Starting phenix.real_space_refine (version: dev) on Wed Apr 13 01:44:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k00_22586/04_2022/7k00_22586_updated.pdb" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "i PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 149338 Number of models: 1 Model: "" Number of chains: 117 Chain: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 742, 'rna3p_pyr': 565, 'rna2p_pur': 120, 'rna2p_pyr': 81} Link IDs: {'rna3p': 1316, 'rna2p': 202} Chain breaks: 2 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: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} 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: {'PTRANS': 4, 'TRANS': 92, 'PCIS': 1} 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115, 'PCIS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 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: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} 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: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna3p': 17, 'rna2p': 7, 'rna3p_pur': 1318, 'rna3p_pyr': 1006, 'rna2p_pur': 267, 'rna2p_pyr': 138} Link IDs: {'rna3p': 2341, 'rna2p': 411} Chain breaks: 3 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: {'rna3p_pyr': 49, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6} Link IDs: {'rna3p': 105, 'rna2p': 13} 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: {'PTRANS': 5, 'TRANS': 202, 'PCIS': 1} 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: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} 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: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'undetermined': 1, 'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: {'TRANS': 101, 'PCIS': 1} 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: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} 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: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} 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: "X" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 3, 'rna2p_pur': 3, 'rna3p_pur': 6} Link IDs: {'rna3p': 9, 'rna2p': 2} Chain: "Y" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1579 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 32, 'rna2p_pyr': 3, 'rna3p_pyr': 32} Link IDs: {'rna3p': 63, 'rna2p': 10} Chain breaks: 1 Chain: "Z" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'rna3p_pyr': 33, 'rna2p_pur': 6, 'rna3p_pur': 33, 'rna2p_pyr': 4} Link IDs: {'rna3p': 66, 'rna2p': 9} Chain: "5" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1} Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 155 Unusual residues: {'PAR': 1, ' MG': 93, 'SPD': 2} Classifications: {'undetermined': 96} Link IDs: {None: 95} Chain: "a" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 362 Unusual residues: {' MG': 208, 'SPD': 14, 'SPM': 1} Classifications: {'undetermined': 223} Link IDs: {None: 222} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" 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} 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: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2063, 2063 Classifications: {'water': 2063} Link IDs: {None: 2062} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "M" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "a" Number of atoms: 4028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4028, 4028 Classifications: {'water': 4028} Link IDs: {None: 4027} Chain: "b" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 171 Classifications: {'water': 171} Link IDs: {None: 170} Chain: "c" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "e" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "f" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "h" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "i" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "j" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "k" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "l" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "m" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "n" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "o" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "p" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "q" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "r" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "s" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "t" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "u" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "v" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "w" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "x" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "z" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "0" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "1" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "X" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "Y" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Z" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0STU SG CYS 3 11 155.053 85.413 164.660 1.00 30.89 S ATOM A0SUJ SG CYS 3 14 152.860 83.203 161.820 1.00 29.35 S ATOM A0SXE SG CYS 3 27 151.871 83.858 165.597 1.00 28.99 S ATOM A0T3H SG CYS 4 16 208.656 151.376 92.607 1.00 47.71 S ATOM A0T3T SG CYS 4 18 212.384 150.725 93.703 1.00 48.51 S ATOM A0T7R SG CYS 4 37 209.961 147.879 93.575 1.00 43.10 S ATOM A0T8C SG CYS 4 40 209.551 150.714 96.153 1.00 44.92 S Time building chain proxies: 62.95, per 1000 atoms: 0.42 Number of scatterers: 149338 At special positions: 0 Unit cell: (230.623, 257.672, 269.06, 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 149 16.00 P 4554 15.00 Mg 309 11.99 O 46650 8.00 N 26483 7.00 C 71191 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.37 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral 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 