Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 16 00:01:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/10_2023/7m4x_23669_updated.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4451 5.49 5 Mg 190 5.21 5 S 141 5.16 5 C 69635 2.51 5 N 25786 2.21 5 O 39239 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 14": "OD1" <-> "OD2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 37": "OD1" <-> "OD2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "P PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 77": "OD1" <-> "OD2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 94": "OD1" <-> "OD2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 70": "OE1" <-> "OE2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "Z ASP 14": "OD1" <-> "OD2" Residue "b TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 118": "OD1" <-> "OD2" Residue "b ASP 161": "OD1" <-> "OD2" Residue "b ASP 196": "OD1" <-> "OD2" Residue "b ARG 210": "NH1" <-> "NH2" Residue "c ASP 110": "OD1" <-> "OD2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 41": "OD1" <-> "OD2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "j TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 81": "OD1" <-> "OD2" Residue "k PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 11": "OD1" <-> "OD2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 38": "OD1" <-> "OD2" Residue "o ASP 74": "OD1" <-> "OD2" Residue "p ASP 41": "OD1" <-> "OD2" Residue "p ASP 47": "OD1" <-> "OD2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "r ASP 27": "OD1" <-> "OD2" Residue "r TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 43": "OD1" <-> "OD2" Residue "u ASP 13": "OD1" <-> "OD2" Residue "u GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 139446 Number of models: 1 Model: "" Number of chains: 73 Chain: "0" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 58566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2730, 58566 Classifications: {'RNA': 2730} Modifications used: {'rna2p': 3, 'rna2p_pur': 254, 'rna2p_pyr': 147, 'rna3p': 12, 'rna3p_pur': 1306, 'rna3p_pyr': 1008} Link IDs: {'rna2p': 403, 'rna3p': 2326} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 9, 'rna3p': 105} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1566 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 204} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 616 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 115, 'rna2p_pyr': 90, 'rna3p': 8, 'rna3p_pur': 748, 'rna3p_pyr': 566} Link IDs: {'rna2p': 205, 'rna3p': 1322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1188 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 793 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "v" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1636 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 31} Link IDs: {'rna2p': 8, 'rna3p': 68} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "3" 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: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 214 Unusual residues: {' MG': 134, 'YQM': 2} Classifications: {'undetermined': 136} Link IDs: {None: 135} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "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: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 91 Unusual residues: {' MG': 51, 'YQM': 1} Classifications: {'undetermined': 52} Link IDs: {None: 51} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 392 Classifications: {'water': 392} Link IDs: {None: 391} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1364 SG CYS 3 11 47.663 109.673 138.795 1.00 20.39 S ATOM 1380 SG CYS 3 14 48.921 111.009 135.450 1.00 20.05 S ATOM 1485 SG CYS 3 27 47.348 113.396 137.972 1.00 20.01 S Time building chain proxies: 49.94, per 1000 atoms: 0.36 Number of scatterers: 139446 At special positions: 0 Unit cell: (229.808, 248.464, 274.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 141 16.00 P 4451 15.00 Mg 190 11.99 F 3 9.00 O 39239 8.00 N 25786 7.00 C 69635 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=0, symmetry=0 Time building additional restraints: 54.56 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " Number of angles added : 3 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10130 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: 166 helices and 70 sheets defined 38.9% alpha, 19.0% beta 1445 base pairs and 2136 stacking pairs defined. Time for finding SS restraints: 61.27 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.164A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.436A 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 Processing helix chain '2' and resid 36 through 45 removed outlier: 5.568A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.293A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.507A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' 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: 3.805A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.112A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.337A 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: 