain 'h' and resid 111 through 116 removed outlier: 3.828A pdb=" N VAL h 115 " --> pdb=" O ALA h 111 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG h 116 " --> pdb=" O LYS h 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 111 through 116' Processing helix chain 'i' and resid 24 through 38 removed outlier: 4.253A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.369A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 3.571A pdb=" N ARG i 120 " --> pdb=" O ARG i 116 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'j' and resid 104 through 109 removed outlier: 3.502A pdb=" N LEU j 107 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER j 109 " --> pdb=" O GLU j 106 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.667A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.097A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.621A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 3.711A pdb=" N ALA l 122 " --> pdb=" O LYS l 118 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 58 removed outlier: 3.591A pdb=" N ARG m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.302A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.626A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 3.692A pdb=" N LEU m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.669A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.176A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 4.099A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.796A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.539A pdb=" N ILE p 17 " --> pdb=" O ARG p 13 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN p 20 " --> pdb=" O LYS p 16 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.709A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.710A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.995A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG p 58 " --> pdb=" O LYS p 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN p 72 " --> pdb=" O ALA p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 removed outlier: 3.505A pdb=" N ALA p 116 " --> pdb=" O LYS p 112 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.761A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 removed outlier: 3.695A pdb=" N TYR r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.740A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL r 50 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 3.710A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.977A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 removed outlier: 3.641A pdb=" N ALA u 23 " --> pdb=" O ARG u 19 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.633A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.089A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 9 removed outlier: 3.736A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) Processing helix chain 'x' and resid 10 through 35 removed outlier: 3.882A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 61 removed outlier: 4.596A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN x 45 " --> pdb=" O HIS x 41 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA x 51 " --> pdb=" O ARG x 47 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 3.558A pdb=" N ARG z 17 " --> pdb=" O ARG z 13 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 19 through 24 removed outlier: 6.464A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 22 through 25 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 6.636A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '4' and resid 20 through 25 removed outlier: 4.516A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '5' and resid 51 through 54 removed outlier: 6.735A pdb=" N VAL 5 27 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '6' and resid 8 through 12 removed outlier: 4.448A pdb=" N SER 6 66 " --> pdb=" O TYR 6 62 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.930A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.501A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 53 through 59 removed outlier: 3.555A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.787A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.957A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.730A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 84 through 88 removed outlier: 4.081A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 15, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.601A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.892A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 72 through 78 removed outlier: 6.698A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR G 85 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.618A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.634A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 5 through 11 removed outlier: 3.508A pdb=" N LYS I 68 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.624A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 23, first strand: chain 'K' and resid 30 through 35 Processing sheet with id= 24, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.273A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 36 through 41 removed outlier: 3.605A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.718A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.794A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'Q' and resid 56 through 59 removed outlier: 7.192A pdb=" N GLY Q 56 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA Q 82 " --> pdb=" O GLY Q 56 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 30 through 33 removed outlier: 4.600A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'W' and resid 91 through 94 removed outlier: 3.865A pdb=" N ALA W 92 " --> pdb=" O LEU W 58 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL W 56 " --> pdb=" O LEU W 94 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS W 59 " --> pdb=" O GLU W 116 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU W 116 " --> pdb=" O LYS W 59 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'X' and resid 107 through 112 removed outlier: 3.815A pdb=" N LEU X 107 " --> pdb=" O ASP X 76 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU X 5 " --> pdb=" O VAL X 149 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN X 151 " --> pdb=" O LEU X 5 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR X 7 " --> pdb=" O ASN X 151 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'X' and resid 174 through 177 removed outlier: 5.155A pdb=" N ALA X 174 " --> pdb=" O LEU X 187 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'X' and resid 264 through 268 removed outlier: 6.788A pdb=" N LEU X 327 " --> pdb=" O TRP X 338 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Y' and resid 106 through 111 removed outlier: 3.786A pdb=" N LEU Y 107 " --> pdb=" O ASP Y 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN Y 151 " --> pdb=" O LEU Y 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE Y 177 " --> pdb=" O PRO Y 152 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA Y 174 " --> pdb=" O LEU Y 187 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Y' and resid 264 through 268 removed outlier: 6.641A pdb=" N LEU Y 327 " --> pdb=" O TRP Y 338 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.434A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'c' and resid 33 through 36 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.549A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.069A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN c 163 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.578A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'd' and resid 3 through 7 removed outlier: 7.153A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.720A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.839A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.679A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.009A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.798A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'f' and resid 65 through 69 removed outlier: 6.059A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS f 33 " --> pdb=" O THR f 157 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR f 158 " --> pdb=" O GLY f 126 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY f 126 " --> pdb=" O THR f 158 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.215A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 41 through 45 Processing sheet with id= 51, first strand: chain 'g' and resid 94 through 99 removed outlier: 7.068A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 121 through 125 removed outlier: 5.827A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 17 through 21 removed outlier: 4.696A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 77 through 82 Processing sheet with id= 55, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.950A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.567A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.279A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.698A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.764A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.681A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.808A pdb=" N ALA m 108 " --> pdb=" O PHE m 102 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE m 102 " --> pdb=" O ALA m 108 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'n' and resid 49 through 52 removed outlier: 3.675A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL n 28 " --> pdb=" O ASP n 93 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.396A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.821A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.642A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.469A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 69, first strand: chain 'q' and resid 65 through 68 removed outlier: 3.534A pdb=" N ALA q 65 " --> pdb=" O ASP q 95 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.217A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'r' and resid 2 through 8 removed outlier: 4.923A pdb=" N THR r 100 " --> pdb=" O GLY r 79 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY r 79 " --> pdb=" O THR r 100 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'r' and resid 81 through 88 removed outlier: 4.445A pdb=" N ARG r 92 " --> pdb=" O ARG r 88 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 's' and resid 28 through 33 removed outlier: 6.074A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 't' and resid 82 through 86 removed outlier: 6.931A pdb=" N ARG t 82 " --> pdb=" O LYS t 97 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG t 94 " --> pdb=" O ILE t 103 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU t 101 " --> pdb=" O PHE t 96 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.883A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 77, first strand: chain 'w' and resid 12 through 19 removed outlier: 3.546A pdb=" N GLY w 15 " --> pdb=" O ARG w 27 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR w 25 " --> pdb=" O ASN w 17 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'w' and resid 34 through 41 Processing sheet with id= 79, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.424A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'z' and resid 28 through 31 removed outlier: 6.495A pdb=" N SER z 29 " --> pdb=" O LYS z 37 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS z 37 " --> pdb=" O SER z 29 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP z 31 " --> pdb=" O GLY z 35 " (cutoff:3.500A) 2333 hydrogen bonds defined for protein. 