Starting phenix.real_space_refine on Tue Mar 19 04:08:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/03_2024/7m4x_23669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/03_2024/7m4x_23669.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/03_2024/7m4x_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_23669/03_2024/7m4x_23669_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/03_2024/7m4x_23669_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/03_2024/7m4x_23669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/03_2024/7m4x_23669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/03_2024/7m4x_23669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4x_23669/03_2024/7m4x_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: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 53.43, per 1000 atoms: 0.38 Number of scatterers: 139446 At special positions: 0 Unit cell: (229.808, 248.464, 274.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 141 16.00 P 4451 15.00 Mg 190 11.99 F 3 9.00 O 39239 8.00 N 25786 7.00 C 69635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 54.27 Conformation dependent library (CDL) restraints added in 6.3 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: 67.29 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: 254.96 Time building geometry restraints manager: 59.07 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' 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 angle pdb=" C1' OMG A2247 " pdb=" N9 OMG A2247 " pdb=" C4 OMG A2247 " ideal model delta sigma weight residual 108.29 125.82 -17.53 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C1' 2MG a 963 " pdb=" N9 2MG a 963 " pdb=" C8 2MG a 963 " ideal model delta sigma weight residual 110.07 127.25 -17.18 3.00e+00 1.11e-01 3.28e+01 ... (remaining 225555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 85318 35.95 - 71.91: 9721 71.91 - 107.86: 1117 107.86 - 143.81: 35 143.81 - 179.77: 74 Dihedral angle restraints: 96265 sinusoidal: 80534 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 96262 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: 7.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.600 Construct map_model_manager: 0.090 Extract box with map and model: 30.270 Check model and map are aligned: 1.520 Set scattering table: 0.950 Process input model: 542.100 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.410 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: 0.030 Load rotamer database and sin/cos tables:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 599.580 ------------------------------------------------------------------------------- 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 : 0.550 20.619 225560 Z= 0.288 Chirality : 0.034 0.403 28819 Planarity : 0.014 0.582 12052 Dihedral : 23.020 179.768 86135 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 83 HIS 0.010 0.001 HIS 2 30 PHE 0.022 0.001 PHE n 42 TYR 0.014 0.001 TYR Q 2 ARG 0.024 0.000 ARG O 92 *********************** 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 : 5.723 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: E 110 GLU cc_start: 0.6904 (tp30) cc_final: 0.6514 (tp30) REVERT: F 13 LYS cc_start: 0.4511 (mmpt) cc_final: 0.3740 (tttp) REVERT: O 91 ARG cc_start: 0.6895 (ttt-90) cc_final: 0.6618 (tmt170) REVERT: g 22 THR cc_start: 0.7481 (m) cc_final: 0.7165 (t) REVERT: l 39 THR cc_start: 0.7683 (p) cc_final: 0.7298 (m) REVERT: s 73 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7994 (mt-10) REVERT: t 29 ARG cc_start: 0.7570 (mtt90) cc_final: 0.7367 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 1172 average time/residue: 2.3142 time to fit residues: 3741.2101 Evaluate side-chains 1043 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1043 time to evaluate : 5.628 ------------------------------------------------------------------------------- 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 114 GLN E 162 ASN 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 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 18 GLN h 38 ASN i 30 ASN i 48 GLN j 56 HIS j 99 GLN k 27 ASN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 48 HIS r 31 GLN t 13 GLN t 82 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 150724 Z= 0.255 Angle : 0.712 15.073 225560 Z= 0.372 Chirality : 0.040 0.427 28819 Planarity : 0.006 0.125 12052 Dihedral : 23.521 179.974 75369 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 3.20 % Allowed : 10.79 % Favored : 86.00 % 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: 0.96 (0.11), residues: 5432 helix: 1.92 (0.12), residues: 1858 sheet: 0.67 (0.16), residues: 1049 loop : -0.31 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 83 HIS 0.017 0.002 HIS M 16 PHE 0.021 0.002 PHE g 26 TYR 0.023 0.002 TYR n 73 ARG 0.009 0.001 ARG i 120 *********************** 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 1207 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1063 time to evaluate : 5.797 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: 0 4 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7964 (mttp) REVERT: 1 29 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: E 110 GLU cc_start: 0.6880 (tp30) cc_final: 0.6454 (tp30) REVERT: F 13 LYS cc_start: 0.4871 (mmpt) cc_final: 0.3869 (tttp) REVERT: F 142 ASP cc_start: 0.5446 (p0) cc_final: 0.4925 (p0) REVERT: J 5 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6522 (tp30) REVERT: K 61 ARG cc_start: 0.8270 (mtp180) cc_final: 0.8032 (mtp180) REVERT: M 43 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: M 69 