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " Number of angles added : 9 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10260 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 176 helices and 71 sheets defined 39.6% alpha, 19.8% beta 1573 base pairs and 2368 stacking pairs defined. Time for finding SS restraints: 63.38 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.723A pdb=" N ILE B 31 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.788A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.048A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.797A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.405A pdb=" N LEU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 130' Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.808A 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: 3.685A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (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 removed outlier: 3.762A pdb=" N GLU C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.877A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.658A 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 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.477A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.788A 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: 5.247A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.649A 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: 3.526A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.431A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.523A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.089A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.202A 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: 3.974A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.657A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.537A pdb=" N ASN E 146 " --> pdb=" O ASP E 142 " (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: 3.710A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 5.366A pdb=" N ASP F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.314A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 5.771A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.687A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) 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: 4.630A 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 91 Processing helix chain 'I' and resid 92 through 102 removed outlier: 5.098A pdb=" N SER I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.715A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.505A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.013A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.700A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.947A 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: 3.569A pdb=" N LYS K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.822A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA K 102 " --> pdb=" O ARG K 98 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.655A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.564A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.582A 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 44 through 49 removed outlier: 4.046A pdb=" N LEU M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 50 through 64 removed outlier: 3.900A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.114A 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 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.651A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'N' and resid 52 through 57 Proline residue: N 57 - end of helix Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.090A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.793A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 removed outlier: 3.731A pdb=" N GLY O 86 " --> pdb=" O ILE O 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.817A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.777A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY R 17 " --> pdb=" O PHE R 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 11 through 17' Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.063A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.616A 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 removed outlier: 3.520A pdb=" N SER S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY S 26 " --> pdb=" O ALA S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.455A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.134A 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 Processing helix chain 'T' and resid 44 through 65 removed outlier: 3.507A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.766A pdb=" N THR T 80 " --> pdb=" O LYS T 76 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN T 82 " --> pdb=" O ASN T 78 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.949A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 68 removed outlier: 4.643A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 17 removed outlier: 4.750A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL c 17 " --> pdb=" O ARG c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.976A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 Proline residue: c 136 - end of helix Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.763A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.776A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.206A 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: 4.700A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'c' and resid 197 through 202 removed outlier: 4.045A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.617A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.658A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.173A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.148A 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: 