6927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3624 hydrogen bonds 5684 hydrogen bond angles 0 basepair planarities 1459 basepair parallelities 2677 stacking parallelities Total time for adding SS restraints: 249.92 Time building geometry restraints manager: 61.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 21957 1.33 - 1.45: 66622 1.45 - 1.57: 66812 1.57 - 1.69: 9275 1.69 - 1.81: 308 Bond restraints: 164974 Sorted by residual: bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.446 0.356 2.00e-02 2.50e+03 3.16e+02 bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.447 0.355 2.00e-02 2.50e+03 3.16e+02 bond pdb=" C4 5MU 7 55 " pdb=" C5 5MU 7 55 " ideal model delta sigma weight residual 1.802 1.449 0.353 2.00e-02 2.50e+03 3.12e+02 bond pdb=" C4 5MU 8 55 " pdb=" C5 5MU 8 55 " ideal model delta sigma weight residual 1.802 1.450 0.352 2.00e-02 2.50e+03 3.11e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.379 0.256 2.00e-02 2.50e+03 1.64e+02 ... (remaining 164969 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.66: 28559 106.66 - 114.28: 104371 114.28 - 121.90: 75835 121.90 - 129.52: 33952 129.52 - 137.14: 3042 Bond angle restraints: 245759 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 128.26 -33.30 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C1' G7M a2069 " pdb=" N9 G7M a2069 " pdb=" C8 G7M a2069 " ideal model delta sigma weight residual 94.96 127.06 -32.10 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 128.33 -22.01 3.00e+00 1.11e-01 5.38e+01 angle pdb=" C2' 2MG A1516 " pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " ideal model delta sigma weight residual 112.00 102.13 9.87 1.50e+00 4.44e-01 4.33e+01 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 142.80 124.42 18.38 3.00e+00 1.11e-01 3.75e+01 ... (remaining 245754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 94237 35.98 - 71.96: 9743 71.96 - 107.94: 1216 107.94 - 143.92: 23 143.92 - 179.90: 10 Dihedral angle restraints: 105229 sinusoidal: 85976 harmonic: 19253 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 52.60 147.40 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 59.66 140.34 1 1.50e+01 4.44e-03 7.55e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 63.55 136.45 1 1.50e+01 4.44e-03 7.36e+01 ... (remaining 105226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 30128 0.083 - 0.166: 1020 0.166 - 0.249: 31 0.249 - 0.332: 2 0.332 - 0.415: 2 Chirality restraints: 31183 Sorted by residual: chirality pdb=" C2' 3TD a1915 " pdb=" C3' 3TD a1915 " pdb=" O2' 3TD a1915 " pdb=" C1' 3TD a1915 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 31180 not shown) Planarity restraints: 13901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 7 55 " 0.081 2.00e-02 2.50e+03 6.40e-01 9.21e+03 pdb=" C4' 5MU 7 55 " 0.442 2.00e-02 2.50e+03 pdb=" O4' 5MU 7 55 " 0.680 2.00e-02 2.50e+03 pdb=" C3' 5MU 7 55 " -0.602 2.00e-02 2.50e+03 pdb=" O3' 5MU 7 55 " -0.711 2.00e-02 2.50e+03 pdb=" C2' 5MU 7 55 " -0.152 2.00e-02 2.50e+03 pdb=" O2' 5MU 7 55 " 1.055 2.00e-02 2.50e+03 pdb=" C1' 5MU 7 55 " 0.193 2.00e-02 2.50e+03 pdb=" N1 5MU 7 55 " -0.988 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 8 55 " 0.079 2.00e-02 2.50e+03 6.35e-01 9.07e+03 pdb=" C4' 5MU 8 55 " 0.444 2.00e-02 2.50e+03 pdb=" O4' 5MU 8 55 " 0.668 2.00e-02 2.50e+03 pdb=" C3' 5MU 8 55 " -0.599 2.00e-02 2.50e+03 pdb=" O3' 5MU 8 55 " -0.707 2.00e-02 2.50e+03 pdb=" C2' 5MU 8 55 " -0.153 2.00e-02 2.50e+03 pdb=" O2' 5MU 8 55 " 1.050 2.00e-02 2.50e+03 pdb=" C1' 5MU 8 55 " 0.197 2.00e-02 2.50e+03 pdb=" N1 5MU 8 55 " -0.978 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " 0.088 2.00e-02 2.50e+03 6.32e-01 8.97e+03 pdb=" C4' 2MG A1207 " 0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " 0.661 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " -0.609 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " -0.703 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " -0.157 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " 1.046 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " 0.199 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " -0.964 2.00e-02 2.50e+03 ... (remaining 13898 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 161 2.26 - 2.92: 57854 2.92 - 3.58: 219043 3.58 - 4.24: 471674 4.24 - 4.90: 631014 Nonbonded interactions: 1379746 Sorted by model distance: nonbonded pdb=" P A Z 1 " pdb=" O3' A Z 4 " model vdw 1.602 3.400 nonbonded pdb=" OP2 A A 621 " pdb="MG MG A1662 " model vdw 1.847 2.170 nonbonded pdb=" O6 G a 570 " pdb="MG MG a6076 " model vdw 1.866 2.170 nonbonded pdb=" OP1 U a 827 " pdb="MG MG a6025 " model vdw 1.907 2.170 nonbonded pdb=" OP1 U a2022 " pdb="MG MG a6071 " model vdw 1.933 2.170 ... (remaining 1379741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '7' selection = (chain '8' and resid 2 through 77) } ncs_group { reference = (chain 'X' and (resid 2 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 192 or (resid 193 and (name N or na \ me CA or name C or name O or name CB )) or resid 194 through 221 or (resid 222 t \ hrough 224 and (name N or name CA or name C or name O or name CB )) or (resid 23 \ 0 through 232 and (name N or name CA or name C or name O or name CB )) or resid \ 233 through 344 or (resid 345 and (name N or name CA or name C or name O or name \ CB )) or resid 346 through 354 or (resid 355 and (name N or name CA or name C o \ r name O or name CB )) or resid 356 through 364 or (resid 365 and (name N or nam \ e CA or name C or name O or name CB )) or resid 366 through 367 or (resid 368 an \ d (name N or name CA or name C or name O or name CB )) or resid 369 through 380 \ or (resid 381 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'Y' and (resid 2 through 218 or (resid 219 and (name N or name CA or name \ C or name O or name CB )) or resid 220 or (resid 221 through 232 and (name N or \ name CA or name C or name O or name CB )) or resid 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB )) or resid 235 through 238 or (resi \ d 239 and (name N or name CA or name C or name O or name CB )) or resid 240 thro \ ugh 241 or (resid 242 and (name N or name CA or name C or name O or name CB )) o \ r resid 243 through 255 or (resid 256 and (name N or name CA or name C or name O \ or name CB )) or resid 257 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 through 310 or (resid 311 and (name \ N or name CA or name C or name O or name CB )) or resid 312 through 347 or (resi \ d 348 and (name N or name CA or name C or name O or name CB )) or resid 349 thro \ ugh 381)) } 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 5.370 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: 0.110 Extract box with map and model: 19.630 Check model and map are aligned: 1.690 Set scattering table: 1.010 Process input model: 567.990 Find NCS groups from input model: 3.280 Set up NCS constraints: 0.380 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 602.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.007 0.356 164974 Z= 0.410 Angle : 0.564 33.305 245759 Z= 0.279 Chirality : 0.034 0.415 31183 Planarity : 0.021 0.640 13901 Dihedral : 21.876 179.901 92797 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 2.16 % Allowed : 5.78 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: -0.44 (0.10), residues: 6620 helix: -0.03 (0.10), residues: 2403 sheet: 0.17 (0.15), residues: 1258 loop : -0.58 (0.11), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 78 HIS 0.005 0.001 HIS c 200 PHE 0.018 0.001 PHE X 45 TYR 0.015 0.002 TYR X 162 ARG 0.006 0.001 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1718 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1600 time to evaluate : 7.022 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: 1 1 MET cc_start: 0.7717 (mtp) cc_final: 0.7496 (mtp) REVERT: 5 38 MET cc_start: 0.8088 (mmp) cc_final: 0.7873 (mmm) REVERT: 5 57 ASN cc_start: 0.7581 (m-40) cc_final: 0.7369 (m110) REVERT: 6 113 LYS cc_start: 0.6612 (mtpp) cc_final: 0.6289 (tptp) REVERT: B 27 MET cc_start: 0.8658 (mmm) cc_final: 0.8296 (mmm) REVERT: B 129 LEU cc_start: 0.7723 (mp) cc_final: 0.7514 (mt) REVERT: B 130 THR cc_start: 0.8529 (p) cc_final: 0.7905 (p) REVERT: B 140 GLU cc_start: 0.7312 (tt0) cc_final: 0.7099 (tt0) REVERT: C 38 LYS cc_start: 0.8560 (mttt) cc_final: 0.8303 (mtmm) REVERT: C 42 TYR cc_start: 0.8908 (t80) cc_final: 0.8611 (t80) REVERT: C 91 VAL cc_start: 0.9384 (p) cc_final: 0.9080 (t) REVERT: C 132 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7380 (ttm-80) REVERT: D 18 ASP cc_start: 0.8487 (t0) cc_final: 0.7916 (t0) REVERT: D 141 ASP cc_start: 0.7464 (m-30) cc_final: 0.7235 (m-30) REVERT: D 195 ILE cc_start: 0.8899 (mp) cc_final: 0.8606 (mt) REVERT: E 14 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8414 (mtpp) REVERT: E 96 MET cc_start: 0.8587 (mtm) cc_final: 0.8344 (mtm) REVERT: E 128 TYR cc_start: 0.8415 (m-80) cc_final: 0.8191 (m-80) REVERT: E 130 SER cc_start: 0.8736 (t) cc_final: 0.8194 (p) REVERT: F 1 MET cc_start: 0.7539 (tpp) cc_final: 0.6705 (mmm) REVERT: F 36 ILE cc_start: 0.9440 (mp) cc_final: 0.9199 (mm) REVERT: F 102 MET cc_start: 0.8818 (mmm) cc_final: 0.8388 (mmm) REVERT: G 37 SER cc_start: 0.8900 (t) cc_final: 0.8694 (t) REVERT: G 63 GLU cc_start: 0.7224 (tm-30) cc_final: 0.7009 (tp30) REVERT: H 38 ASN cc_start: 0.8706 (m-40) cc_final: 0.8416 (m-40) REVERT: H 79 SER cc_start: 0.8712 (t) cc_final: 0.8032 (p) REVERT: I 52 LEU cc_start: 0.9248 (mt) cc_final: 0.9044 (mp) REVERT: I 64 TYR cc_start: 0.8397 (t80) cc_final: 0.7977 (t80) REVERT: J 16 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.7976 (mtm-85) REVERT: J 48 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8187 (mtt180) REVERT: K 53 ARG cc_start: 0.8595 (mmm160) cc_final: 0.8207 (mmm160) REVERT: L 44 LYS cc_start: 0.8637 (mttt) cc_final: 0.8254 (mmtt) REVERT: L 73 ASN cc_start: 0.8533 (p0) cc_final: 0.8185 (p0) REVERT: M 66 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8436 (mm-30) REVERT: M 78 LYS cc_start: 0.8851 (tptm) cc_final: 0.8647 (tptp) REVERT: N 6 MET cc_start: 0.9177 (mmm) cc_final: 0.8878 (mmm) REVERT: N 10 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6993 (mm-30) REVERT: N 12 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8497 (tttt) REVERT: O 64 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.8102 (tpm170) REVERT: O 89 ARG cc_start: 0.7024 (ptp90) cc_final: 0.6656 (ptm-80) REVERT: P 24 SER cc_start: 0.8938 (p) cc_final: 0.8685 (p) REVERT: Q 53 CYS cc_start: 0.7859 (m) cc_final: 0.7594 (m) REVERT: R 48 ARG cc_start: 0.7388 (mpt180) cc_final: 0.6986 (mpt180) REVERT: T 39 ILE cc_start: 0.9116 (mm) cc_final: 0.8861 (mt) REVERT: T 48 GLN cc_start: 0.8704 (mm110) cc_final: 0.8410 (mm-40) REVERT: U 10 GLU cc_start: 0.7381 (tt0) cc_final: 0.6950 (tt0) REVERT: X 117 GLN cc_start: 0.8084 (pp30) cc_final: 0.7652 (pp30) REVERT: X 321 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6857 (m-70) REVERT: Y 73 ASN cc_start: 0.8237 (p0) cc_final: 0.7866 (p0) REVERT: Y 255 TRP cc_start: 0.8332 (t-100) cc_final: 0.7823 (t-100) REVERT: Y 274 ASP cc_start: 0.8014 (m-30) cc_final: 0.7779 (m-30) REVERT: c 20 VAL cc_start: 0.8531 (t) cc_final: 0.8317 (m) REVERT: c 97 LYS