5.123A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.079A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.630A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 91' Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.989A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 5.721A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.842A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.530A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 183 removed outlier: 5.753A pdb=" N ASP E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 4 through 21 removed outlier: 4.050A pdb=" N LEU F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.956A pdb=" N ILE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 4.442A pdb=" N ILE F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.857A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.001A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 removed outlier: 3.655A pdb=" N VAL I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN I 12 " --> pdb=" O PRO I 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 7 through 12' Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.937A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.651A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY I 107 " --> pdb=" O ARG I 103 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 109 " --> pdb=" O VAL I 105 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.541A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.783A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.807A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 4.108A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 3.921A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 88' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.668A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Proline residue: L 126 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 57 removed outlier: 3.929A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.270A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.832A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.810A 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 3 through 23 removed outlier: 4.337A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 3.714A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.628A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 107' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.752A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.844A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.736A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.936A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.876A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.218A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.763A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.378A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 3.975A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 5.030A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.837A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN 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: 4.272A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 35 Processing helix chain 'X' and resid 40 through 61 removed outlier: 4.353A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.571A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 4.832A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.909A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 78 through 90 Processing helix chain 'b' and resid 105 through 126 removed outlier: 3.878A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 150 Processing helix chain 'b' and resid 167 through 172 Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 227 removed outlier: 4.444A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.573A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 4.797A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 4.031A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.632A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.249A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.701A 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 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.593A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.295A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.575A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 148 through 153 removed outlier: 5.449A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 4.114A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.504A pdb=" N LEU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) Proline residue: d 194 - end of helix No H-bonds generated for 'chain 'd' and resid 189 through 194' Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.034A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS d 208 " --> pdb=" O GLU d 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.229A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 3.664A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 14 through 33 removed outlier: 4.069A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLY f 20 " --> pdb=" O ASP f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.576A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 