3.776A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.423A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (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: 3.598A pdb=" N PHE e 158 " --> pdb=" O ASP e 154 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.679A 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: 5.071A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 29 removed outlier: 3.974A pdb=" N VAL f 28 " --> pdb=" O SER f 24 " (cutoff:3.500A) Proline residue: f 29 - end of helix No H-bonds generated for 'chain 'f' and resid 24 through 29' Processing helix chain 'f' and resid 42 through 47 removed outlier: 4.051A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 62 removed outlier: 3.507A pdb=" N ASN f 52 " --> pdb=" O LYS f 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.581A 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: 3.639A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.689A 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 7 removed outlier: 3.740A pdb=" N LYS g 6 " --> pdb=" O SER g 2 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 81 removed outlier: 6.202A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.022A 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 Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.919A 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: 4.167A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.599A 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 123 removed outlier: 3.758A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.732A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.018A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.896A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.871A 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: 4.126A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.907A 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 57 removed outlier: 4.335A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.298A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.025A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 5.004A 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: 4.503A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.841A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 removed outlier: 3.523A pdb=" N LYS n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.913A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.657A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.298A 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 Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.633A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.753A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.774A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (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 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.552A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 40 removed outlier: 5.705A pdb=" N ASN r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.564A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 4.244A 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: 3.997A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.253A 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 Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.798A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.140A 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: 3.749A pdb=" N LEU x 6 " --> pdb=" O LYS x 2 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) Processing helix chain 'x' and resid 10 through 35 removed outlier: 4.491A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.678A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (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 18 Processing helix chain '0' and resid 26 through 31 Proline residue: 0 31 - end of helix No H-bonds generated for 'chain '0' and resid 26 through 31' Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.282A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.626A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 4.481A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.329A 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 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.560A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.189A 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 65 removed outlier: 3.732A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.942A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 67 through 71 Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 removed outlier: 3.509A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 170 removed outlier: 6.103A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 145 removed outlier: 4.093A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 145 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 174 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.549A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.614A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 43 removed outlier: 5.720A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.431A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.046A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.839A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 5 through 11 removed outlier: 3.570A pdb=" N GLY I 24 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS I 60 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.659A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 16, first strand: chain 'K' and resid 42 through 45 removed outlier: 7.082A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.263A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 36 through 41 removed outlier: 3.731A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.529A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 7 through 12 removed outlier: 4.894A pdb=" N ASP Q 57 