cc_start: 0.8233 (tppt) cc_final: 0.8016 (mmtt) REVERT: c 108 LYS cc_start: 0.8223 (tttt) cc_final: 0.7923 (tttp) REVERT: c 111 LYS cc_start: 0.8533 (pttp) cc_final: 0.8122 (ptpp) REVERT: c 114 ASP cc_start: 0.8054 (m-30) cc_final: 0.7749 (m-30) REVERT: c 225 MET cc_start: 0.7362 (mtt) cc_final: 0.7125 (mtt) REVERT: d 4 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8233 (mp) REVERT: d 108 ASP cc_start: 0.8103 (m-30) cc_final: 0.7832 (m-30) REVERT: d 128 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7336 (mmt-90) REVERT: d 199 SER cc_start: 0.9004 (m) cc_final: 0.8505 (p) REVERT: e 21 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7520 (ptp-110) REVERT: e 119 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.9006 (mt) REVERT: e 152 GLU cc_start: 0.7204 (pm20) cc_final: 0.6981 (pt0) REVERT: f 51 ASP cc_start: 0.7737 (m-30) cc_final: 0.7445 (m-30) REVERT: f 148 ARG cc_start: 0.7521 (mtp-110) cc_final: 0.7036 (mtp85) REVERT: f 175 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: g 3 ARG cc_start: 0.7665 (mtt-85) cc_final: 0.7335 (mtt180) REVERT: g 25 THR cc_start: 0.8538 (m) cc_final: 0.8300 (p) REVERT: g 42 GLU cc_start: 0.7731 (tp30) cc_final: 0.7105 (tp30) REVERT: g 137 ASP cc_start: 0.8339 (t0) cc_final: 0.7733 (t0) REVERT: h 109 GLU cc_start: 0.5566 (mm-30) cc_final: 0.5214 (tp30) REVERT: i 69 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7769 (ttm-80) REVERT: j 93 GLN cc_start: 0.8661 (mm110) cc_final: 0.8411 (mm-40) REVERT: j 98 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7574 (mtp85) REVERT: l 1 MET cc_start: 0.7968 (mtm) cc_final: 0.7699 (mtm) REVERT: l 47 GLU cc_start: 0.7956 (tp30) cc_final: 0.7506 (tp30) REVERT: l 70 ASP cc_start: 0.8894 (p0) cc_final: 0.8573 (p0) REVERT: l 127 LYS cc_start: 0.8224 (mttt) cc_final: 0.7921 (mtpp) REVERT: n 45 SER cc_start: 0.8342 (p) cc_final: 0.7975 (m) REVERT: n 116 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8122 (tp40) REVERT: o 6 LYS cc_start: 0.8354 (mtpp) cc_final: 0.8134 (mtpt) REVERT: o 10 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8040 (mt0) REVERT: o 38 LYS cc_start: 0.7778 (ttpp) cc_final: 0.7517 (ttpt) REVERT: o 68 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6412 (tp30) REVERT: p 52 GLN cc_start: 0.8742 (mt0) cc_final: 0.8526 (mt0) REVERT: r 11 ARG cc_start: 0.8468 (tpt90) cc_final: 0.7931 (tpt90) REVERT: r 28 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7667 (mtpp) REVERT: s 27 SER cc_start: 0.8566 (m) cc_final: 0.8348 (p) REVERT: s 76 ARG cc_start: 0.8361 (ptm-80) cc_final: 0.8108 (ptm160) REVERT: s 91 GLN cc_start: 0.8528 (mp10) cc_final: 0.8170 (mm110) REVERT: u 58 SER cc_start: 0.8617 (m) cc_final: 0.8235 (p) REVERT: v 39 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7266 (mtp180) REVERT: v 83 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7418 (mt-10) REVERT: x 49 ASP cc_start: 0.7753 (m-30) cc_final: 0.7533 (m-30) REVERT: x 55 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8648 (t) REVERT: x 58 ASN cc_start: 0.8952 (t0) cc_final: 0.8662 (t0) REVERT: y 19 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7933 (ttmt) REVERT: y 21 LYS cc_start: 0.8997 (mttt) cc_final: 0.8453 (mttp) REVERT: y 49 ASN cc_start: 0.8660 (t0) cc_final: 0.8362 (t0) outliers start: 118 outliers final: 53 residues processed: 1681 average time/residue: 1.4492 time to fit residues: 4144.0821 Evaluate side-chains 1319 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1261 time to evaluate : 6.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain q residue 37 GLU Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain x residue 55 THR Chi-restraints excluded: chain y residue 8 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 938 optimal weight: 10.0000 chunk 842 optimal weight: 0.7980 chunk 467 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 568 optimal weight: 10.0000 chunk 450 optimal weight: 10.0000 chunk 871 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 529 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 1009 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 136 GLN D 140 ASN E 78 ASN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN G 86 GLN I 5 GLN J 64 GLN J 99 GLN K 38 GLN P 63 GLN Q 51 ASN R 31 ASN T 13 GLN T 52 ASN X 89 GLN X 122 HIS ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 211 ASN Y 321 HIS g 22 GLN i 76 HIS n 116 GLN o 12 GLN p 71 GLN p 81 ASN q 6 GLN q 18 GLN q 86 GLN u 49 ASN x 15 ASN x 27 ASN z 6 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 164974 Z= 0.226 Angle : 0.621 16.555 245759 Z= 0.338 Chirality : 0.037 0.401 31183 Planarity : 0.006 0.135 13901 Dihedral : 22.652 179.867 79848 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.56 % Allowed : 10.46 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.32 (0.10), residues: 6620 helix: 1.18 (0.11), residues: 2439 sheet: 0.17 (0.15), residues: 1248 loop : -0.52 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS X 122 PHE 0.023 0.001 PHE Y 17 TYR 0.025 0.002 TYR B 213 ARG 0.006 0.000 ARG X 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1447 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1307 time to evaluate : 7.044 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: 5 38 MET cc_start: 0.7977 (mmp) cc_final: 0.7761 (mmm) REVERT: 5 57 ASN cc_start: 0.7632 (m-40) cc_final: 0.7417 (m-40) REVERT: B 27 MET cc_start: 0.8626 (mmm) cc_final: 0.8284 (mmm) REVERT: C 41 GLN cc_start: 0.8159 (tt0) cc_final: 0.7872 (tt0) REVERT: C 42 TYR cc_start: 0.8942 (t80) cc_final: 0.8611 (t80) REVERT: C 91 VAL cc_start: 0.9432 (p) cc_final: 0.9225 (t) REVERT: C 136 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6937 (ttm-80) REVERT: D 18 ASP cc_start: 0.8200 (t0) cc_final: 0.7993 (t0) REVERT: D 141 ASP cc_start: 0.7558 (m-30) cc_final: 0.7215 (m-30) REVERT: D 195 ILE cc_start: 0.8947 (mp) cc_final: 0.8666 (mt) REVERT: E 14 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8462 (mtpp) REVERT: E 23 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8198 (tttp) REVERT: E 69 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.7051 (mtp85) REVERT: F 1 MET cc_start: 0.7375 (tpp) cc_final: 0.6906 (mmm) REVERT: F 36 ILE cc_start: 0.9420 (mp) cc_final: 0.9216 (mm) REVERT: F 102 MET cc_start: 0.8803 (mmm) cc_final: 0.8400 (mmm) REVERT: G 63 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6930 (tp30) REVERT: G 136 LYS cc_start: 0.7969 (ttpp) cc_final: 0.7277 (ttmm) REVERT: H 79 SER cc_start: 0.8633 (t) cc_final: 0.8026 (p) REVERT: I 52 LEU cc_start: 0.9207 (mt) cc_final: 0.8976 (mp) REVERT: I 64 TYR cc_start: 0.8303 (t80) cc_final: 0.7838 (t80) REVERT: J 48 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8101 (mtt180) REVERT: K 53 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8124 (mmm160) REVERT: L 44 LYS cc_start: 0.8644 (mttt) cc_final: 0.8247 (mmtt) REVERT: L 73 ASN cc_start: 0.8514 (p0) cc_final: 0.8222 (p0) REVERT: N 6 MET cc_start: 0.8979 (mmm) cc_final: 0.8674 (mmm) REVERT: O 64 ARG cc_start: 0.8562 (tpp-160) cc_final: 0.8341 (tpp-160) REVERT: O 73 LYS cc_start: 0.8493 (tppt) cc_final: 0.8242 (tptp) REVERT: O 89 ARG cc_start: 0.7071 (ptp90) cc_final: 0.6715 (ptm-80) REVERT: Q 5 ILE cc_start: 0.8607 (tp) cc_final: 0.8338 (pt) REVERT: Q 53 CYS cc_start: 0.7661 (m) cc_final: 0.7260 (m) REVERT: R 70 TYR cc_start: 0.9105 (m-80) cc_final: 0.8596 (m-80) REVERT: S 38 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8494 (m) REVERT: T 39 ILE cc_start: 0.9155 (mm) cc_final: 0.8888 (mt) REVERT: T 48 GLN cc_start: 0.8537 (mm110) cc_final: 0.8300 (mm-40) REVERT: U 10 GLU cc_start: 0.7312 (tt0) cc_final: 0.7003 (tt0) REVERT: U 36 GLU cc_start: 0.7525 (tt0) cc_final: 0.7296 (tt0) REVERT: X 117 GLN cc_start: 0.7966 (pp30) cc_final: 0.7639 (pp30) REVERT: X 143 ASN cc_start: 0.6924 (p0) cc_final: 0.6255 (p0) REVERT: c 108 LYS cc_start: 0.8135 (tttt) cc_final: 0.7916 (tttp) REVERT: c 225 MET cc_start: 0.7435 (mtt) cc_final: 0.7184 (mtt) REVERT: d 4 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8353 (mp) REVERT: d 74 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7510 (mp0) REVERT: d 128 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7405 (mmt-90) REVERT: d 199 SER cc_start: 0.9001 (m) cc_final: 0.8518 (p) REVERT: e 152 GLU cc_start: 0.7133 (pm20) cc_final: 0.6925 (pt0) REVERT: f 51 ASP cc_start: 0.7713 (m-30) cc_final: 0.7360 (m-30) REVERT: f 134 GLU cc_start: 0.7098 (tt0) cc_final: 0.6759 (pt0) REVERT: f 148 ARG cc_start: 0.7453 (mtp-110) cc_final: 0.7039 (mtp85) REVERT: f 175 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: g 3 ARG cc_start: 0.7683 (mtt-85) cc_final: 0.7474 (mtt180) REVERT: g 42 GLU cc_start: 0.7725 (tp30) cc_final: 0.7391 (tp30) REVERT: g 55 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7237 (tpp80) REVERT: g 130 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: g 137 ASP cc_start: 0.8024 (t0) cc_final: 0.7360 (t0) REVERT: h 4 ILE cc_start: 0.7272 (mm) cc_final: 0.7031 (mt) REVERT: j 28 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8315 (t) REVERT: j 98 ARG cc_start: 0.7754 (mtp180) cc_final: 0.7524 (mtp85) REVERT: l 1 MET cc_start: 0.7973 (mtm) cc_final: 0.7717 (mtm) REVERT: l 47 GLU cc_start: 0.7795 (tp30) cc_final: 0.7433 (tp30) REVERT: l 70 ASP cc_start: 0.8921 (p0) cc_final: 0.8611 (p0) REVERT: l 127 LYS cc_start: 0.8162 (mttt) cc_final: 0.7820 (mtpp) REVERT: m 13 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8175 (p0) REVERT: m 43 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8269 (mm-30) REVERT: m 51 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8609 (mt) REVERT: o 38 LYS cc_start: 0.7822 (ttpp) cc_final: 0.7580 (ttpt) REVERT: o 44 GLU cc_start: 0.7787 (tt0) cc_final: 0.7237 (tt0) REVERT: o 68 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6370 (tp30) REVERT: p 52 GLN cc_start: 0.8660 (mt0) cc_final: 0.8238 (mt0) REVERT: r 11 ARG cc_start: 0.8472 (tpt90) cc_final: 0.8231 (mmm160) REVERT: r 28 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7689 (mtpp) REVERT: s 25 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6928 (mm-30) REVERT: s 26 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7295 (ttpt) REVERT: s 27 SER cc_start: 0.8618 (m) cc_final: 0.8396 (p) REVERT: s 76 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.8098 (ptm160) REVERT: u 58 SER cc_start: 0.8461 (m) cc_final: 0.8212 (p) REVERT: u 76 ASP cc_start: 0.7667 (t70) cc_final: 0.7438 (t70) REVERT: v 39 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7349 (mtp180) REVERT: v 83 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7495 (mt-10) REVERT: y 49 ASN cc_start: 0.8607 (t0) cc_final: 0.8373 (t0) outliers start: 140 outliers final: 97 residues processed: 1386 average time/residue: 1.3559 time to fit residues: 3210.3657 Evaluate side-chains 1334 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1230 time to evaluate : 6.