5.710A pdb=" N SER g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 113 through 121 Processing helix chain 'i' and resid 32 through 37 Processing helix chain 'i' and resid 39 through 54 Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.671A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 4.824A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.657A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.681A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.741A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 75 removed outlier: 4.404A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.182A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.565A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.991A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.807A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix 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 34 removed outlier: 5.081A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA n 32 " --> pdb=" O LYS n 28 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN n 33 " --> pdb=" O ALA n 29 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL n 34 " --> pdb=" O THR n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.617A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY n 91 " --> pdb=" O THR n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.552A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.843A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 71 through 82 Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.583A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.740A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.128A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.267A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 41 removed outlier: 3.753A pdb=" N LYS t 16 " --> pdb=" O ARG t 12 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 4.096A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA t 87 " --> pdb=" O VAL 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: 4.925A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 21 removed outlier: 6.268A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 13 through 19 removed outlier: 8.117A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.061A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.976A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 138 through 142 removed outlier: 3.763A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N SER C 170 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.094A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.660A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.629A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 80 through 85 removed outlier: 4.783A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 11, first strand: chain 'D' and resid 25 through 29 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.402A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.940A pdb=" N ARG E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA E 86 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 116 through 119 removed outlier: 4.051A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.736A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 40 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 17, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 18, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.204A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 20, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.608A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.125A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.198A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE J 86 " --> pdb=" O ALA J 11 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP J 37 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 68 through 71 removed outlier: 4.119A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 63 through 66 removed outlier: 3.863A pdb=" N LYS J 66 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASP J 81 " --> pdb=" O LYS J 66 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 39 through 42 Processing sheet with id= 26, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.534A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'L' and resid 74 through 77 removed outlier: 6.925A pdb=" N ILE L 74 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 33 through 37 removed outlier: 3.973A pdb=" N ALA M 108 " --> pdb=" O ARG M 103 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY M 101 " --> pdb=" O MET M 110 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.753A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.593A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.968A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.109A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 17 through 22 removed outlier: 3.903A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 35, first strand: chain 'Q' and resid 65 through 69 removed outlier: 3.772A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 37, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.413A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 38 through 44 removed outlier: 5.466A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'T' and resid 80 through 85 removed outlier: 6.691A pdb=" N ARG T 80 " --> pdb=" O LYS T 95 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 41, first strand: chain 'U' and resid 41 through 46 removed outlier: 3.501A pdb=" N ARG U 97 " --> pdb=" O TYR U 35 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.526A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 34 through 37 removed outlier: 4.183A pdb=" N ASN V 35 " --> pdb=" O ALA V 61 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASN V 50 " --> pdb=" O THR V 62 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 45 through 48 removed outlier: 6.216A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.536A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.168A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Z' and resid 28 through 31 Processing sheet with id= 48, first strand: chain 'b' and resid 17 through 20 removed outlier: 5.157A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'b' and resid 92 through 95 removed outlier: 3.875A pdb=" N ILE b 166 " --> pdb=" O VAL b 72 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 19 through 22 removed outlier: 5.798A pdb=" N ASN c 19 " --> pdb=" O ILE c 55 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG c 59 " --> pdb=" O ASN c 21 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.666A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 143 through 147 removed outlier: 3.813A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU d 180 " --> pdb=" O VAL d 147 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 10 through 15 removed outlier: 7.019A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.822A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 32 through 40 removed outlier: 6.604A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 38 through 42 removed outlier: 5.876A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.864A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'g' and resid 73 through 79 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.035A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.777A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'i' and resid 3 through 9 removed outlier: 3.613A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.800A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 44 through 53 removed outlier: 8.184A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'k' and resid 29 through 34 Processing sheet with id= 65, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.249A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.894A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.721A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 8 through 12 removed outlier: 7.174A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 20 through 32 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 30 through 34 removed outlier: 4.999A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1899 hydrogen bonds defined for protein. 5622 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3624 hydrogen bonds 5712 hydrogen bond angles 0 basepair planarities 1445 basepair parallelities 2136 stacking parallelities Total time for adding SS restraints: 221.39 Time building geometry restraints manager: 58.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12516 1.31 - 1.43: 67341 1.43 - 1.56: 61690 1.56 - 1.69: 8926 1.69 - 1.82: 251 Bond restraints: 150724 Sorted by residual: bond pdb=" C14 YQM A3201 " pdb=" C15 YQM A3201 " ideal model delta sigma weight residual 1.035 1.581 -0.546 2.00e-02 2.50e+03 7.45e+02 bond pdb=" C14 YQM A3202 " pdb=" C15 YQM A3202 " ideal model delta sigma weight residual 1.035 1.576 -0.541 2.00e-02 2.50e+03 7.31e+02 bond pdb=" C14 YQM a1601 " pdb=" C15 YQM a1601 " ideal model delta sigma weight residual 1.035 1.558 -0.523 2.00e-02 2.50e+03 6.85e+02 bond pdb=" C08 YQM a1601 " pdb=" C09 YQM a1601 " ideal model delta sigma weight residual 1.951 1.549 0.402 2.00e-02 2.50e+03 4.03e+02 bond pdb=" C08 YQM A3201 " pdb=" C09 YQM A3201 " ideal model delta sigma weight residual 1.951 1.550 0.401 2.00e-02 2.50e+03 4.02e+02 ... (remaining 150719 not shown) Histogram of bond angle deviations from ideal: 98.43 - 108.11: 42405 108.11 - 117.80: 99101 117.80 - 127.48: 75041 127.48 - 137.17: 9009 137.17 - 146.85: 4 Bond angle restraints: 225560 Sorted by residual: angle pdb=" C1' G7M A2065 " pdb=" N9 G7M A2065 " pdb=" C8 G7M A2065 " ideal model delta sigma weight residual 94.96 121.93 -26.97 3.00e+00 1.11e-01 8.08e+01 angle pdb=" C1' G7M a 524 " pdb=" N9 G7M a 524 " pdb=" C8 G7M a 524 " ideal model delta sigma weight residual 94.96 121.66 -26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 146.85 -20.62 3.00e+00 1.11e-01 4.72e+01 angle pdb=" C1' 2MG a1204 " pdb=" N9 2MG a1204 " pdb=" C8 2MG a1204 " ideal model delta sigma weight residual 110.07 128.65 -18.58 3.00e+00 1.11e-01 3.83e+01 angle pdb=" C1' 2MG A2441 " pdb=" N9 2MG A2441 " pdb=" C8 2MG A2441 " ideal model delta sigma weight residual 110.07 128.21 -18.14 3.00e+00 1.11e-01 3.65e+01 ... (remaining 225555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 77682 35.95 - 71.91: 2394 71.91 - 107.86: 204 107.86 - 143.81: 34 143.81 - 179.77: 74 Dihedral angle restraints: 80388 sinusoidal: 64657 harmonic: 15731 Sorted by residual: dihedral pdb=" O4' C A 715 " pdb=" C1' C A 715 " pdb=" N1 C A 715 " pdb=" C2 C A 715 " ideal model delta sinusoidal sigma weight residual 200.00 21.27 178.