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'Q' and resid 56 through 59 removed outlier: 7.166A pdb=" N GLY Q 56 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA Q 82 " --> pdb=" O GLY Q 56 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.483A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'c' and resid 75 through 78 removed outlier: 4.499A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 80 through 83 removed outlier: 5.278A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 162 through 165 removed outlier: 6.381A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'd' and resid 11 through 16 removed outlier: 4.021A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 79 through 84 removed outlier: 6.065A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 179 through 182 Processing sheet with id= 30, first strand: chain 'd' and resid 24 through 28 Processing sheet with id= 31, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.461A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 1 through 5 removed outlier: 4.283A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL e 14 " --> pdb=" O MET e 1 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU e 5 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 44 through 47 removed outlier: 6.628A pdb=" N ARG e 44 " --> pdb=" O PRO e 89 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA e 87 " --> pdb=" O GLN e 46 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.690A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.732A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.427A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 41 through 44 removed outlier: 3.589A pdb=" N GLY g 53 " --> pdb=" O GLU g 42 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS g 44 " --> pdb=" O THR g 51 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.911A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 121 through 125 removed outlier: 6.161A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY g 135 " --> pdb=" O PHE g 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE g 83 " --> pdb=" O GLY g 135 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'h' and resid 1 through 5 removed outlier: 3.617A pdb=" N VAL h 3 " --> pdb=" O VAL h 19 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.779A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.349A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.208A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU j 86 " --> pdb=" O ALA j 11 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP j 37 " --> pdb=" O VAL j 62 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'j' and resid 68 through 71 removed outlier: 4.175A pdb=" N SER j 75 " --> pdb=" O ARG j 71 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'j' and resid 63 through 66 removed outlier: 3.901A pdb=" N LYS j 66 " --> pdb=" O GLY j 81 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY j 81 " --> pdb=" O LYS j 66 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'l' and resid 62 through 65 removed outlier: 6.458A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'l' and resid 30 through 36 removed outlier: 8.038A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.866A pdb=" N ALA m 108 " --> pdb=" O PHE m 102 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE m 102 " --> pdb=" O ALA m 108 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'n' and resid 49 through 52 Processing sheet with id= 51, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.459A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.705A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'q' and resid 11 through 14 removed outlier: 6.990A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.149A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 56, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 57, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.025A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 59, first strand: chain 's' and resid 12 through 15 removed outlier: 5.218A pdb=" N VAL s 31 " --> pdb=" O HIS s 15 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 't' and resid 40 through 45 removed outlier: 4.765A pdb=" N ASN t 40 " --> pdb=" O ALA t 63 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.662A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.198A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 64, first strand: chain 'w' and resid 11 through 19 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'w' and resid 35 through 41 Processing sheet with id= 66, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.310A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'z' and resid 28 through 31 removed outlier: 6.397A pdb=" N SER z 29 " --> pdb=" O LYS z 37 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS z 37 " --> pdb=" O SER z 29 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP z 31 " --> pdb=" O GLY z 35 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '0' and resid 19 through 25 removed outlier: 6.226A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '2' and resid 22 through 25 removed outlier: 5.686A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '3' and resid 1 through 5 removed outlier: 6.878A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '4' and resid 20 through 25 removed outlier: 4.232A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) 1901 hydrogen bonds defined for protein. 5616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3954 hydrogen bonds 6176 hydrogen bond angles 0 basepair planarities 1573 basepair parallelities 2368 stacking parallelities Total time for adding SS restraints: 852.44 Time building geometry restraints manager: 66.