Starting phenix.real_space_refine on Mon Nov 20 23:28:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/11_2023/7m4x_23669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/11_2023/7m4x_23669.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/11_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_23669/11_2023/7m4x_23669_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/11_2023/7m4x_23669_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/11_2023/7m4x_23669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/11_2023/7m4x_23669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/11_2023/7m4x_23669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/11_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: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 54.55, per 1000 atoms: 0.39 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: 58.94 Conformation dependent library (CDL) restraints added in 7.3 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 for structures that cannot fit in PDB format. 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: 75.96 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: 276.49 Time building geometry restraints manager: 63.82 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: 77751 35.95 - 71.91: 2423 71.91 - 107.86: 205 107.86 - 143.81: 34 143.81 - 179.77: 74 Dihedral angle restraints: 80487 sinusoidal: 64756 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 80484 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.630 Construct map_model_manager: 0.110 Extract box with map and model: 29.940 Check model and map are aligned: 1.530 Set scattering table: 0.890 Process input model: 589.960 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.400 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: 0.040 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 644.860 ------------------------------------------------------------------------------- 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 : 15.144 179.768 70357 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 : 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 outliers start: 0 outliers final: 0 residues processed: 1172 average time/residue: 2.3641 time to fit residues: 3831.6816 Evaluate side-chains 1042 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1042 time to evaluate : 5.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3587 ------------------------------------------------------------------------------- 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 E 162 ASN 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 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: 0.7183 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 150724 Z= 0.258 Angle : 0.704 16.485 225560 Z= 0.367 Chirality : 0.040 0.428 28819 Planarity : 0.006 0.131 12052 Dihedral : 15.247 179.814 59591 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.28 % Rotamer: Outliers : 3.14 % Allowed : 10.97 % Favored : 85.89 % 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: 1.00 (0.11), residues: 5432 helix: 1.98 (0.12), residues: 1854 sheet: 0.65 (0.16), residues: 1059 loop : -0.29 (0.12), residues: 2519 *********************** 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 1196 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1055 time to evaluate : 6.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 56 residues processed: 1090 average time/residue: 2.3828 time to fit residues: 3620.0586 Evaluate side-chains 1084 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1028 time to evaluate : 5.994 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 20 residues processed: 36 average time/residue: 1.3860 time to fit residues: 88.9185 ------------------------------------------------------------------------------- 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: 9.9990 chunk 736 optimal weight: 5.9990 chunk 602 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 887 optimal weight: 0.7980 chunk 958 optimal weight: 2.9990 chunk 789 optimal weight: 7.9990 chunk 879 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 711 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 HIS C 58 HIS C 153 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN J 29 HIS L 17 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** e 81 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN h 38 ASN i 30 ASN i 48 GLN j 56 HIS ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN t 80 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 150724 Z= 0.362 Angle : 0.814 15.153 225560 Z= 0.419 Chirality : 0.046 0.495 28819 Planarity : 0.007 0.136 12052 Dihedral : 15.557 179.745 59591 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.00 % Rotamer: Outliers : 3.87 % Allowed : 14.15 % Favored : 81.98 % 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: 1.43 (0.12), residues: 1849 sheet: 0.51 (0.16), residues: 1036 loop : -0.55 (0.11), residues: 2547 *********************** 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 1250 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1076 time to evaluate : 6.057 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: 174 outliers final: 91 residues processed: 1139 average time/residue: 2.3217 time to fit residues: 3681.6088 Evaluate side-chains 1129 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1038 time to evaluate : 6.005 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 40 residues processed: 53 average time/residue: 1.4571 time to fit residues: 130.9305 ------------------------------------------------------------------------------- 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: 8.9990 chunk 666 optimal weight: 4.9990 chunk 460 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 423 optimal weight: 7.9990 chunk 595 optimal weight: 4.9990 chunk 890 optimal weight: 6.9990 chunk 942 optimal weight: 1.9990 chunk 465 optimal weight: 2.9990 chunk 843 optimal weight: 0.6980 chunk 253 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 J 29 HIS L 17 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 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN i 48 GLN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 150724 Z= 0.282 Angle : 0.726 17.821 225560 Z= 0.380 Chirality : 0.042 0.452 28819 Planarity : 0.006 0.130 12052 Dihedral : 15.379 179.600 59591 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 3.74 % Allowed : 15.73 % Favored : 80.53 % 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: 0.49 (0.11), residues: 5432 helix: 1.49 (0.12), residues: 1853 sheet: 0.51 (0.16), residues: 1037 loop : -0.60 (0.11), residues: 2542 *********************** 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 1212 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1044 time to evaluate : 6.088 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: 168 outliers final: 93 residues processed: 1115 average time/residue: 2.4026 time to fit residues: 3745.9925 Evaluate side-chains 1101 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1008 time to evaluate : 5.721 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 48 residues processed: 48 average time/residue: 1.5304 time to fit residues: 124.2740 ------------------------------------------------------------------------------- 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: 20.0000 chunk 534 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 701 optimal weight: 7.9990 chunk 388 optimal weight: 40.0000 chunk 804 optimal weight: 0.9980 chunk 651 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 481 optimal weight: 10.0000 chunk 845 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 J 29 HIS 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 W 6 GLN Y 43 ASN Z 4 GLN b 120 GLN c 25 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 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 150724 Z= 0.362 Angle : 0.814 18.202 225560 Z= 0.418 Chirality : 0.046 0.469 28819 Planarity : 0.007 0.135 12052 Dihedral : 15.572 179.748 59591 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 4.12 % Allowed : 16.42 % Favored : 79.46 % 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: 0.29 (0.11), residues: 5432 helix: 1.30 (0.12), residues: 1848 sheet: 0.36 (0.16), residues: 1041 loop : -0.68 (0.11), residues: 2543 *********************** 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 1204 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1019 time to evaluate : 5.326 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: 185 outliers final: 105 residues processed: 1103 average time/residue: 2.3204 time to fit residues: 3568.7822 Evaluate side-chains 1123 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1018 time to evaluate : 5.935 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 55 residues processed: 52 average time/residue: 1.4681 time to fit residues: 130.4679 ------------------------------------------------------------------------------- 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: 6.9990 chunk 848 optimal weight: 0.0470 chunk 186 optimal weight: 6.9990 chunk 553 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 943 optimal weight: 2.9990 chunk 783 optimal weight: 6.9990 chunk 436 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 495 optimal weight: 9.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 114 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN I 63 GLN K 56 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 R 61 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 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 150724 Z= 0.360 Angle : 0.798 16.287 225560 Z= 0.411 Chirality : 0.045 0.435 28819 Planarity : 0.007 0.133 12052 Dihedral : 15.510 179.725 59591 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 4.12 % Allowed : 17.38 % Favored : 78.50 % 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: 0.25 (0.11), residues: 5432 helix: 1.27 (0.12), residues: 1850 sheet: 0.35 (0.16), residues: 1024 loop : -0.71 (0.11), residues: 2558 *********************** 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 1216 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1031 time to evaluate : 6.111 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: 185 outliers final: 113 residues processed: 1110 average time/residue: 2.3728 time to fit residues: 3679.9049 Evaluate side-chains 1126 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1013 time to evaluate : 5.981 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 61 residues processed: 54 average time/residue: 1.4782 time to fit residues: 135.7961 ------------------------------------------------------------------------------- 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: 0.9980 chunk 106 optimal weight: 10.0000 chunk 537 optimal weight: 6.9990 chunk 688 optimal weight: 10.0000 chunk 533 optimal weight: 10.0000 chunk 794 optimal weight: 0.0970 chunk 526 optimal weight: 10.0000 chunk 939 optimal weight: 9.9990 chunk 588 optimal weight: 5.9990 chunk 572 optimal weight: 40.0000 chunk 433 optimal weight: 2.9990 overall best weight: 3.4184 ------------------------------------------------------------------------------- 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** D 63 ASN F 37 ASN 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 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 150724 Z= 0.345 Angle : 0.790 16.165 225560 Z= 0.408 Chirality : 0.045 0.390 28819 Planarity : 0.007 0.133 12052 Dihedral : 15.486 179.877 59591 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 4.12 % Allowed : 17.96 % Favored : 77.93 % 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: 0.22 (0.11), residues: 5432 helix: 1.26 (0.12), residues: 1844 sheet: 0.34 (0.16), residues: 1031 loop : -0.74 (0.11), residues: 2557 *********************** 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 1204 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1019 time to evaluate : 5.682 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: 185 outliers final: 114 residues processed: 1110 average time/residue: 2.4406 time to fit residues: 3790.0648 Evaluate side-chains 1131 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1017 time to evaluate : 6.163 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 67 residues processed: 50 average time/residue: 1.4552 time to fit residues: 125.6121 ------------------------------------------------------------------------------- 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: 50.0000 chunk 561 optimal weight: 0.6980 chunk 283 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 597 optimal weight: 5.9990 chunk 640 optimal weight: 4.9990 chunk 464 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 738 optimal weight: 40.