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C a1448 " pdb=" C1' C a1448 " pdb=" N1 C a1448 " pdb=" C2 C a1448 " ideal model delta sinusoidal sigma weight residual -160.00 17.59 -177.59 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2473 " pdb=" C1' U A2473 " pdb=" N1 U A2473 " pdb=" C2 U A2473 " ideal model delta sinusoidal sigma weight residual -160.00 14.73 -174.73 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 80385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 27786 0.081 - 0.161: 993 0.161 - 0.242: 30 0.242 - 0.323: 4 0.323 - 0.403: 6 Chirality restraints: 28819 Sorted by residual: chirality pdb=" C05 YQM A3201 " pdb=" C04 YQM A3201 " pdb=" C06 YQM A3201 " pdb=" C19 YQM A3201 " both_signs ideal model delta sigma weight residual False 2.36 2.76 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C05 YQM A3202 " pdb=" C04 YQM A3202 " pdb=" C06 YQM A3202 " pdb=" C19 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.36 2.76 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1* PSU a 513 " pdb=" O4* PSU a 513 " pdb=" C2* PSU a 513 " pdb=" C5 PSU a 513 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 28816 not shown) Planarity restraints: 12052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2247 " -0.038 2.00e-02 2.50e+03 5.82e-01 7.61e+03 pdb=" C4' OMG A2247 " -0.438 2.00e-02 2.50e+03 pdb=" O4' OMG A2247 " -0.655 2.00e-02 2.50e+03 pdb=" C3' OMG A2247 " 0.591 2.00e-02 2.50e+03 pdb=" O3' OMG A2247 " 0.583 2.00e-02 2.50e+03 pdb=" C2' OMG A2247 " 0.207 2.00e-02 2.50e+03 pdb=" O2' OMG A2247 " -0.920 2.00e-02 2.50e+03 pdb=" C1' OMG A2247 " -0.221 2.00e-02 2.50e+03 pdb=" N9 OMG A2247 " 0.891 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.032 2.00e-02 2.50e+03 5.70e-01 7.31e+03 pdb=" C4' 2MG a1204 " 0.436 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.637 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.565 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.213 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.902 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.226 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.868 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2441 " 0.036 2.00e-02 2.50e+03 5.70e-01 7.31e+03 pdb=" C4' 2MG A2441 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 2MG A2441 " 0.626 2.00e-02 2.50e+03 pdb=" C3' 2MG A2441 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG A2441 " -0.569 2.00e-02 2.50e+03 pdb=" C2' 2MG A2441 " -0.213 2.00e-02 2.50e+03 pdb=" O2' 2MG A2441 " 0.914 2.00e-02 2.50e+03 pdb=" C1' 2MG A2441 " 0.225 2.00e-02 2.50e+03 pdb=" N9 2MG A2441 " -0.859 2.00e-02 2.50e+03 ... (remaining 12049 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 913 2.41 - 3.03: 75318 3.03 - 3.66: 244723 3.66 - 4.28: 395558 4.28 - 4.90: 532660 Nonbonded interactions: 1249172 Sorted by model distance: nonbonded pdb=" O2' 5MU v 55 " pdb=" O4* PSU v 56 " model vdw 1.789 3.040 nonbonded pdb="MG MG a1636 " pdb=" O HOH a1769 " model vdw 1.802 2.170 nonbonded pdb="MG MG a1643 " pdb=" O HOH a1771 " model vdw 1.804 2.170 nonbonded pdb=" OP2 C a1066 " pdb="MG MG a1652 " model vdw 1.814 2.170 nonbonded pdb="MG MG a1645 " pdb=" O HOH a1801 " model vdw 1.821 2.170 ... (remaining 1249167 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.610 Construct map_model_manager: 0.110 Extract box with map and model: 29.870 Check model and map are aligned: 1.470 Set scattering table: 0.980 Process input model: 495.170 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 545.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 : 0.006 0.546 150724 Z= 0.392 Angle : 0.556 26.967 225560 Z= 0.290 Chirality : 0.034 0.403 28819 Planarity : 0.014 0.582 12052 Dihedral : 15.109 179.768 70258 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.52 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.11), residues: 5432 helix: 2.35 (0.12), residues: 1870 sheet: 0.66 (0.16), residues: 1033 loop : -0.11 (0.12), residues: 2529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1172 time to evaluate : 7.950 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: 0 outliers final: 0 residues processed: 1172 average time/residue: 2.3518 time to fit residues: 3822.9761 Evaluate side-chains 1042 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1042 time to evaluate : 5.