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 15933 1.32 - 1.45: 68666 1.45 - 1.58: 60240 1.58 - 1.71: 8984 1.71 - 1.84: 264 Bond restraints: 154087 Sorted by residual: bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.805 1.485 0.320 2.00e-02 2.50e+03 2.57e+02 bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.805 1.487 0.318 2.00e-02 2.50e+03 2.52e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.638 1.327 0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.638 1.336 0.302 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.150 1.389 -0.239 2.00e-02 2.50e+03 1.43e+02 ... (remaining 154082 not shown) Histogram of bond angle deviations from ideal: 95.00 - 103.60: 11994 103.60 - 112.21: 95773 112.21 - 120.82: 74390 120.82 - 129.43: 44714 129.43 - 138.03: 3633 Bond angle restraints: 230504 Sorted by residual: angle pdb=" N LYS v 44 " pdb=" CA LYS v 44 " pdb=" C LYS v 44 " ideal model delta sigma weight residual 111.07 103.31 7.76 1.07e+00 8.73e-01 5.25e+01 angle pdb=" N6 MA6 A1519 " pdb=" C6 MA6 A1519 " pdb=" N1 MA6 A1519 " ideal model delta sigma weight residual 98.71 119.19 -20.48 3.00e+00 1.11e-01 4.66e+01 angle pdb=" N6 MA6 A1518 " pdb=" C6 MA6 A1518 " pdb=" N1 MA6 A1518 " ideal model delta sigma weight residual 98.71 119.11 -20.40 3.00e+00 1.11e-01 4.63e+01 angle pdb=" C1' OMG a2251 " pdb=" N9 OMG a2251 " pdb=" C8 OMG a2251 " ideal model delta sigma weight residual 106.81 127.16 -20.35 3.00e+00 1.11e-01 4.60e+01 angle pdb=" N ALA L 17 " pdb=" CA ALA L 17 " pdb=" C ALA L 17 " ideal model delta sigma weight residual 110.91 118.70 -7.79 1.17e+00 7.31e-01 4.44e+01 ... (remaining 230499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 78635 35.41 - 70.81: 3198 70.81 - 106.22: 277 106.22 - 141.63: 18 141.63 - 177.04: 10 Dihedral angle restraints: 82138 sinusoidal: 66233 harmonic: 15905 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual 180.00 -121.53 -58.47 0 5.00e+00 4.00e-02 1.37e+02 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 56.94 143.06 1 1.50e+01 4.44e-03 7.68e+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 62.94 137.06 1 1.50e+01 4.44e-03 7.39e+01 ... (remaining 82135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 27336 0.091 - 0.183: 1873 0.183 - 0.274: 130 0.274 - 0.365: 17 0.365 - 0.457: 5 Chirality restraints: 29361 Sorted by residual: chirality pdb=" CA GLU M 66 " pdb=" N GLU M 66 " pdb=" C GLU M 66 " pdb=" CB GLU M 66 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.45 0.43 2.00e-01 2.50e+01 4.73e+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 2.12 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 29358 not shown) Planarity restraints: 12246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2445 " -0.058 2.00e-02 2.50e+03 6.08e-01 8.32e+03 pdb=" C4' 2MG a2445 " -0.453 2.00e-02 2.50e+03 pdb=" O4' 2MG a2445 " -0.723 2.00e-02 2.50e+03 pdb=" C3' 2MG a2445 " 0.603 2.00e-02 2.50e+03 pdb=" O3' 2MG a2445 " 0.620 2.00e-02 2.50e+03 pdb=" C2' 2MG a2445 " 0.210 2.00e-02 2.50e+03 pdb=" O2' 2MG a2445 " -0.937 2.00e-02 2.50e+03 pdb=" C1' 2MG a2445 " -0.203 2.00e-02 2.50e+03 pdb=" N9 2MG a2445 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.052 2.00e-02 2.50e+03 6.06e-01 8.25e+03 pdb=" C4' 2MG A1516 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.645 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.641 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.173 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.973 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.226 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.944 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.051 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 2MG A1207 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.636 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.631 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.182 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.967 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.222 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.922 2.00e-02 2.50e+03 ... (remaining 12243 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 1281 2.25 - 2.91: 62785 2.91 - 3.58: 253124 3.58 - 4.24: 515644 4.24 - 4.90: 665353 Nonbonded interactions: 1498187 Sorted by model distance: nonbonded pdb="MG MG A1654 " pdb=" O HOH A3224 " model vdw 1.588 2.170 nonbonded pdb="MG MG a6144 " pdb=" O HOH a9878 " model vdw 1.609 2.170 nonbonded pdb=" OP1 G a 962 " pdb="MG MG a6030 " model vdw 1.630 2.170 nonbonded pdb=" O HOH a8897 " pdb=" O HOH d 433 " model vdw 1.639 2.440 nonbonded pdb=" OP1 G a 760 " pdb="MG MG a6129 " model vdw 1.655 2.170 ... (remaining 1498182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4554 5.49 5 Mg 309 5.21 5 S 149 5.16 5 C 71191 2.51 5 N 26483 2.21 5 O 46650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.230 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: 0.180 Extract box with map and model: 35.930 Check model and map are aligned: 1.670 Convert atoms to be neutral: 0.920 Process input model: 1174.240 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1236.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 0.320 154087 Z= 0.424 Angle : 0.966 20.481 230504 Z= 0.499 Chirality : 0.050 0.457 29361 Planarity : 0.020 0.608 12246 Dihedral : 15.242 177.037 71878 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Rotamer Outliers : 6.