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain X residue 8 CYS Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 13 ASN Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain p residue 71 GLN Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 561 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 840 optimal weight: 9.9990 chunk 687 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 1011 optimal weight: 4.9990 chunk 1092 optimal weight: 0.9980 chunk 900 optimal weight: 9.9990 chunk 1003 optimal weight: 3.9990 chunk 344 optimal weight: 7.9990 chunk 811 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 28 ASN ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN I 5 GLN K 38 GLN R 31 ASN T 13 GLN T 48 GLN X 101 GLN X 131 ASN ** Y 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 136 GLN f 63 GLN m 13 ASN n 100 HIS q 18 GLN q 86 GLN u 49 ASN x 27 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 164974 Z= 0.388 Angle : 0.671 14.887 245759 Z= 0.361 Chirality : 0.041 0.406 31183 Planarity : 0.007 0.144 13901 Dihedral : 22.570 179.868 79825 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.64 % Allowed : 12.13 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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 (0.10), residues: 6620 helix: 1.32 (0.11), residues: 2443 sheet: 0.10 (0.14), residues: 1272 loop : -0.59 (0.11), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 201 HIS 0.006 0.001 HIS c 200 PHE 0.023 0.002 PHE X 45 TYR 0.026 0.002 TYR B 213 ARG 0.011 0.001 ARG X 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1244 time to evaluate : 6.999 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: B 27 MET cc_start: 0.8713 (mmm) cc_final: 0.8351 (mmm) REVERT: B 59 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7296 (ptmm) REVERT: C 41 GLN cc_start: 0.8213 (tt0) cc_final: 0.7911 (tt0) REVERT: C 42 TYR cc_start: 0.8968 (t80) cc_final: 0.8616 (t80) REVERT: C 91 VAL cc_start: 0.9414 (p) cc_final: 0.9202 (t) REVERT: D 141 ASP cc_start: 0.7549 (m-30) cc_final: 0.7102 (m-30) REVERT: D 195 ILE cc_start: 0.8943 (mp) cc_final: 0.8659 (mt) REVERT: E 14 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8451 (mtpp) REVERT: E 69 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.7132 (mtp85) REVERT: E 130 SER cc_start: 0.8550 (p) cc_final: 0.8303 (p) REVERT: F 1 MET cc_start: 0.7539 (tpp) cc_final: 0.6545 (mmm) REVERT: F 36 ILE cc_start: 0.9469 (mp) cc_final: 0.9210 (mm) REVERT: F 102 MET cc_start: 0.8857 (mmt) cc_final: 0.8524 (mmm) REVERT: G 63 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7022 (tp30) REVERT: G 136 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7613 (ttmm) REVERT: H 79 SER cc_start: 0.8687 (t) cc_final: 0.8087 (p) REVERT: I 52 LEU cc_start: 0.9232 (mt) cc_final: 0.8993 (mp) REVERT: I 57 MET cc_start: 0.7677 (ttm) cc_final: 0.7407 (ttm) REVERT: I 64 TYR cc_start: 0.8326 (t80) cc_final: 0.7911 (t80) REVERT: J 48 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8076 (mtt180) REVERT: K 53 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8110 (mmm160) REVERT: L 44 LYS cc_start: 0.8664 (mttt) cc_final: 0.8325 (mmtt) REVERT: L 73 ASN cc_start: 0.8597 (p0) cc_final: 0.8300 (p0) REVERT: N 6 MET cc_start: 0.8942 (mmm) cc_final: 0.8636 (mmm) REVERT: O 73 LYS cc_start: 0.8562 (tppt) cc_final: 0.8300 (tptp) REVERT: O 89 ARG cc_start: 0.7231 (ptp90) cc_final: 0.6811 (ptm-80) REVERT: Q 38 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8809 (pt) REVERT: R 70 TYR cc_start: 0.9107 (m-80) cc_final: 0.8551 (m-80) REVERT: S 38 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8556 (m) REVERT: T 48 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8248 (mm-40) REVERT: U 10 GLU cc_start: 0.7276 (tt0) cc_final: 0.6908 (tt0) REVERT: X 321 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6103 (t-90) REVERT: X 353 ASN cc_start: 0.8776 (t0) cc_final: 0.8350 (t0) REVERT: c 108 LYS cc_start: 0.8168 (tttt) cc_final: 0.7963 (tttp) REVERT: c 111 LYS cc_start: 0.8762 (ptpp) cc_final: 0.8527 (ptpp) REVERT: c 225 MET cc_start: 0.7383 (mtt) cc_final: 0.7099 (mtt) REVERT: d 74 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7529 (mp0) REVERT: d 128 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7438 (mmt-90) REVERT: d 157 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7542 (ttpt) REVERT: d 199 SER cc_start: 0.9098 (m) cc_final: 0.8575 (p) REVERT: e 152 GLU cc_start: 0.7214 (pm20) cc_final: 0.6880 (pt0) REVERT: f 51 ASP cc_start: 0.7625 (m-30) cc_final: 0.7309 (m-30) REVERT: f 135 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: f 148 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.7062 (mtp85) REVERT: f 175 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: g 3 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7546 (mtt180) REVERT: g 137 ASP cc_start: 0.7972 (t0) cc_final: 0.7386 (t0) REVERT: j 98 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7530 (mtp85) REVERT: l 1 MET cc_start: 0.7947 (mtm) cc_final: 0.7627 (mtm) REVERT: l 47 GLU cc_start: 0.7802 (tp30) cc_final: 0.7439 (tp30) REVERT: l 70 ASP cc_start: 0.8909 (p0) cc_final: 0.8598 (p0) REVERT: l 127 LYS cc_start: 0.8222 (mttt) cc_final: 0.7881 (mtpp) REVERT: m 43 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8311 (mm-30) REVERT: o 38 LYS cc_start: 0.7990 (ttpp) cc_final: 0.7763 (ttpt) REVERT: o 44 GLU cc_start: 0.7889 (tt0) cc_final: 0.7363 (tt0) REVERT: o 68 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6343 (tp30) REVERT: q 37 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6641 (mm-30) REVERT: r 11 ARG cc_start: 0.8461 (tpt90) cc_final: 0.8187 (mmm160) REVERT: r 28 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7667 (mtpp) REVERT: s 26 LYS cc_start: 0.7833 (mmtm) cc_final: 0.7334 (ttpt) REVERT: s 76 ARG cc_start: 0.8357 (ptm-80) cc_final: 0.8050 (ptm160) REVERT: u 12 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: u 58 SER cc_start: 0.8599 (m) cc_final: 0.8330 (p) REVERT: u 76 ASP cc_start: 0.7679 (t70) cc_final: 0.7428 (t70) REVERT: v 39 ARG cc_start: 0.7710 (mtp180) cc_final: 0.7420 (mtp180) REVERT: v 83 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7564 (mt-10) REVERT: y 49 ASN cc_start: 0.8615 (t0) cc_final: 0.8400 (t0) outliers start: 199 outliers final: 153 residues processed: 1363 average time/residue: 1.3583 time to fit residues: 3178.3309 Evaluate side-chains 1374 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1213 time to evaluate : 6.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain X residue 8 CYS Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain X residue 356 THR Chi-restraints excluded: chain X residue 361 ARG Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 61 SER Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 239 ASP Chi-restraints excluded: chain Y residue 258 LEU Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 20 MET Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 42 THR Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 65 ASP Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 999 optimal weight: 10.0000 chunk 760 optimal weight: 8.9990 chunk 525 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 482 optimal weight: 2.9990 chunk 679 optimal weight: 10.0000 chunk 1015 optimal weight: 8.9990 chunk 1074 optimal weight: 0.9990 chunk 530 optimal weight: 10.0000 chunk 962 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN K 38 GLN R 31 ASN T 13 GLN X 131 ASN ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 GLN p 71 GLN q 12 HIS q 86 GLN u 49 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 164974 Z= 0.340 Angle : 0.645 17.177 245759 Z= 0.350 Chirality : 0.039 0.405 31183 Planarity : 0.006 0.138 13901 Dihedral : 22.535 179.786 79823 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.28 % Favored : 96.71 % Rotamer: Outliers : 3.62 % Allowed : 13.14 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.42 (0.10), residues: 6620 helix: 1.42 (0.11), residues: 2451 sheet: 0.10 (0.14), residues: 1257 loop : -0.58 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS c 200 PHE 0.023 0.002 PHE X 45 TYR 0.027 0.002 TYR B 213 ARG 0.007 0.000 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1246 time to evaluate : 7.072 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: 5 96 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6326 (m-10) REVERT: B 27 MET cc_start: 0.8704 (mmm) cc_final: 0.8418 (mmm) REVERT: B 59 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7148 (ptmm) REVERT: C 41 GLN cc_start: 0.8226 (tt0) cc_final: 0.7915 (tt0) REVERT: D 105 MET cc_start: 0.8322 (mmm) cc_final: 0.8044 (mtt) REVERT: D 141 ASP cc_start: 0.7546 (m-30) cc_final: 0.7078 (m-30) REVERT: D 195 ILE cc_start: 0.8943 (mp) cc_final: 0.8684 (mt) REVERT: E 14 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8446 (mtpp) REVERT: E 69 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.7099 (mtp85) REVERT: E 157 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8475 (mtp180) REVERT: F 1 MET cc_start: 0.7587 (tpp) cc_final: 0.6601 (mmm) REVERT: F 36 ILE cc_start: 0.9454 (mp) cc_final: 0.9212 (mm) REVERT: F 102 MET cc_start: 0.8785 (mmt) cc_final: 0.8496 (mmm) REVERT: G 136 LYS cc_start: 0.7750 (ttpp) cc_final: 0.7506 (tttp) REVERT: H 79 SER cc_start: 0.8679 (t) cc_final: 0.8073 (p) REVERT: I 52 LEU cc_start: 0.9236 (mt) cc_final: 0.8988 (mp) REVERT: I 64 TYR cc_start: 0.8331 (t80) cc_final: 0.7894 (t80) REVERT: J 48 ARG cc_start: 0.8405 (mtt180) cc_final: 0.7909 (mtt180) REVERT: J 66 GLU cc_start: 0.7660 (tt0) cc_final: 0.7399 (tt0) REVERT: L 44 LYS cc_start: 0.8665 (mttt) cc_final: 0.8318 (mmtt) REVERT: L 73 ASN cc_start: 0.8632 (p0) cc_final: 0.8306 (p0) REVERT: N 6 MET cc_start: 0.8908 (mmm) cc_final: 0.8615 (mmm) REVERT: O 73 LYS cc_start: 0.8555 (tppt) cc_final: 0.8286 (tptp) REVERT: O 89 ARG cc_start: 0.7218 (ptp90) cc_final: 0.6801 (ptm-80) REVERT: Q 38 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8813 (pt) REVERT: R 21 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8697 (mm) REVERT: R 70 TYR cc_start: 0.9116 (m-80) cc_final: 0.8595 (m-80) REVERT: S 38 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8546 (m) REVERT: T 48 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8247 (mm-40) REVERT: U 10 GLU cc_start: 0.7236 (tt0) cc_final: 0.6859 (tt0) REVERT: X 224 LEU cc_start: 0.8614 (mp) cc_final: 0.8400 (mp) REVERT: X 321 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6115 (t-90) REVERT: X 353 ASN cc_start: 0.8765 (t0) cc_final: 0.8416 (t0) REVERT: c 108 LYS cc_start: 0.8182 (tttt) cc_final: 0.7967 (tttp) REVERT: c 225 MET cc_start: 0.7401 (mtt) cc_final: 0.7096 (mtt) REVERT: d 128 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7475 (mmt-90) REVERT: d 157 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7537 (ttpt) REVERT: d 199 SER cc_start: 0.8961 (m) cc_final: 0.8496 (p) REVERT: e 152 GLU cc_start: 0.7229 (pm20) cc_final: 0.6874 (pt0) REVERT: f 51 ASP cc_start: 0.7749 (m-30) cc_final: 0.7394 (m-30) REVERT: f 135 GLN cc_start: 0.7915 (pt0) cc_final: 0.7330 (pm20) REVERT: f 148 ARG cc_start: 0.7486 (mtp-110) cc_final: 0.7076 (mtp85) REVERT: f 175 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: g 3 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7481 (mtt180) REVERT: g 137 ASP cc_start: 0.7767 (t0) cc_final: 0.7428 (t0) REVERT: j 1 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7712 (mtt) REVERT: j 98 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7524 (mtp85) REVERT: l 1 MET cc_start: 0.7995 (mtm) cc_final: 0.7655 (mtm) REVERT: l 47 GLU cc_start: 0.7856 (tp30) cc_final: 0.7475 (tp30) REVERT: l 70 ASP cc_start: 0.8912 (p0) cc_final: 0.8590 (p0) REVERT: l 127 LYS cc_start: 0.8243 (mttt) cc_final: 0.7878 (mtpp) REVERT: m 43 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8365 (mm-30) REVERT: o 38 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7780 (ttpt) REVERT: o 44 GLU cc_start: 0.7916 (tt0) cc_final: 0.7375 (tt0) REVERT: o 68 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6339 (tp30) REVERT: r 11 ARG cc_start: 0.8429 (tpt90) cc_final: 0.8150 (mmm160) REVERT: r 28 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7647 (mtpp) REVERT: s 26 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7343 (ttpt) REVERT: s 76 ARG cc_start: 0.8356 (ptm-80) cc_final: 0.8055 (ptm160) REVERT: u 12 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7749 (mt0) REVERT: u 58 SER cc_start: 0.8618 (m) cc_final: 0.8355 (p) REVERT: u 68 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8019 (mptt) REVERT: v 30 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8657 (m) REVERT: v 39 ARG cc_start: 0.7724 (mtp180) cc_final: 0.7424 (mtp180) REVERT: x 23 ARG cc_start: 0.8505 (mtm180) cc_final: 0.8106 (mtt90) REVERT: y 49 ASN cc_start: 0.8609 (t0) cc_final: 0.8402 (t0) outliers start: 198 outliers final: 161 residues processed: 1364 average time/residue: 1.3342 time to fit residues: 3129.1944 Evaluate side-chains 1380 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1207 time to evaluate : 6.