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 823 optimal weight: 7.9990 chunk 739 optimal weight: 10.0000 chunk 410 optimal weight: 0.9990 chunk 252 optimal weight: 10.0000 chunk 498 optimal weight: 10.0000 chunk 394 optimal weight: 9.9990 chunk 764 optimal weight: 6.9990 chunk 295 optimal weight: 20.0000 chunk 464 optimal weight: 0.8980 chunk 568 optimal weight: 0.9990 chunk 885 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 HIS C 197 ASN C 200 ASN E 29 GLN E 40 GLN I 63 GLN J 29 HIS J 110 GLN L 17 ASN M 26 ASN O 44 GLN O 55 ASN Q 11 GLN R 34 ASN R 37 ASN R 57 ASN S 58 ASN U 79 GLN U 82 GLN U 92 HIS V 17 ASN Z 37 HIS b 105 ASN c 38 GLN c 139 GLN d 36 ASN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN i 30 ASN i 48 GLN j 56 HIS j 99 GLN k 27 ASN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 48 HIS r 31 GLN t 13 GLN t 82 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 150724 Z= 0.258 Angle : 0.703 16.584 225560 Z= 0.368 Chirality : 0.040 0.426 28819 Planarity : 0.006 0.127 12052 Dihedral : 15.203 179.890 59492 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.28 % Rotamer: Outliers : 3.09 % Allowed : 10.99 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.11), residues: 5432 helix: 1.98 (0.12), residues: 1855 sheet: 0.64 (0.16), residues: 1057 loop : -0.28 (0.12), residues: 2520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1066 time to evaluate : 5.681 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: 139 outliers final: 54 residues processed: 1103 average time/residue: 2.3254 time to fit residues: 3561.4359 Evaluate side-chains 1095 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1041 time to evaluate : 5.719 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 20 residues processed: 34 average time/residue: 1.3967 time to fit residues: 84.4933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 492 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 736 optimal weight: 5.9990 chunk 602 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 887 optimal weight: 0.4980 chunk 958 optimal weight: 0.9990 chunk 789 optimal weight: 7.9990 chunk 879 optimal weight: 9.9990 chunk 302 optimal weight: 0.9980 chunk 711 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS C 153 GLN E 162 ASN I 63 GLN J 29 HIS L 17 ASN O 44 GLN O 55 ASN Q 86 GLN R 34 ASN R 37 ASN S 58 ASN U 82 GLN V 17 ASN Z 41 HIS b 105 ASN c 139 GLN d 56 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 HIS e 81 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN h 18 GLN h 38 ASN i 30 ASN i 48 GLN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 150724 Z= 0.264 Angle : 0.707 14.734 225560 Z= 0.372 Chirality : 0.041 0.420 28819 Planarity : 0.006 0.132 12052 Dihedral : 15.293 179.240 59492 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.69 % Favored : 97.20 % Rotamer: Outliers : 3.52 % Allowed : 14.04 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 5432 helix: 1.66 (0.12), residues: 1858 sheet: 0.60 (0.16), residues: 1040 loop : -0.42 (0.12), residues: 2534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1056 time to evaluate : 5.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 75 residues processed: 1109 average time/residue: 2.3223 time to fit residues: 3585.9272 Evaluate side-chains 1100 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1025 time to evaluate : 5.699 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 33 residues processed: 42 average time/residue: 1.4691 time to fit residues: 104.8001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 876 optimal weight: 4.9990 chunk 666 optimal weight: 4.9990 chunk 460 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 423 optimal weight: 9.9990 chunk 595 optimal weight: 5.9990 chunk 890 optimal weight: 5.9990 chunk 942 optimal weight: 0.0030 chunk 465 optimal weight: 6.9990 chunk 843 optimal weight: 0.8980 chunk 253 optimal weight: 10.0000 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN L 17 ASN O 44 GLN O 55 ASN Q 86 GLN R 34 ASN R 37 ASN S 58 ASN U 82 GLN V 17 ASN ** b 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 56 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS t 80 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 150724 Z= 0.288 Angle : 0.734 17.584 225560 Z= 0.384 Chirality : 0.042 0.469 28819 Planarity : 0.006 0.131 12052 Dihedral : 15.331 179.543 59492 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Rotamer: Outliers : 3.83 % Allowed : 15.51 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.11), residues: 5432 helix: 1.55 (0.12), residues: 1857 sheet: 0.54 (0.16), residues: 1047 loop : -0.54 (0.11), residues: 2528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1050 time to evaluate : 6.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 83 residues processed: 1118 average time/residue: 2.3325 time to fit residues: 3626.1647 Evaluate side-chains 1104 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1021 time to evaluate : 5.679 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 40 residues processed: 43 average time/residue: 1.2972 time to fit residues: 101.2679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 784 optimal weight: 7.9990 chunk 534 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 701 optimal weight: 7.9990 chunk 388 optimal weight: 40.0000 chunk 804 optimal weight: 4.9990 chunk 651 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 481 optimal weight: 2.9990 chunk 845 optimal weight: 0.5980 chunk 237 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN O 44 GLN Q 86 GLN R 34 ASN R 37 ASN S 58 ASN U 82 GLN V 17 ASN W 6 GLN Z 4 GLN b 120 GLN d 56 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS t 80 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 150724 Z= 0.335 Angle : 0.782 18.958 225560 Z= 0.405 Chirality : 0.044 0.462 28819 Planarity : 0.007 0.134 12052 Dihedral : 15.453 179.723 59492 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 4.21 % Allowed : 16.27 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 5432 helix: 1.41 (0.12), residues: 1842 sheet: 0.39 (0.16), residues: 1029 loop : -0.64 (0.11), residues: 2561 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1031 time to evaluate : 6.