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.10), residues: 5474 helix: -1.16 (0.10), residues: 1831 sheet: -0.91 (0.14), residues: 1050 loop : -1.15 (0.11), residues: 2593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1748 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1459 time to evaluate : 6.546 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 outliers start: 289 outliers final: 47 residues processed: 1645 average time/residue: 2.4318 time to fit residues: 5692.8781 Evaluate side-chains 1194 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1147 time to evaluate : 6.656 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 37 residues processed: 10 average time/residue: 1.8102 time to fit residues: 35.9233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 834 optimal weight: 7.9990 chunk 748 optimal weight: 9.9990 chunk 415 optimal weight: 20.0000 chunk 255 optimal weight: 30.0000 chunk 505 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 774 optimal weight: 0.9990 chunk 299 optimal weight: 7.9990 chunk 470 optimal weight: 20.0000 chunk 576 optimal weight: 10.0000 chunk 897 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS B 58 ASN B 89 GLN B 103 ASN B 109 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 74 ASN D 89 ASN D 100 ASN D 140 ASN D 152 GLN D 196 ASN E 12 GLN E 70 ASN E 73 ASN E 82 GLN E 97 GLN E 148 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 130 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN J 56 HIS K 15 GLN K 40 ASN K 64 GLN M 14 HIS N 4 GLN N 35 ASN N 43 ASN N 66 GLN O 35 GLN P 9 HIS P 26 ASN P 63 GLN R 31 ASN S 14 HIS S 52 HIS S 83 HIS T 20 HIS T 68 HIS c 90 ASN c 117 GLN c 197 ASN c 243 HIS d 94 GLN f 81 GLN g 38 ASN g 48 ASN g 115 HIS g 139 GLN h 20 ASN i 128 ASN i 136 GLN l 13 HIS m 31 HIS m 62 ASN n 100 HIS o 3 ASN o 7 GLN o 12 GLN p 37 GLN p 52 GLN p 71 GLN q 66 HIS q 87 GLN r 7 HIS r 40 ASN s 28 ASN s 48 GLN s 91 GLN t 40 ASN t 53 ASN t 74 ASN u 5 ASN u 12 GLN u 49 ASN v 50 ASN v 57 HIS w 6 GLN w 20 HIS x 15 ASN x 39 GLN y 20 HIS z 6 ASN z 42 HIS 2 31 HIS 4 30 HIS Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 154087 Z= 0.327 Angle : 0.815 17.682 230504 Z= 0.423 Chirality : 0.043 0.410 29361 Planarity : 0.008 0.145 12246 Dihedral : 13.713 177.957 60850 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer Outliers : 5.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.11), residues: 5474 helix: 0.44 (0.11), residues: 1870 sheet: -0.42 (0.15), residues: 1066 loop : -0.64 (0.11), residues: 2538 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1173 time to evaluate : 6.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 250 outliers final: 104 residues processed: 1332 average time/residue: 2.4621 time to fit residues: 4677.3526 Evaluate side-chains 1212 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1108 time to evaluate : 6.668 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 68 residues processed: 36 average time/residue: 1.5992 time to fit residues: 102.7145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 498 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 746 optimal weight: 4.9990 chunk 610 optimal weight: 10.9990 chunk 247 optimal weight: 30.0000 chunk 898 optimal weight: 0.8980 chunk 970 optimal weight: 0.9980 chunk 800 optimal weight: 9.9990 chunk 891 optimal weight: 3.9990 chunk 306 optimal weight: 10.0000 chunk 721 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN D 74 ASN D 89 ASN E 70 ASN E 73 ASN E 132 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN K 64 GLN L 112 GLN N 49 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN c 117 GLN c 163 GLN d 32 ASN d 94 GLN f 81 GLN g 143 GLN i 128 ASN l 22 GLN m 73 ASN o 3 ASN o 7 GLN p 44 GLN p 71 GLN q 87 GLN ** s 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 12 GLN u 49 ASN x 15 ASN x 39 GLN ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 61 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 154087 Z= 0.191 Angle : 0.651 15.271 230504 Z= 0.353 Chirality : 0.037 0.380 29361 Planarity : 0.006 0.138 12246 Dihedral : 13.447 178.065 60850 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Rotamer Outliers : 4.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5474 helix: 1.21 (0.12), residues: 1862 sheet: -0.17 (0.15), residues: 1036 loop : -0.34 (0.12), residues: 2576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1382 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1162 time to evaluate : 6.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 220 outliers final: 99 residues processed: 1300 average time/residue: 2.4618 time to fit residues: 4585.5015 Evaluate side-chains 1206 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1107 time to evaluate : 6.630 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 69 residues processed: 30 average time/residue: 1.9135 time to fit residues: 96.1843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 888 optimal weight: 7.9990 chunk 675 optimal weight: 10.0000 chunk 466 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 428 optimal weight: 10.0000 chunk 603 optimal weight: 10.0000 chunk 902 optimal weight: 4.9990 chunk 955 optimal weight: 7.9990 chunk 471 optimal weight: 30.0000 chunk 854 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN D 131 ASN E 12 GLN E 73 ASN E 78 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN K 64 GLN L 112 GLN N 49 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 ASN c 163 GLN d 32 ASN d 94 GLN f 27 GLN f 52 ASN f 81 GLN g 143 GLN i 128 ASN i 138 GLN j 90 ASN m 73 ASN o 3 ASN o 7 GLN s 28 ASN u 12 GLN u 49 ASN x 15 ASN x 39 GLN 4 61 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 154087 Z= 0.354 Angle : 0.829 19.302 230504 Z= 0.427 Chirality : 0.043 0.403 29361 Planarity : 0.008 0.150 12246 Dihedral : 13.633 179.483 60850 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer Outliers : 5.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.11), residues: 5474 helix: 1.00 (0.12), residues: 1875 sheet: -0.21 (0.15), residues: 1071 loop : -0.41 (0.12), residues: 2528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1126 time to evaluate : 6.