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 16 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 4 residue 61 ASN Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain X residue 8 CYS Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain X residue 328 VAL Chi-restraints excluded: chain X residue 356 THR Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 61 SER Chi-restraints excluded: chain Y residue 239 ASP Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 258 LEU Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 20 MET Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 42 THR Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain p residue 71 GLN Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 65 ASP Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain y residue 56 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 895 optimal weight: 8.9990 chunk 610 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 800 optimal weight: 20.0000 chunk 443 optimal weight: 20.0000 chunk 917 optimal weight: 4.9990 chunk 742 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 548 optimal weight: 10.0000 chunk 964 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN K 38 GLN R 31 ASN T 13 GLN X 180 GLN Y 147 GLN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 86 GLN u 49 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 164974 Z= 0.343 Angle : 0.648 14.496 245759 Z= 0.351 Chirality : 0.039 0.408 31183 Planarity : 0.007 0.139 13901 Dihedral : 22.517 179.676 79823 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 3.92 % Allowed : 14.16 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.45 (0.10), residues: 6620 helix: 1.48 (0.11), residues: 2444 sheet: 0.09 (0.14), residues: 1267 loop : -0.57 (0.11), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS c 200 PHE 0.023 0.002 PHE X 45 TYR 0.035 0.002 TYR B 213 ARG 0.009 0.000 ARG p 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1237 time to evaluate : 7.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 9 TYR cc_start: 0.8604 (t80) cc_final: 0.8402 (t80) REVERT: 5 96 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6395 (m-10) REVERT: B 27 MET cc_start: 0.8708 (mmm) cc_final: 0.8456 (mmm) REVERT: C 41 GLN cc_start: 0.8221 (tt0) cc_final: 0.7933 (tt0) REVERT: C 42 TYR cc_start: 0.8952 (t80) cc_final: 0.8646 (t80) REVERT: C 121 THR cc_start: 0.9250 (m) cc_final: 0.8980 (m) REVERT: D 141 ASP cc_start: 0.7560 (m-30) cc_final: 0.7096 (m-30) REVERT: D 195 ILE cc_start: 0.8930 (mp) cc_final: 0.8666 (mt) REVERT: E 14 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8460 (mtpp) REVERT: E 157 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8426 (mtp180) REVERT: F 1 MET cc_start: 0.7682 (tpp) cc_final: 0.6726 (mmm) REVERT: F 36 ILE cc_start: 0.9482 (mp) cc_final: 0.9230 (mm) REVERT: F 102 MET cc_start: 0.8759 (mmt) cc_final: 0.8493 (mmm) REVERT: H 79 SER cc_start: 0.8677 (t) cc_final: 0.8075 (p) REVERT: I 52 LEU cc_start: 0.9241 (mt) cc_final: 0.9022 (mp) REVERT: I 64 TYR cc_start: 0.8334 (t80) cc_final: 0.7899 (t80) REVERT: J 48 ARG cc_start: 0.8383 (mtt180) cc_final: 0.7942 (mtt180) REVERT: J 66 GLU cc_start: 0.7687 (tt0) cc_final: 0.7455 (tt0) REVERT: L 44 LYS cc_start: 0.8658 (mttt) cc_final: 0.8306 (mmtt) REVERT: L 73 ASN cc_start: 0.8585 (p0) cc_final: 0.8271 (p0) REVERT: N 6 MET cc_start: 0.8900 (mmm) cc_final: 0.8603 (mmm) REVERT: O 73 LYS cc_start: 0.8555 (tppt) cc_final: 0.8340 (tptp) REVERT: O 89 ARG cc_start: 0.7245 (ptp90) cc_final: 0.6790 (ptm-80) REVERT: Q 38 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8811 (pt) REVERT: R 21 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8719 (mm) REVERT: R 70 TYR cc_start: 0.9105 (m-80) cc_final: 0.8602 (m-80) REVERT: S 38 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8551 (m) REVERT: T 48 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8259 (mm-40) REVERT: U 10 GLU cc_start: 0.7165 (tt0) cc_final: 0.6782 (tt0) REVERT: X 117 GLN cc_start: 0.8070 (pp30) cc_final: 0.7733 (pp30) REVERT: X 321 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6113 (t-90) REVERT: X 353 ASN cc_start: 0.8815 (t0) cc_final: 0.8439 (t0) REVERT: X 375 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: Y 255 TRP cc_start: 0.8190 (t-100) cc_final: 0.7374 (t-100) REVERT: c 108 LYS cc_start: 0.8187 (tttt) cc_final: 0.7970 (tttp) REVERT: c 225 MET cc_start: 0.7377 (mtt) cc_final: 0.7045 (mtt) REVERT: d 128 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7430 (mmt-90) REVERT: d 157 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7541 (ttpt) REVERT: d 199 SER cc_start: 0.8963 (m) cc_final: 0.8499 (p) REVERT: e 152 GLU cc_start: 0.7209 (pm20) cc_final: 0.6831 (pt0) REVERT: f 51 ASP cc_start: 0.7799 (m-30) cc_final: 0.7473 (m-30) REVERT: f 135 GLN cc_start: 0.7640 (pt0) cc_final: 0.7017 (pm20) REVERT: f 148 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.7099 (mtp85) REVERT: g 3 ARG cc_start: 0.7739 (mtt-85) cc_final: 0.7479 (mtt180) REVERT: g 137 ASP cc_start: 0.7761 (t0) cc_final: 0.7490 (t0) REVERT: j 1 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7695 (mtt) REVERT: j 98 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7518 (mtp85) REVERT: l 1 MET cc_start: 0.7926 (mtm) cc_final: 0.7623 (mtm) REVERT: l 47 GLU cc_start: 0.7864 (tp30) cc_final: 0.7512 (tp30) REVERT: l 70 ASP cc_start: 0.8913 (p0) cc_final: 0.8587 (p0) REVERT: l 127 LYS cc_start: 0.8255 (mttt) cc_final: 0.7871 (mtpp) REVERT: o 38 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7776 (ttpt) REVERT: o 44 GLU cc_start: 0.7924 (tt0) cc_final: 0.7365 (tt0) REVERT: o 68 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6308 (tp30) REVERT: r 11 ARG cc_start: 0.8413 (tpt90) cc_final: 0.8129 (mmm160) REVERT: r 28 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7646 (mtpp) REVERT: s 26 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7343 (ttpt) REVERT: s 76 ARG cc_start: 0.8352 (ptm-80) cc_final: 0.8058 (ptm160) REVERT: u 12 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: u 49 ASN cc_start: 0.8418 (m-40) cc_final: 0.8089 (m-40) REVERT: u 58 SER cc_start: 0.8625 (m) cc_final: 0.8351 (p) REVERT: u 68 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8109 (mmmt) REVERT: v 30 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8660 (m) REVERT: v 39 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7418 (mtp180) REVERT: x 23 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8108 (mtt90) outliers start: 214 outliers final: 184 residues processed: 1365 average time/residue: 1.3593 time to fit residues: 3192.7641 Evaluate side-chains 1412 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1217 time to evaluate : 6.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 16 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain X residue 8 CYS Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain X residue 328 VAL Chi-restraints excluded: chain X residue 356 THR Chi-restraints excluded: chain X residue 375 ARG Chi-restraints excluded: chain X residue 376 LEU Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 61 SER Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 239 ASP Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 258 LEU Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 20 MET Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 42 THR Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 73 ILE Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 65 ASP Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 12 SER Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 361 optimal weight: 1.9990 chunk 967 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 631 optimal weight: 40.0000 chunk 265 optimal weight: 4.9990 chunk 1075 optimal weight: 10.0000 chunk 893 optimal weight: 8.9990 chunk 498 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 355 optimal weight: 0.6980 chunk 564 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN K 38 GLN R 31 ASN T 13 GLN X 131 ASN X 180 GLN g 38 ASN h 135 HIS m 18 GLN p 71 GLN x 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 164974 Z= 0.197 Angle : 0.606 14.053 245759 Z= 0.334 Chirality : 0.035 0.515 31183 Planarity : 0.006 0.164 13901 Dihedral : 22.546 179.566 79820 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.52 % Favored : 96.47 % Rotamer: Outliers : 3.64 % Allowed : 14.64 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.56 (0.10), residues: 6620 helix: 1.58 (0.11), residues: 2449 sheet: 0.12 (0.14), residues: 1260 loop : -0.51 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.010 0.001 HIS h 135 PHE 0.023 0.001 PHE X 45 TYR 0.038 0.002 TYR B 213 ARG 0.019 0.000 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1237 time to evaluate : 7.210 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: 5 96 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6375 (m-10) REVERT: B 27 MET cc_start: 0.8700 (mmm) cc_final: 0.8441 (mmm) REVERT: C 41 GLN cc_start: 0.8193 (tt0) cc_final: 0.7912 (tt0) REVERT: C 42 TYR cc_start: 0.8963 (t80) cc_final: 0.8643 (t80) REVERT: C 121 THR cc_start: 0.9231 (m) cc_final: 0.8935 (m) REVERT: D 141 ASP cc_start: 0.7546 (m-30) cc_final: 0.7105 (m-30) REVERT: D 195 ILE cc_start: 0.8892 (mp) cc_final: 0.8638 (mt) REVERT: E 14 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8459 (mtpp) REVERT: E 157 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8433 (mtp180) REVERT: F 1 MET cc_start: 0.7669 (tpp) cc_final: 0.6730 (mmm) REVERT: F 36 ILE cc_start: 0.9484 (mp) cc_final: 0.9232 (mm) REVERT: F 102 MET cc_start: 0.8730 (mmt) cc_final: 0.8493 (mmm) REVERT: H 79 SER cc_start: 0.8649 (t) cc_final: 0.8052 (p) REVERT: I 52 LEU cc_start: 0.9235 (mt) cc_final: 0.9013 (mp) REVERT: I 64 TYR cc_start: 0.8319 (t80) cc_final: 0.7808 (t80) REVERT: J 48 ARG cc_start: 0.8356 (mtt180) cc_final: 0.7910 (mtt180) REVERT: J 66 GLU cc_start: 0.7665 (tt0) cc_final: 0.7450 (tt0) REVERT: K 94 GLU cc_start: 0.7058 (pm20) cc_final: 0.6656 (pp20) REVERT: K 98 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7314 (mtm-85) REVERT: L 44 LYS cc_start: 0.8643 (mttt) cc_final: 0.8305 (mmtt) REVERT: L 73 ASN cc_start: 0.8566 (p0) cc_final: 0.8258 (p0) REVERT: N 6 MET cc_start: 0.8884 (mmm) cc_final: 0.8567 (mmm) REVERT: O 73 LYS cc_start: 0.8556 (tppt) cc_final: 0.8275 (tptp) REVERT: O 89 ARG cc_start: 0.7261 (ptp90) cc_final: 0.6780 (ptm-80) REVERT: Q 38 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8810 (pt) REVERT: R 70 TYR cc_start: 0.9094 (m-80) cc_final: 0.8604 (m-80) REVERT: S 38 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8537 (m) REVERT: T 48 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8264 (mm-40) REVERT: U 10 GLU cc_start: 0.7136 (tt0) cc_final: 0.6763 (tt0) REVERT: X 117 GLN cc_start: 0.8012 (pp30) cc_final: 0.7715 (pp30) REVERT: X 321 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6075 (t-90) REVERT: X 353 ASN cc_start: 0.8770 (t0) cc_final: 0.8388 (t0) REVERT: Y 255 TRP cc_start: 0.8134 (t-100) cc_final: 0.7387 (t-100) REVERT: c 108 LYS cc_start: 0.8176 (tttt) cc_final: 0.7973 (tttp) REVERT: c 225 MET cc_start: 0.7416 (mtt) cc_final: 0.7134 (mtt) REVERT: d 128 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7405 (mmt-90) REVERT: d 157 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7548 (ttpt) REVERT: d 199 SER cc_start: 0.8959 (m) cc_final: 0.8502 (p) REVERT: e 152 GLU cc_start: 0.7213 (pm20) cc_final: 0.6821 (pt0) REVERT: f 51 ASP cc_start: 0.7794 (m-30) cc_final: 0.7464 (m-30) REVERT: f 135 GLN cc_start: 0.7566 (pt0) cc_final: 0.7074 (pm20) REVERT: f 148 ARG cc_start: 0.7526 (mtp-110) cc_final: 0.7055 (mtp85) REVERT: f 175 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: g 3 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7255 (mtt180) REVERT: g 137 ASP cc_start: 0.7730 (t0) cc_final: 0.7463 (t0) REVERT: j 98 ARG cc_start: 0.7758 (mtp180) cc_final: 0.7504 (mtp85) REVERT: k 51 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7500 (mt-10) REVERT: l 1 MET cc_start: 0.7982 (mtm) cc_final: 0.7661 (mtm) REVERT: l 47 GLU cc_start: 0.7833 (tp30) cc_final: 0.7475 (tp30) REVERT: l 70 ASP cc_start: 0.8913 (p0) cc_final: 0.8589 (p0) REVERT: l 127 LYS cc_start: 0.8218 (mttt) cc_final: 0.7819 (mtpp) REVERT: o 38 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7815 (ttpt) REVERT: o 44 GLU cc_start: 0.7913 (tt0) cc_final: 0.7342 (tt0) REVERT: o 68 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6313 (tp30) REVERT: r 11 ARG cc_start: 0.8404 (tpt90) cc_final: 0.8146 (mmm160) REVERT: r 28 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7626 (mtpp) REVERT: s 26 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7348 (ttpt) REVERT: s 76 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.8066 (ptm160) REVERT: u 12 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: u 49 ASN cc_start: 0.8446 (m-40) cc_final: 0.8103 (m-40) REVERT: u 58 SER cc_start: 0.8623 (m) cc_final: 0.8353 (p) REVERT: u 68 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8038 (mmmt) REVERT: v 30 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8659 (m) REVERT: v 39 ARG cc_start: 0.7710 (mtp180) cc_final: 0.7401 (mtp180) outliers start: 199 outliers final: 174 residues processed: 1359 average time/residue: 1.3214 time to fit residues: 3089.9682 Evaluate side-chains 1392 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1209 time to evaluate : 6.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 16 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain X residue 350 LEU Chi-restraints excluded: chain X residue 356 THR Chi-restraints excluded: chain X residue 376 LEU Chi-restraints excluded: chain Y residue 61 SER Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 239 ASP Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 73 ILE Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 71 GLN Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain t residue 70 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 65 ASP Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 12 SER Chi-restraints excluded: chain y residue 41 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 1037 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 613 optimal weight: 40.0000 chunk 785 optimal weight: 8.9990 chunk 608 optimal weight: 8.9990 chunk 905 optimal weight: 0.0670 chunk 600 optimal weight: 8.9990 chunk 1071 optimal weight: 5.9990 chunk 670 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 494 optimal weight: 0.9980 overall best weight: 5.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN R 31 ASN T 13 GLN X 131 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 86 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 164974 Z= 0.344 Angle : 0.647 14.488 245759 Z= 0.350 Chirality : 0.040 0.416 31183 Planarity : 0.007 0.138 13901 Dihedral : 22.499 179.233 79820 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 4.04 % Allowed : 14.95 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.50 (0.10), residues: 6620 helix: 1.53 (0.11), residues: 2449 sheet: 0.11 (0.14), residues: 1264 loop : -0.55 (0.11), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS c 200 PHE 0.024 0.002 PHE X 45 TYR 0.039 0.002 TYR B 213 ARG 0.007 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1227 time to evaluate : 6.991 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: 4 63 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7395 (ttp80) REVERT: 5 96 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6390 (m-10) REVERT: B 27 MET cc_start: 0.8678 (mmm) cc_final: 0.8454 (mmm) REVERT: C 41 GLN cc_start: 0.8223 (tt0) cc_final: 0.7940 (tt0) REVERT: C 42 TYR cc_start: 0.8973 (t80) cc_final: 0.8637 (t80) REVERT: C 121 THR cc_start: 0.9293 (m) cc_final: 0.8999 (m) REVERT: D 141 ASP cc_start: 0.7504 (m-30) cc_final: 0.7037 (m-30) REVERT: D 195 ILE cc_start: 0.8914 (mp) cc_final: 0.8639 (mt) REVERT: E 14 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8456 (mtpp) REVERT: E 157 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8461 (mtp180) REVERT: F 1 MET cc_start: 0.7899 (tpp) cc_final: 0.7033 (mmm) REVERT: F 36 ILE cc_start: 0.9513 (mp) cc_final: 0.9274 (mm) REVERT: F 102 MET cc_start: 0.8730 (mmt) cc_final: 0.8493 (mmm) REVERT: H 79 SER cc_start: 0.8648 (t) cc_final: 0.8045 (p) REVERT: I 52 LEU cc_start: 0.9274 (mt) cc_final: 0.9053 (mp) REVERT: J 48 ARG cc_start: 0.8392 (mtt180) cc_final: 0.7930 (mtt180) REVERT: J 66 GLU cc_start: 0.7649 (tt0) cc_final: 0.7428 (tt0) REVERT: K 98 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7321 (mtm-85) REVERT: L 44 LYS cc_start: 0.8648 (mttt) cc_final: 0.8314 (mmtt) REVERT: L 73 ASN cc_start: 0.8599 (p0) cc_final: 0.8395 (p0) REVERT: O 73 LYS cc_start: 0.8529 (tppt) cc_final: 0.8319 (tptp) REVERT: O 89 ARG cc_start: 0.7262 (ptp90) cc_final: 0.6794 (ptm-80) REVERT: Q 38 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8811 (pt) REVERT: R 70 TYR cc_start: 0.9097 (m-80) cc_final: 0.8589 (m-80) REVERT: S 38 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8553 (m) REVERT: T 48 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8280 (mm-40) REVERT: U 10 GLU cc_start: 0.7136 (tt0) cc_final: 0.6751 (tt0) REVERT: X 117 GLN cc_start: 0.8104 (pp30) cc_final: 0.7788 (pp30) REVERT: X 321 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6102 (t-90) REVERT: X 353 ASN cc_start: 0.8781 (t0) cc_final: 0.8384 (t0) REVERT: Y 255 TRP cc_start: 0.8161 (t-100) cc_final: 0.7348 (t-100) REVERT: Y 296 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7850 (mtm180) REVERT: c 108 LYS cc_start: 0.8187 (tttt) cc_final: 0.7973 (tttp) REVERT: c 225 MET cc_start: 0.7358 (mtt) cc_final: 0.7092 (mtt) REVERT: c 229 ASP cc_start: 0.7782 (m-30) cc_final: 0.7530 (m-30) REVERT: d 128 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7441 (mmt-90) REVERT: d 157 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7551 (ttpt) REVERT: d 199 SER cc_start: 0.8961 (m) cc_final: 0.8501 (p) REVERT: e 140 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7319 (p0) REVERT: e 152 GLU cc_start: 0.7286 (pm20) cc_final: 0.6885 (pt0) REVERT: f 51 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: f 135 GLN cc_start: 0.7764 (pt0) cc_final: 0.7221 (pm20) REVERT: f 148 ARG cc_start: 0.7538 (mtp-110) cc_final: 0.7057 (mtp85) REVERT: f 175 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: g 3 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.7318 (mtt180) REVERT: g 137 ASP cc_start: 0.7712 (t0) cc_final: 0.7451 (t0) REVERT: j 1 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: j 28 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8198 (t) REVERT: j 98 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7528 (mtp85) REVERT: k 126 ARG cc_start: 0.8524 (mtm180) cc_final: 0.8280 (mtm180) REVERT: l 1 MET cc_start: 0.7934 (mtm) cc_final: 0.7644 (mtm) REVERT: l 47 GLU cc_start: 0.7866 (tp30) cc_final: 0.7552 (tp30) REVERT: l 70 ASP cc_start: 0.8871 (p0) cc_final: 0.8543 (p0) REVERT: l 127 LYS cc_start: 0.8199 (mttt) cc_final: 0.7832 (mtpp) REVERT: o 38 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7837 (ttpt) REVERT: o 44 GLU cc_start: 0.7895 (tt0) cc_final: 0.7324 (tt0) REVERT: o 68 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6264 (tp30) REVERT: r 11 ARG cc_start: 0.8407 (tpt90) cc_final: 0.8119 (mmm160) REVERT: r 28 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7644 (mtpp) REVERT: s 1 MET cc_start: 0.6992 (ppp) cc_final: 0.6361 (ttt) REVERT: s 26 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7435 (ttpt) REVERT: s 76 ARG cc_start: 0.8353 (ptm-80) cc_final: 0.8066 (ptm160) REVERT: u 12 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: u 49 ASN cc_start: 0.8435 (m-40) cc_final: 0.8062 (m-40) REVERT: u 58 SER cc_start: 0.8673 (m) cc_final: 0.8410 (p) REVERT: u 68 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8055 (mptt) REVERT: v 30 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8668 (m) REVERT: v 39 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7405 (mtp180) REVERT: x 23 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8131 (mtt90) outliers start: 221 outliers final: 196 residues processed: 1360 average time/residue: 1.3751 time to fit residues: 3238.9257 Evaluate side-chains 1421 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1211 time to evaluate : 7.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 16 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 4 residue 61 ASN Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain X residue 8 CYS Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 237 PHE Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain X residue 356 THR Chi-restraints excluded: chain X residue 375 ARG Chi-restraints excluded: chain X residue 376 LEU Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 61 SER Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 239 ASP Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 296 ARG Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 73 ILE Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 141 LYS Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain t residue 70 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 65 ASP Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 12 SER Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 663 optimal weight: 10.0000 chunk 428 optimal weight: 0.5980 chunk 640 optimal weight: 8.9990 chunk 322 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 681 optimal weight: 8.9990 chunk 730 optimal weight: 7.9990 chunk 529 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 842 optimal weight: 2.