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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** D 63 ASN 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 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN r 31 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 150724 Z= 0.411 Angle : 0.862 18.813 225560 Z= 0.439 Chirality : 0.048 0.430 28819 Planarity : 0.007 0.137 12052 Dihedral : 15.580 179.818 59591 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 3.98 % Allowed : 18.42 % Favored : 77.59 % 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: 0.07 (0.11), residues: 5432 helix: 1.09 (0.12), residues: 1854 sheet: 0.28 (0.16), residues: 1029 loop : -0.80 (0.11), residues: 2549 *********************** 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 1194 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1015 time to evaluate : 5.995 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: 179 outliers final: 105 residues processed: 1105 average time/residue: 2.3028 time to fit residues: 3555.3923 Evaluate side-chains 1112 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1007 time to evaluate : 5.976 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 68 residues processed: 40 average time/residue: 1.2545 time to fit residues: 93.5062 ------------------------------------------------------------------------------- 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: 0.9980 chunk 900 optimal weight: 4.9990 chunk 821 optimal weight: 5.9990 chunk 875 optimal weight: 2.9990 chunk 527 optimal weight: 5.9990 chunk 381 optimal weight: 50.0000 chunk 687 optimal weight: 50.0000 chunk 268 optimal weight: 7.9990 chunk 791 optimal weight: 4.9990 chunk 828 optimal weight: 2.9990 chunk 872 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** D 63 ASN 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 ** 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 ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN j 99 GLN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN r 31 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 150724 Z= 0.342 Angle : 0.782 18.984 225560 Z= 0.404 Chirality : 0.044 0.439 28819 Planarity : 0.007 0.132 12052 Dihedral : 15.443 179.889 59591 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 3.12 % Allowed : 19.51 % 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: 0.17 (0.11), residues: 5432 helix: 1.22 (0.12), residues: 1853 sheet: 0.35 (0.16), residues: 1028 loop : -0.78 (0.11), residues: 2551 *********************** 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 1164 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1024 time to evaluate : 6.064 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: 140 outliers final: 99 residues processed: 1101 average time/residue: 2.3643 time to fit residues: 3628.4921 Evaluate side-chains 1099 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1000 time to evaluate : 6.010 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 69 residues processed: 33 average time/residue: 1.4371 time to fit residues: 84.5413 ------------------------------------------------------------------------------- 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: 10.0000 chunk 926 optimal weight: 2.9990 chunk 565 optimal weight: 0.9980 chunk 439 optimal weight: 2.9990 chunk 643 optimal weight: 4.9990 chunk 971 optimal weight: 3.9990 chunk 894 optimal weight: 0.9990 chunk 773 optimal weight: 0.0470 chunk 80 optimal weight: 7.9990 chunk 597 optimal weight: 5.9990 chunk 474 optimal weight: 0.9980 overall best weight: 1.2082 ------------------------------------------------------------------------------- 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** D 63 ASN 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 ** 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 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 58 HIS ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN r 31 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2087 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= 0.160 Angle : 0.622 14.695 225560 Z= 0.334 Chirality : 0.036 0.435 28819 Planarity : 0.005 0.124 12052 Dihedral : 15.105 179.961 59591 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 2.31 % Allowed : 20.78 % Favored : 76.90 % 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: 0.54 (0.11), residues: 5432 helix: 1.63 (0.12), residues: 1849 sheet: 0.54 (0.16), residues: 1004 loop : -0.64 (0.11), residues: 2579 ********************** 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 1121 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1017 time to evaluate : 6.124 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: 104 outliers final: 75 residues processed: 1088 average time/residue: 2.4185 time to fit residues: 3676.0737 Evaluate side-chains 1084 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1009 time to evaluate : 6.070 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 62 residues processed: 15 average time/residue: 1.5460 time to fit residues: 44.5254 ------------------------------------------------------------------------------- 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: 5.9990 chunk 823 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 713 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 chunk 774 optimal weight: 3.9990 chunk 324 optimal weight: 8.9990 chunk 795 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 30 HIS ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN K 107 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN O 55 ASN Q 86 GLN R 34 ASN S 36 ASN S 58 ASN U 82 GLN V 17 ASN Y 43 ASN 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 ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN r 31 GLN t 80 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133212 restraints weight = 181707.232| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 0.46 r_work: 0.3394 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 150724 Z= 0.398 Angle : 0.830 15.905 225560 Z= 0.423 Chirality : 0.046 0.538 28819 Planarity : 0.007 0.134 12052 Dihedral : 15.394 179.988 59591 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 2.58 % Allowed : 20.65 % Favored : 76.77 % 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: 0.21 (0.11), residues: 5432 helix: 1.25 (0.12), residues: 1853 sheet: 0.38 (0.16), residues: 1026 loop : -0.77 (0.11), residues: 2553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49531.51 seconds wall clock time: 856 minutes 11.99 seconds (51371.99 seconds total)