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 105 residues processed: 1108 average time/residue: 2.3884 time to fit residues: 3723.3906 Evaluate side-chains 1122 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1017 time to evaluate : 5.719 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 46 residues processed: 62 average time/residue: 1.4595 time to fit residues: 153.1109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 317 optimal weight: 2.9990 chunk 848 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 553 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 943 optimal weight: 2.9990 chunk 783 optimal weight: 8.9990 chunk 436 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 312 optimal weight: 10.0000 chunk 495 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 30 HIS C 142 HIS ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN O 44 GLN Q 86 GLN R 34 ASN R 37 ASN R 61 ASN S 36 ASN S 58 ASN U 82 GLN V 17 ASN W 6 GLN Y 43 ASN d 56 GLN d 61 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS t 80 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 150724 Z= 0.342 Angle : 0.781 14.646 225560 Z= 0.404 Chirality : 0.044 0.465 28819 Planarity : 0.007 0.133 12052 Dihedral : 15.436 179.721 59492 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 3.76 % Allowed : 17.94 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.11), residues: 5432 helix: 1.37 (0.12), residues: 1844 sheet: 0.38 (0.16), residues: 1037 loop : -0.70 (0.11), residues: 2551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1040 time to evaluate : 5.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 100 residues processed: 1113 average time/residue: 2.3420 time to fit residues: 3633.6971 Evaluate side-chains 1116 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1016 time to evaluate : 5.718 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 57 residues processed: 46 average time/residue: 1.3081 time to fit residues: 108.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 909 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 537 optimal weight: 0.8980 chunk 688 optimal weight: 10.0000 chunk 533 optimal weight: 9.9990 chunk 794 optimal weight: 6.9990 chunk 526 optimal weight: 9.9990 chunk 939 optimal weight: 10.0000 chunk 588 optimal weight: 5.9990 chunk 572 optimal weight: 30.0000 chunk 433 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN I 61 GLN I 63 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN Q 86 GLN R 34 ASN R 37 ASN S 36 ASN S 58 ASN U 82 GLN V 17 ASN Y 43 ASN d 56 GLN d 61 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 28 GLN o 37 ASN o 71 ASN o 75 HIS r 31 GLN t 80 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 150724 Z= 0.451 Angle : 0.899 14.684 225560 Z= 0.455 Chirality : 0.050 0.437 28819 Planarity : 0.008 0.139 12052 Dihedral : 15.642 179.798 59492 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 3.94 % Allowed : 18.36 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.11), residues: 5432 helix: 1.07 (0.12), residues: 1847 sheet: 0.27 (0.15), residues: 1044 loop : -0.81 (0.11), residues: 2541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1002 time to evaluate : 5.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 115 residues processed: 1084 average time/residue: 2.3413 time to fit residues: 3544.2613 Evaluate side-chains 1110 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 995 time to evaluate : 5.700 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 63 residues processed: 55 average time/residue: 1.4760 time to fit residues: 138.1371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 581 optimal weight: 9.9990 chunk 375 optimal weight: 0.9980 chunk 561 optimal weight: 7.9990 chunk 283 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 597 optimal weight: 4.9990 chunk 640 optimal weight: 3.9990 chunk 464 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 738 optimal weight: 40.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN Q 86 GLN R 34 ASN R 37 ASN S 36 ASN S 58 ASN U 82 GLN V 17 ASN Y 43 ASN c 25 ASN d 56 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 58 HIS h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS r 31 GLN t 80 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 150724 Z= 0.378 Angle : 0.813 15.772 225560 Z= 0.418 Chirality : 0.046 0.404 28819 Planarity : 0.007 0.134 12052 Dihedral : 15.487 179.916 59492 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.67 % Rotamer: Outliers : 3.78 % Allowed : 18.85 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5432 helix: 1.13 (0.12), residues: 1853 sheet: 0.31 (0.16), residues: 1022 loop : -0.82 (0.11), residues: 2557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1006 time to evaluate : 5.