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 231 outliers final: 128 residues processed: 1267 average time/residue: 2.4775 time to fit residues: 4474.3148 Evaluate side-chains 1230 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1102 time to evaluate : 6.356 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 86 residues processed: 42 average time/residue: 1.7793 time to fit residues: 125.5934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 795 optimal weight: 0.9990 chunk 542 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 711 optimal weight: 3.9990 chunk 394 optimal weight: 10.0000 chunk 814 optimal weight: 8.9990 chunk 660 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 487 optimal weight: 40.0000 chunk 857 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN B 58 ASN C 8 ASN C 41 GLN D 54 GLN D 74 ASN D 131 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN E 73 ASN E 97 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN I 50 GLN K 64 GLN L 112 GLN N 49 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN d 32 ASN d 94 GLN f 81 GLN g 143 GLN i 128 ASN i 138 GLN m 73 ASN o 3 ASN o 7 GLN s 28 ASN s 70 HIS u 49 ASN x 39 GLN 4 61 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 154087 Z= 0.206 Angle : 0.668 15.688 230504 Z= 0.359 Chirality : 0.037 0.384 29361 Planarity : 0.006 0.141 12246 Dihedral : 13.444 178.033 60850 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer Outliers : 4.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 5474 helix: 1.33 (0.12), residues: 1873 sheet: -0.16 (0.15), residues: 1048 loop : -0.29 (0.12), residues: 2553 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1133 time to evaluate : 6.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 123 residues processed: 1264 average time/residue: 2.5278 time to fit residues: 4564.4721 Evaluate side-chains 1209 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1086 time to evaluate : 6.664 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 90 residues processed: 34 average time/residue: 1.6722 time to fit residues: 100.6000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 321 optimal weight: 4.9990 chunk 860 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 560 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 955 optimal weight: 1.9990 chunk 793 optimal weight: 20.0000 chunk 442 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 501 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 58 ASN B 93 ASN C 8 ASN C 41 GLN D 74 ASN D 131 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 70 ASN F 11 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN I 37 GLN I 50 GLN K 64 GLN L 112 GLN N 49 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 ASN c 163 GLN d 32 ASN d 94 GLN f 52 ASN f 81 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 143 GLN i 128 ASN i 138 GLN m 73 ASN o 3 ASN o 7 GLN s 28 ASN u 49 ASN x 39 GLN 4 61 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 154087 Z= 0.281 Angle : 0.747 18.266 230504 Z= 0.393 Chirality : 0.040 0.400 29361 Planarity : 0.007 0.146 12246 Dihedral : 13.533 179.938 60850 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer Outliers : 4.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.11), residues: 5474 helix: 1.22 (0.12), residues: 1873 sheet: -0.18 (0.15), residues: 1076 loop : -0.33 (0.12), residues: 2525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1109 time to evaluate : 6.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 125 residues processed: 1240 average time/residue: 2.5112 time to fit residues: 4460.2411 Evaluate side-chains 1212 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1087 time to evaluate : 6.755 Switching outliers to nearest non-outliers outliers start: 125 outliers final: 91 residues processed: 35 average time/residue: 1.7066 time to fit residues: 105.4439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 921 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 698 optimal weight: 8.9990 chunk 540 optimal weight: 10.0000 chunk 804 optimal weight: 4.9990 chunk 533 optimal weight: 10.0000 chunk 952 optimal weight: 0.8980 chunk 595 optimal weight: 10.0000 chunk 580 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 overall best weight: 6.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 58 ASN C 41 GLN D 36 GLN D 54 GLN D 74 ASN D 131 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN I 5 GLN I 37 GLN I 50 GLN L 112 GLN N 49 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 HIS d 32 ASN d 94 GLN f 27 GLN f 52 ASN f 81 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 143 GLN h 33 GLN i 128 ASN i 138 GLN m 73 ASN o 3 ASN o 7 GLN s 28 ASN u 49 ASN x 39 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.108 154087 Z= 0.346 Angle : 0.824 19.325 230504 Z= 0.425 Chirality : 0.043 0.414 29361 Planarity : 0.008 0.148 12246 Dihedral : 13.665 179.304 60850 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer Outliers : 4.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.11), residues: 5474 helix: 1.01 (0.12), residues: 1875 sheet: -0.28 (0.15), residues: 1085 loop : -0.44 (0.12), residues: 2514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1127 time to evaluate : 6.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 120 residues processed: 1258 average time/residue: 2.5200 time to fit residues: 4538.9681 Evaluate side-chains 1215 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1095 time to evaluate : 6.483 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 94 residues processed: 27 average time/residue: 1.6757 time to fit residues: 84.9159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 589 optimal weight: 10.0000 chunk 380 optimal weight: 1.9990 chunk 568 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 605 optimal weight: 10.0000 chunk 648 optimal weight: 20.0000 chunk 470 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 748 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 58 ASN D 74 ASN D 131 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 70 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN I 50 GLN L 112 GLN N 49 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 ASN d 32 ASN d 94 GLN f 81 GLN g 73 ASN h 33 GLN i 128 ASN i 138 GLN m 73 ASN o 3 ASN o 7 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 28 ASN s 70 HIS u 49 ASN x 39 GLN ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.164 154087 Z= 0.221 Angle : 0.695 15.478 230504 Z= 0.371 Chirality : 0.038 0.388 29361 Planarity : 0.007 0.141 12246 Dihedral : 13.498 178.537 60850 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.33 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.11), residues: 5474 helix: 1.32 (0.12), residues: 1864 sheet: -0.21 (0.15), residues: 1074 loop : -0.33 (0.12), residues: 2536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1113 time to evaluate : 6.