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7121 (mtm-85) REVERT: M 86 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.6127 (ttp-110) REVERT: N 20 ARG cc_start: 0.6597 (tpp-160) cc_final: 0.6079 (tpp-160) REVERT: O 75 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8125 (ttt180) REVERT: P 15 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7890 (ttpp) REVERT: Q 97 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7860 (tttt) REVERT: R 75 TYR cc_start: 0.8499 (p90) cc_final: 0.8262 (p90) REVERT: b 219 MET cc_start: 0.3695 (ptm) cc_final: 0.3425 (ptm) REVERT: d 72 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7291 (ttt180) REVERT: e 110 MET cc_start: 0.8377 (mtp) cc_final: 0.8075 (mtm) REVERT: g 22 THR cc_start: 0.7561 (m) cc_final: 0.7315 (t) REVERT: g 38 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7796 (mp) REVERT: g 96 ARG cc_start: 0.6903 (mtm-85) cc_final: 0.6701 (mtm110) REVERT: h 3 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7438 (ttp) REVERT: i 97 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: j 16 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7222 (mtm-85) REVERT: m 56 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6742 (mp) outliers start: 144 outliers final: 56 residues processed: 1103 average time/residue: 2.2667 time to fit residues: 3470.3703 Evaluate side-chains 1101 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1031 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain C residue 4 GLN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 5 GLU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain Q residue 97 LYS Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 126 LYS Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 22 LYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 90 ILE Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 63 THR Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain t residue 80 ASN Chi-restraints excluded: chain u residue 34 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 492 optimal weight: 9.9990 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: 0.0010 chunk 958 optimal weight: 2.9990 chunk 789 optimal weight: 1.9990 chunk 879 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 711 optimal weight: 3.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS C 153 GLN I 63 GLN J 29 HIS L 17 ASN O 44 GLN O 55 ASN Q 86 GLN R 34 ASN R 37 ASN S 58 ASN U 82 GLN V 17 ASN c 139 GLN d 56 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 HIS e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN h 38 ASN i 30 ASN i 48 GLN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN o 37 ASN o 75 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 150724 Z= 0.273 Angle : 0.712 14.979 225560 Z= 0.373 Chirality : 0.041 0.424 28819 Planarity : 0.006 0.133 12052 Dihedral : 23.508 179.463 75369 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % Rotamer: Outliers : 3.87 % Allowed : 14.04 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 5432 helix: 1.69 (0.12), residues: 1852 sheet: 0.59 (0.16), residues: 1042 loop : -0.44 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 201 HIS 0.020 0.002 HIS b 96 PHE 0.021 0.002 PHE g 26 TYR 0.020 0.002 TYR i 5 ARG 0.009 0.001 ARG i 120 *********************** 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 1229 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1055 time to evaluate : 5.717 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: 0 4 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8002 (mttp) REVERT: E 110 GLU cc_start: 0.6904 (tp30) cc_final: 0.6387 (tp30) REVERT: F 13 LYS cc_start: 0.4399 (mmpt) cc_final: 0.3982 (tttp) REVERT: F 38 MET cc_start: 0.5000 (mpm) cc_final: 0.3857 (tmt) REVERT: K 61 ARG cc_start: 0.8273 (mtp180) cc_final: 0.8034 (mtp180) REVERT: M 43 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: M 86 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6137 (ttp-110) REVERT: N 16 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7641 (mtt180) REVERT: N 20 ARG cc_start: 0.6599 (tpp-160) cc_final: 0.6172 (tpp-160) REVERT: O 75 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8139 (ttt180) REVERT: P 15 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7979 (tttm) REVERT: R 75 TYR cc_start: 0.8545 (p90) cc_final: 0.8252 (p90) REVERT: S 43 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7121 (tptm) REVERT: T 32 VAL cc_start: 0.8071 (p) cc_final: 0.7851 (t) REVERT: d 71 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: e 110 MET cc_start: 0.8381 (mtp) cc_final: 0.8096 (mtm) REVERT: e 155 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7412 (ptmm) REVERT: g 22 THR cc_start: 0.7566 (m) cc_final: 0.7291 (t) REVERT: g 96 ARG cc_start: 0.6965 (mtm-85) cc_final: 0.6712 (mtm110) REVERT: h 3 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7437 (ttp) REVERT: i 97 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8013 (ttm-80) REVERT: j 16 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7277 (mtm-85) REVERT: m 56 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6755 (mp) REVERT: m 107 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.6944 (mmt180) REVERT: p 19 MET cc_start: 0.7604 (ptm) cc_final: 0.7362 (ptp) REVERT: u 46 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6471 (mttt) outliers start: 174 outliers final: 84 residues processed: 1119 average time/residue: 2.2724 time to fit residues: 3526.6718 Evaluate side-chains 1131 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1033 time to evaluate : 5.