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN R 31 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 60 GLN ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 164974 Z= 0.401 Angle : 0.684 14.807 245759 Z= 0.367 Chirality : 0.042 0.414 31183 Planarity : 0.007 0.142 13901 Dihedral : 22.539 178.907 79820 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 4.28 % Allowed : 14.97 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.37 (0.10), residues: 6620 helix: 1.40 (0.11), residues: 2450 sheet: 0.09 (0.14), residues: 1259 loop : -0.62 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 201 HIS 0.006 0.001 HIS c 200 PHE 0.034 0.002 PHE R 13 TYR 0.039 0.002 TYR B 213 ARG 0.011 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1206 time to evaluate : 7.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 39 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8192 (mttp) REVERT: 4 63 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7376 (ttp80) REVERT: 5 96 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6341 (m-10) REVERT: B 27 MET cc_start: 0.8672 (mmm) cc_final: 0.8471 (mmm) REVERT: C 41 GLN cc_start: 0.8240 (tt0) cc_final: 0.7946 (tt0) REVERT: C 42 TYR cc_start: 0.9012 (t80) cc_final: 0.8728 (t80) REVERT: D 141 ASP cc_start: 0.7537 (m-30) cc_final: 0.7064 (m-30) REVERT: D 195 ILE cc_start: 0.8915 (mp) cc_final: 0.8634 (mt) REVERT: E 14 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8302 (mtpp) REVERT: E 157 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8463 (mtp180) REVERT: F 1 MET cc_start: 0.8096 (tpp) cc_final: 0.7353 (mmm) REVERT: F 36 ILE cc_start: 0.9488 (mp) cc_final: 0.9228 (mm) REVERT: H 79 SER cc_start: 0.8702 (t) cc_final: 0.8114 (p) REVERT: I 52 LEU cc_start: 0.9307 (mt) cc_final: 0.9106 (mp) REVERT: K 98 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7467 (mtm-85) REVERT: L 44 LYS cc_start: 0.8600 (mttt) cc_final: 0.8235 (mmtt) REVERT: L 73 ASN cc_start: 0.8578 (p0) cc_final: 0.8374 (p0) REVERT: L 89 ASP cc_start: 0.8582 (p0) cc_final: 0.8238 (p0) REVERT: N 6 MET cc_start: 0.8868 (mmm) cc_final: 0.8602 (mmm) REVERT: O 73 LYS cc_start: 0.8531 (tppt) cc_final: 0.8277 (tptp) REVERT: O 89 ARG cc_start: 0.7273 (ptp90) cc_final: 0.6744 (ptm-80) REVERT: Q 38 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8806 (pt) REVERT: R 70 TYR cc_start: 0.9097 (m-80) cc_final: 0.8563 (m-80) REVERT: S 38 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8568 (m) REVERT: T 48 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8274 (mm-40) REVERT: X 117 GLN cc_start: 0.8216 (pp30) cc_final: 0.7849 (pp30) REVERT: X 321 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6163 (t-90) REVERT: X 353 ASN cc_start: 0.8733 (t0) cc_final: 0.8404 (t0) REVERT: X 375 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7950 (ttm170) REVERT: Y 162 TYR cc_start: 0.8341 (m-80) cc_final: 0.8048 (m-80) REVERT: Y 255 TRP cc_start: 0.8141 (t-100) cc_final: 0.7366 (t-100) REVERT: Y 296 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7959 (mtm180) REVERT: c 108 LYS cc_start: 0.8185 (tttt) cc_final: 0.7963 (tttp) REVERT: c 225 MET cc_start: 0.7376 (mtt) cc_final: 0.7108 (mtt) REVERT: c 229 ASP cc_start: 0.7781 (m-30) cc_final: 0.7533 (m-30) REVERT: d 128 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7432 (mmt-90) REVERT: d 157 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7527 (ttpt) REVERT: d 199 SER cc_start: 0.8964 (m) cc_final: 0.8494 (p) REVERT: e 152 GLU cc_start: 0.7465 (pm20) cc_final: 0.7086 (pt0) REVERT: f 135 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: f 148 ARG cc_start: 0.7533 (mtp-110) cc_final: 0.6981 (mtp85) REVERT: f 175 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: g 3 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7345 (mtt180) REVERT: g 137 ASP cc_start: 0.7660 (t0) cc_final: 0.7381 (t0) REVERT: j 1 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7742 (mtt) REVERT: j 98 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7522 (mtp85) REVERT: j 108 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7282 (mtp85) REVERT: k 126 ARG cc_start: 0.8539 (mtm180) cc_final: 0.8295 (mtm180) REVERT: l 1 MET cc_start: 0.7955 (mtm) cc_final: 0.7640 (mtm) REVERT: l 47 GLU cc_start: 0.7870 (tp30) cc_final: 0.7573 (tp30) REVERT: l 70 ASP cc_start: 0.8875 (p0) cc_final: 0.8536 (p0) REVERT: l 127 LYS cc_start: 0.8145 (mttt) cc_final: 0.7767 (mtpp) REVERT: o 38 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7855 (ttpt) REVERT: o 44 GLU cc_start: 0.7912 (tt0) cc_final: 0.7330 (tt0) REVERT: o 68 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6313 (tp30) REVERT: q 37 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6692 (mm-30) REVERT: r 11 ARG cc_start: 0.8411 (tpt90) cc_final: 0.8119 (mmm160) REVERT: r 28 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7693 (mtpp) REVERT: s 1 MET cc_start: 0.7124 (ppp) cc_final: 0.6589 (ttt) REVERT: s 26 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7481 (ttpt) REVERT: s 76 ARG cc_start: 0.8342 (ptm-80) cc_final: 0.8044 (ptm160) REVERT: u 12 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: u 49 ASN cc_start: 0.8434 (m-40) cc_final: 0.8075 (m-40) REVERT: u 58 SER cc_start: 0.8769 (m) cc_final: 0.8482 (p) REVERT: u 68 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8185 (mmmt) REVERT: v 30 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8681 (m) REVERT: x 23 ARG cc_start: 0.8537 (mtm180) cc_final: 0.8149 (mtt90) outliers start: 234 outliers final: 206 residues processed: 1353 average time/residue: 1.3451 time to fit residues: 3142.7272 Evaluate side-chains 1421 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1202 time to evaluate : 6.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 57 LEU Chi-restraints excluded: chain 3 residue 16 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain X residue 8 CYS Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 138 HIS Chi-restraints excluded: chain X residue 182 SER Chi-restraints excluded: chain X residue 237 PHE Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain X residue 350 LEU Chi-restraints excluded: chain X residue 356 THR Chi-restraints excluded: chain X residue 375 ARG Chi-restraints excluded: chain X residue 376 LEU Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 61 SER Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 239 ASP Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 296 ARG Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 155 GLU Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 147 ASP Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 20 MET Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 42 THR Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 141 LYS Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 71 GLN Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain t residue 70 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 65 ASP Chi-restraints excluded: chain x residue 8 GLU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 12 SER Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 974 optimal weight: 5.9990 chunk 1026 optimal weight: 1.9990 chunk 936 optimal weight: 20.0000 chunk 998 optimal weight: 2.9990 chunk 601 optimal weight: 6.9990 chunk 435 optimal weight: 0.9980 chunk 784 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 902 optimal weight: 9.9990 chunk 944 optimal weight: 0.9980 chunk 995 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN D 152 GLN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN R 31 ASN X 131 ASN X 180 GLN ** X 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 211 ASN g 48 ASN ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 86 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 164974 Z= 0.180 Angle : 0.603 13.879 245759 Z= 0.334 Chirality : 0.036 0.421 31183 Planarity : 0.006 0.187 13901 Dihedral : 22.573 178.647 79818 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 3.68 % Allowed : 15.72 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.53 (0.10), residues: 6620 helix: 1.55 (0.11), residues: 2448 sheet: 0.13 (0.14), residues: 1259 loop : -0.53 (0.11), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.005 0.001 HIS o 77 PHE 0.026 0.001 PHE R 13 TYR 0.046 0.002 TYR I 90 ARG 0.009 0.000 ARG X 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1228 time to evaluate : 6.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 96 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6342 (m-10) REVERT: C 41 GLN cc_start: 0.8180 (tt0) cc_final: 0.7910 (tt0) REVERT: C 42 TYR cc_start: 0.9012 (t80) cc_final: 0.8722 (t80) REVERT: C 121 THR cc_start: 0.9277 (m) cc_final: 0.9033 (m) REVERT: D 141 ASP cc_start: 0.7520 (m-30) cc_final: 0.7108 (m-30) REVERT: D 195 ILE cc_start: 0.8881 (mp) cc_final: 0.8631 (mt) REVERT: E 14 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8447 (mtpp) REVERT: E 157 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8480 (mtp180) REVERT: F 1 MET cc_start: 0.8110 (tpp) cc_final: 0.7207 (mmm) REVERT: F 36 ILE cc_start: 0.9491 (mp) cc_final: 0.9224 (mm) REVERT: H 43 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8018 (mm-30) REVERT: H 79 SER cc_start: 0.8664 (t) cc_final: 0.8075 (p) REVERT: I 52 LEU cc_start: 0.9297 (mt) cc_final: 0.9089 (mp) REVERT: K 98 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7450 (mtm-85) REVERT: L 44 LYS cc_start: 0.8608 (mttt) cc_final: 0.8237 (mmtt) REVERT: N 6 MET cc_start: 0.8829 (mmm) cc_final: 0.8553 (mmm) REVERT: O 73 LYS cc_start: 0.8525 (tppt) cc_final: 0.8301 (tptp) REVERT: O 89 ARG cc_start: 0.7230 (ptp90) cc_final: 0.6727 (ptm-80) REVERT: Q 38 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8804 (pt) REVERT: R 70 TYR cc_start: 0.9080 (m-80) cc_final: 0.8569 (m-80) REVERT: S 38 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8538 (m) REVERT: T 48 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8290 (mm-40) REVERT: X 117 GLN cc_start: 0.8108 (pp30) cc_final: 0.7828 (pp30) REVERT: X 321 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.6110 (t-90) REVERT: X 353 ASN cc_start: 0.8691 (t0) cc_final: 0.8349 (t0) REVERT: Y 255 TRP cc_start: 0.8093 (t-100) cc_final: 0.7336 (t-100) REVERT: Y 296 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7865 (mtm180) REVERT: c 108 LYS cc_start: 0.8186 (tttt) cc_final: 0.7981 (tttp) REVERT: c 225 MET cc_start: 0.7421 (mtt) cc_final: 0.7178 (mtt) REVERT: d 128 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7423 (mmt-90) REVERT: d 157 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7533 (ttpt) REVERT: d 199 SER cc_start: 0.8958 (m) cc_final: 0.8505 (p) REVERT: e 152 GLU cc_start: 0.7436 (pm20) cc_final: 0.7073 (pt0) REVERT: e 191 ASP cc_start: 0.7415 (m-30) cc_final: 0.7146 (m-30) REVERT: f 51 ASP cc_start: 0.7688 (m-30) cc_final: 0.7402 (m-30) REVERT: f 135 GLN cc_start: 0.7665 (pt0) cc_final: 0.7094 (pm20) REVERT: f 148 ARG cc_start: 0.7579 (mtp-110) cc_final: 0.7057 (mtp85) REVERT: f 175 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: g 3 ARG cc_start: 0.7722 (mtt-85) cc_final: 0.7297 (mtt180) REVERT: g 137 ASP cc_start: 0.7660 (t0) cc_final: 0.7412 (t0) REVERT: j 98 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7504 (mtp85) REVERT: j 108 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7218 (mtp85) REVERT: k 126 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8273 (mtm180) REVERT: l 1 MET cc_start: 0.7921 (mtm) cc_final: 0.7617 (mtm) REVERT: l 47 GLU cc_start: 0.7814 (tp30) cc_final: 0.7476 (tp30) REVERT: l 70 ASP cc_start: 0.8876 (p0) cc_final: 0.8540 (p0) REVERT: l 127 LYS cc_start: 0.8203 (mttt) cc_final: 0.7830 (mtpp) REVERT: o 38 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7844 (ttpt) REVERT: o 44 GLU cc_start: 0.7911 (tt0) cc_final: 0.7320 (tt0) REVERT: o 68 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6307 (tp30) REVERT: q 37 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6752 (mm-30) REVERT: r 11 ARG cc_start: 0.8287 (tpt90) cc_final: 0.8026 (mmm160) REVERT: r 28 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7631 (mtpp) REVERT: s 26 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7492 (ttpt) REVERT: s 76 ARG cc_start: 0.8321 (ptm-80) cc_final: 0.8054 (ptm160) REVERT: u 12 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: u 49 ASN cc_start: 0.8434 (m-40) cc_final: 0.8057 (m-40) REVERT: u 58 SER cc_start: 0.8765 (m) cc_final: 0.8461 (p) REVERT: u 68 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8182 (mmmt) REVERT: v 30 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8665 (m) REVERT: v 39 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7351 (mtp180) REVERT: x 23 ARG cc_start: 0.8514 (mtm180) cc_final: 0.8121 (mtt90) outliers start: 201 outliers final: 177 residues processed: 1350 average time/residue: 1.4777 time to fit residues: 3476.1374 Evaluate side-chains 1382 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1195 time to evaluate : 7.