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 112 residues processed: 1225 average time/residue: 2.5145 time to fit residues: 4400.1491 Evaluate side-chains 1209 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1097 time to evaluate : 6.625 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 92 residues processed: 20 average time/residue: 1.8142 time to fit residues: 65.5361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 866 optimal weight: 9.9990 chunk 912 optimal weight: 9.9990 chunk 832 optimal weight: 9.9990 chunk 887 optimal weight: 7.9990 chunk 534 optimal weight: 30.0000 chunk 386 optimal weight: 20.0000 chunk 696 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 801 optimal weight: 4.9990 chunk 839 optimal weight: 2.9990 chunk 884 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN D 74 ASN D 131 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 70 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN I 50 GLN L 112 GLN N 49 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN d 94 GLN f 52 ASN f 81 GLN g 73 ASN h 33 GLN i 128 ASN i 138 GLN m 73 ASN o 3 ASN o 7 GLN q 86 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 28 ASN u 49 ASN x 39 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.235 154087 Z= 0.318 Angle : 0.789 16.913 230504 Z= 0.411 Chirality : 0.042 0.406 29361 Planarity : 0.008 0.146 12246 Dihedral : 13.578 179.222 60850 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 5474 helix: 1.13 (0.12), residues: 1864 sheet: -0.25 (0.15), residues: 1085 loop : -0.40 (0.12), residues: 2525 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1098 time to evaluate : 6.622 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 160 outliers final: 122 residues processed: 1215 average time/residue: 2.5789 time to fit residues: 4474.5096 Evaluate side-chains 1201 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1079 time to evaluate : 6.629 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 99 residues processed: 23 average time/residue: 1.8152 time to fit residues: 74.1918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 582 optimal weight: 10.0000 chunk 938 optimal weight: 8.9990 chunk 572 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 chunk 652 optimal weight: 20.0000 chunk 984 optimal weight: 10.0000 chunk 905 optimal weight: 0.1980 chunk 783 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 58 ASN C 8 ASN D 74 ASN D 131 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 70 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN H 67 GLN I 50 GLN L 112 GLN N 49 GLN T 20 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 ASN d 32 ASN d 94 GLN f 52 ASN f 81 GLN g 73 ASN g 116 GLN i 128 ASN i 138 GLN m 73 ASN o 3 ASN o 7 GLN q 86 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 49 ASN x 39 GLN ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.429 154087 Z= 0.326 Angle : 0.785 26.138 230504 Z= 0.411 Chirality : 0.041 0.399 29361 Planarity : 0.007 0.145 12246 Dihedral : 13.569 179.913 60850 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.13 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 5474 helix: 1.11 (0.12), residues: 1864 sheet: -0.26 (0.15), residues: 1081 loop : -0.41 (0.12), residues: 2529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1084 time to evaluate : 6.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 115 residues processed: 1193 average time/residue: 2.5664 time to fit residues: 4392.9776 Evaluate side-chains 1190 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1075 time to evaluate : 6.714 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 103 residues processed: 12 average time/residue: 1.7756 time to fit residues: 42.1055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 622 optimal weight: 10.0000 chunk 834 optimal weight: 0.0970 chunk 240 optimal weight: 10.0000 chunk 722 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 785 optimal weight: 3.9990 chunk 328 optimal weight: 9.9990 chunk 806 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN C 8 ASN D 74 ASN D 131 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 70 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN H 67 GLN I 50 GLN L 112 GLN N 49 GLN T 20 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN d 94 GLN f 81 GLN g 73 ASN i 128 ASN i 138 GLN m 73 ASN o 3 ASN o 7 GLN q 86 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 49 ASN x 39 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.145880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110673 restraints weight = 158315.798| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.55 r_work: 0.3318 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 0.84 restraints_weight: 0.2500 r_work: 0.3272 rms_B_bonded: 1.11 restraints_weight: 0.1250 r_work: 0.3239 rms_B_bonded: 1.52 restraints_weight: 0.0625 r_work: 0.3192 rms_B_bonded: 2.15 restraints_weight: 0.0312 r_work: 0.3120 rms_B_bonded: 3.26 restraints_weight: 0.0156 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.489 154087 Z= 0.283 Angle : 0.746 46.765 230504 Z= 0.395 Chirality : 0.039 0.390 29361 Planarity : 0.007 0.143 12246 Dihedral : 13.557 179.426 60850 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 5474 helix: 1.19 (0.12), residues: 1864 sheet: -0.25 (0.15), residues: 1078 loop : -0.38 (0.12), residues: 2532 =============================================================================== Job complete usr+sys time: 58295.92 seconds wall clock time: 996 minutes 59.97 seconds (59819.97 seconds total)