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 170 outliers final: 104 residues processed: 1094 average time/residue: 2.3462 time to fit residues: 3588.5272 Evaluate side-chains 1111 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1007 time to evaluate : 5.749 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 66 residues processed: 41 average time/residue: 1.4074 time to fit residues: 99.9389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 854 optimal weight: 0.6980 chunk 900 optimal weight: 0.5980 chunk 821 optimal weight: 4.9990 chunk 875 optimal weight: 3.9990 chunk 527 optimal weight: 5.9990 chunk 381 optimal weight: 40.0000 chunk 687 optimal weight: 40.0000 chunk 268 optimal weight: 8.9990 chunk 791 optimal weight: 3.9990 chunk 828 optimal weight: 0.7980 chunk 872 optimal weight: 0.0470 overall best weight: 1.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN Q 86 GLN R 34 ASN R 37 ASN S 36 ASN S 58 ASN U 82 GLN V 17 ASN Y 43 ASN c 25 ASN d 56 GLN d 61 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 58 HIS h 38 ASN h 41 GLN i 30 ASN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN o 75 HIS r 31 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 0.048 150724 Z= 0.167 Angle : 0.631 14.586 225560 Z= 0.338 Chirality : 0.037 0.368 28819 Planarity : 0.005 0.125 12052 Dihedral : 15.105 179.759 59492 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 20.16 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 5432 helix: 1.58 (0.12), residues: 1856 sheet: 0.51 (0.16), residues: 1022 loop : -0.68 (0.12), residues: 2554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1029 time to evaluate : 6.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 78 residues processed: 1102 average time/residue: 2.3200 time to fit residues: 3573.9181 Evaluate side-chains 1093 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1015 time to evaluate : 5.759 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 62 residues processed: 18 average time/residue: 1.2301 time to fit residues: 45.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 575 optimal weight: 9.9990 chunk 926 optimal weight: 5.9990 chunk 565 optimal weight: 10.0000 chunk 439 optimal weight: 3.9990 chunk 643 optimal weight: 5.9990 chunk 971 optimal weight: 4.9990 chunk 894 optimal weight: 7.9990 chunk 773 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 597 optimal weight: 6.9990 chunk 474 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN O 44 GLN Q 86 GLN R 34 ASN ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN S 58 ASN U 82 GLN V 17 ASN Y 43 ASN d 56 GLN d 61 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 58 HIS h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS r 31 GLN t 80 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.123 150724 Z= 0.470 Angle : 0.904 14.529 225560 Z= 0.455 Chirality : 0.050 0.554 28819 Planarity : 0.008 0.138 12052 Dihedral : 15.503 179.787 59492 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 2.47 % Allowed : 20.43 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.11), residues: 5432 helix: 1.10 (0.12), residues: 1854 sheet: 0.30 (0.16), residues: 1037 loop : -0.84 (0.11), residues: 2541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 998 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 88 residues processed: 1066 average time/residue: 2.3356 time to fit residues: 3481.1560 Evaluate side-chains 1081 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 993 time to evaluate : 5.390 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 62 residues processed: 28 average time/residue: 1.4005 time to fit residues: 71.0992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 614 optimal weight: 4.9990 chunk 823 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 713 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 774 optimal weight: 0.8980 chunk 324 optimal weight: 0.9990 chunk 795 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN K 107 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN O 44 GLN Q 86 GLN R 34 ASN R 37 ASN S 36 ASN S 58 ASN U 82 GLN V 17 ASN Y 43 ASN d 56 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 58 HIS h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS r 31 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135081 restraints weight = 182335.599| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 0.40 r_work: 0.3427 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 150724 Z= 0.231 Angle : 0.686 14.613 225560 Z= 0.363 Chirality : 0.039 0.382 28819 Planarity : 0.006 0.129 12052 Dihedral : 15.206 179.831 59492 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 2.34 % Allowed : 20.69 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5432 helix: 1.44 (0.12), residues: 1847 sheet: 0.45 (0.16), residues: 1027 loop : -0.74 (0.11), residues: 2558 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47974.95 seconds wall clock time: 829 minutes 37.49 seconds (49777.49 seconds total)