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 16 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 138 HIS Chi-restraints excluded: chain X residue 237 PHE Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain X residue 350 LEU Chi-restraints excluded: chain X residue 356 THR Chi-restraints excluded: chain X residue 361 ARG Chi-restraints excluded: chain X residue 376 LEU Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 61 SER Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 239 ASP Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 296 ARG Chi-restraints excluded: chain Y residue 328 VAL Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 155 GLU Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 20 MET Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 73 ILE Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 141 LYS Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 86 THR Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 70 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 65 ASP Chi-restraints excluded: chain x residue 8 GLU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 655 optimal weight: 10.0000 chunk 1056 optimal weight: 2.9990 chunk 644 optimal weight: 10.0000 chunk 501 optimal weight: 1.9990 chunk 734 optimal weight: 20.0000 chunk 1107 optimal weight: 6.9990 chunk 1019 optimal weight: 5.9990 chunk 882 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 681 optimal weight: 10.0000 chunk 540 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN G 86 GLN R 31 ASN X 131 ASN ** X 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN g 48 ASN o 12 GLN ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 164974 Z= 0.267 Angle : 0.615 13.991 245759 Z= 0.337 Chirality : 0.037 0.411 31183 Planarity : 0.006 0.134 13901 Dihedral : 22.493 178.675 79816 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.57 % Rotamer: Outliers : 3.51 % Allowed : 16.14 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.55 (0.10), residues: 6620 helix: 1.57 (0.11), residues: 2451 sheet: 0.12 (0.14), residues: 1263 loop : -0.51 (0.11), residues: 2906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS c 200 PHE 0.026 0.002 PHE R 13 TYR 0.040 0.002 TYR B 213 ARG 0.012 0.000 ARG F 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13240 Ramachandran restraints generated. 6620 Oldfield, 0 Emsley, 6620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1384 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1192 time to evaluate : 6.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 96 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6334 (m-10) REVERT: C 41 GLN cc_start: 0.8212 (tt0) cc_final: 0.7935 (tt0) REVERT: C 42 TYR cc_start: 0.9011 (t80) cc_final: 0.8733 (t80) REVERT: C 121 THR cc_start: 0.9294 (m) cc_final: 0.9040 (m) REVERT: D 141 ASP cc_start: 0.7514 (m-30) cc_final: 0.7045 (m-30) REVERT: D 195 ILE cc_start: 0.8906 (mp) cc_final: 0.8635 (mt) REVERT: E 14 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8457 (mtpp) REVERT: E 157 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8447 (mtp180) REVERT: F 1 MET cc_start: 0.8096 (tpp) cc_final: 0.7280 (mmm) REVERT: F 36 ILE cc_start: 0.9485 (mp) cc_final: 0.9216 (mm) REVERT: H 43 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8000 (mm-30) REVERT: H 79 SER cc_start: 0.8628 (t) cc_final: 0.8029 (p) REVERT: I 52 LEU cc_start: 0.9297 (mt) cc_final: 0.9088 (mp) REVERT: L 44 LYS cc_start: 0.8609 (mttt) cc_final: 0.8248 (mmtt) REVERT: L 89 ASP cc_start: 0.8486 (p0) cc_final: 0.8132 (p0) REVERT: N 6 MET cc_start: 0.8836 (mmm) cc_final: 0.8534 (mmm) REVERT: O 73 LYS cc_start: 0.8523 (tppt) cc_final: 0.8301 (tptp) REVERT: O 89 ARG cc_start: 0.7183 (ptp90) cc_final: 0.6760 (ptm-80) REVERT: Q 38 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8808 (pt) REVERT: R 70 TYR cc_start: 0.9088 (m-80) cc_final: 0.8585 (m-80) REVERT: S 38 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8542 (m) REVERT: T 48 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8295 (mm-40) REVERT: X 117 GLN cc_start: 0.8128 (pp30) cc_final: 0.7785 (pp30) REVERT: X 321 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6100 (t-90) REVERT: X 353 ASN cc_start: 0.8673 (t0) cc_final: 0.8330 (t0) REVERT: Y 255 TRP cc_start: 0.8091 (t-100) cc_final: 0.7306 (t-100) REVERT: Y 296 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7914 (mtm180) REVERT: c 108 LYS cc_start: 0.8195 (tttt) cc_final: 0.7980 (tttp) REVERT: c 225 MET cc_start: 0.7381 (mtt) cc_final: 0.7087 (mtt) REVERT: d 128 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7447 (mmt-90) REVERT: d 157 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7546 (ttpt) REVERT: d 199 SER cc_start: 0.8959 (m) cc_final: 0.8505 (p) REVERT: e 152 GLU cc_start: 0.7471 (pm20) cc_final: 0.7153 (pt0) REVERT: f 51 ASP cc_start: 0.7688 (m-30) cc_final: 0.7412 (m-30) REVERT: f 135 GLN cc_start: 0.7775 (pt0) cc_final: 0.7175 (pm20) REVERT: f 148 ARG cc_start: 0.7582 (mtp-110) cc_final: 0.7050 (mtp85) REVERT: f 175 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: g 3 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7316 (mtt180) REVERT: g 137 ASP cc_start: 0.7673 (t0) cc_final: 0.7434 (t0) REVERT: j 28 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8264 (t) REVERT: j 98 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7509 (mtp85) REVERT: j 108 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7223 (mtp85) REVERT: k 126 ARG cc_start: 0.8525 (mtm180) cc_final: 0.8279 (mtm180) REVERT: l 1 MET cc_start: 0.7929 (mtm) cc_final: 0.7640 (mtm) REVERT: l 47 GLU cc_start: 0.7839 (tp30) cc_final: 0.7530 (tp30) REVERT: l 70 ASP cc_start: 0.8918 (p0) cc_final: 0.8581 (p0) REVERT: l 127 LYS cc_start: 0.8109 (mttt) cc_final: 0.7746 (mtpp) REVERT: o 38 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7853 (ttpt) REVERT: o 44 GLU cc_start: 0.7908 (tt0) cc_final: 0.7316 (tt0) REVERT: o 68 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6283 (tp30) REVERT: r 11 ARG cc_start: 0.8318 (tpt90) cc_final: 0.8049 (mmm160) REVERT: r 28 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7629 (mtpp) REVERT: s 26 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7488 (ttpt) REVERT: s 76 ARG cc_start: 0.8379 (ptm-80) cc_final: 0.8095 (ptm160) REVERT: u 12 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: u 49 ASN cc_start: 0.8417 (m-40) cc_final: 0.8034 (m-40) REVERT: u 58 SER cc_start: 0.8823 (m) cc_final: 0.8509 (p) REVERT: u 68 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8188 (mmmt) REVERT: v 30 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8666 (m) REVERT: v 39 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7401 (mtp180) REVERT: x 23 ARG cc_start: 0.8519 (mtm180) cc_final: 0.8126 (mtt90) outliers start: 192 outliers final: 174 residues processed: 1312 average time/residue: 1.4520 time to fit residues: 3310.9524 Evaluate side-chains 1374 residues out of total 5513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1189 time to evaluate : 7.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 16 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 6 residue 82 LYS Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 138 HIS Chi-restraints excluded: chain X residue 237 PHE Chi-restraints excluded: chain X residue 240 VAL Chi-restraints excluded: chain X residue 294 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 321 HIS Chi-restraints excluded: chain X residue 350 LEU Chi-restraints excluded: chain X residue 356 THR Chi-restraints excluded: chain X residue 376 LEU Chi-restraints excluded: chain Y residue 61 SER Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 239 ASP Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 296 ARG Chi-restraints excluded: chain Y residue 328 VAL Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 374 VAL Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 ASP Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 155 GLU Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain f residue 175 PHE Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 138 VAL Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 20 MET Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 73 ILE Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 141 LYS Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 28 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 86 THR Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 70 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 65 ASP Chi-restraints excluded: chain x residue 8 GLU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 700 optimal weight: 8.9990 chunk 939 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 chunk 813 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 883 optimal weight: 3.9990 chunk 369 optimal weight: 10.0000 chunk 907 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 140 ASN R 31 ASN X 131 ASN ** X 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 48 ASN o 12 GLN ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 86 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.086444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.063818 restraints weight = 264111.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.063779 restraints weight = 561903.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.064802 restraints weight = 264241.401| |-----------------------------------------------------------------------------| r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 164974 Z= 0.491 Angle : 0.729 15.294 245759 Z= 0.385 Chirality : 0.045 0.423 31183 Planarity : 0.007 0.147 13901 Dihedral : 22.536 179.611 79816 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.03 % Rotamer: Outliers : 3.75 % Allowed : 16.17 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.04 % 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: 0.33 (0.10), residues: 6620 helix: 1.37 (0.11), residues: 2451 sheet: 0.08 (0.14), residues: 1248 loop : -0.66 (0.11), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 201 HIS 0.006 0.001 HIS c 200 PHE 0.030 0.002 PHE R 13 TYR 0.038 0.002 TYR B 213 ARG 0.014 0.001 ARG F 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41686.39 seconds wall clock time: 726 minutes 34.89 seconds (43594.89 seconds total)