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 0 residue 33 LYS Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain C residue 4 GLN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain V residue 72 LYS Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 126 LYS Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 211 MET Chi-restraints excluded: chain d residue 34 LYS Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 22 LYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 90 ILE Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 70 LYS Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 42 MET Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain t residue 80 ASN Chi-restraints excluded: chain u residue 34 LYS Chi-restraints excluded: chain u residue 46 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 876 optimal weight: 3.9990 chunk 666 optimal weight: 4.9990 chunk 460 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 423 optimal weight: 4.9990 chunk 595 optimal weight: 5.9990 chunk 890 optimal weight: 6.9990 chunk 942 optimal weight: 3.9990 chunk 465 optimal weight: 6.9990 chunk 843 optimal weight: 0.5980 chunk 253 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 HIS C 153 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN 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 ** b 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 56 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS t 80 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 150724 Z= 0.372 Angle : 0.819 17.984 225560 Z= 0.420 Chirality : 0.046 0.512 28819 Planarity : 0.007 0.134 12052 Dihedral : 23.594 179.741 75369 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 4.12 % Allowed : 15.31 % Favored : 80.57 % 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: 0.39 (0.11), residues: 5432 helix: 1.37 (0.12), residues: 1856 sheet: 0.46 (0.16), residues: 1027 loop : -0.62 (0.11), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP c 201 HIS 0.013 0.002 HIS M 16 PHE 0.026 0.002 PHE g 26 TYR 0.026 0.003 TYR d 78 ARG 0.011 0.001 ARG m 107 *********************** 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 1244 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1059 time to evaluate : 5.866 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: 0 4 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7964 (mttp) REVERT: C 174 ILE cc_start: 0.5709 (OUTLIER) cc_final: 0.5425 (pp) REVERT: E 110 GLU cc_start: 0.6894 (tp30) cc_final: 0.6325 (tp30) REVERT: E 187 MET cc_start: 0.8101 (ttm) cc_final: 0.7812 (ttm) REVERT: F 10 ASP cc_start: 0.4566 (p0) cc_final: 0.4340 (p0) REVERT: F 13 LYS cc_start: 0.4542 (mmpt) cc_final: 0.4011 (tttp) REVERT: F 132 LEU cc_start: 0.3439 (OUTLIER) cc_final: 0.2786 (tp) REVERT: K 61 ARG cc_start: 0.8277 (mtp180) cc_final: 0.8033 (mtp180) REVERT: M 43 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: M 86 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.6874 (ttp-170) REVERT: N 16 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7678 (mtt180) REVERT: N 20 ARG cc_start: 0.6593 (tpp-160) cc_final: 0.6189 (tpp-160) REVERT: O 75 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8156 (ttt180) REVERT: P 15 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7960 (ttpp) REVERT: R 75 TYR cc_start: 0.8578 (p90) cc_final: 0.8219 (p90) REVERT: S 43 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7132 (tptm) REVERT: T 32 VAL cc_start: 0.8079 (p) cc_final: 0.7871 (t) REVERT: U 69 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7855 (p) REVERT: V 53 MET cc_start: 0.7927 (ttt) cc_final: 0.7641 (ttt) REVERT: e 110 MET cc_start: 0.8414 (mtp) cc_final: 0.8172 (mtm) REVERT: e 155 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7451 (ptmm) REVERT: g 22 THR cc_start: 0.7653 (m) cc_final: 0.7338 (t) REVERT: g 38 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7788 (mp) REVERT: g 96 ARG cc_start: 0.6998 (mtm-85) cc_final: 0.6733 (mtm110) REVERT: h 3 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7513 (ttp) REVERT: h 31 LYS cc_start: 0.7127 (mtmm) cc_final: 0.6885 (pttt) REVERT: i 97 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.8057 (ttm-80) REVERT: j 16 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7340 (mtm-85) REVERT: m 56 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6774 (mp) REVERT: m 107 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7162 (mmt180) REVERT: p 19 MET cc_start: 0.7671 (ptm) cc_final: 0.7448 (ptp) REVERT: t 34 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6381 (mtt90) REVERT: u 46 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6597 (mttm) outliers start: 185 outliers final: 103 residues processed: 1125 average time/residue: 2.3114 time to fit residues: 3590.9298 Evaluate side-chains 1143 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1022 time to evaluate : 5.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 0 residue 33 LYS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain C residue 4 GLN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 126 LYS Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain c residue 211 MET Chi-restraints excluded: chain d residue 34 LYS Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 22 LYS Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 63 THR Chi-restraints excluded: chain h residue 70 LYS Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 98 GLN Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 42 MET Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain u residue 34 LYS Chi-restraints excluded: chain u residue 46 LYS Chi-restraints excluded: chain u residue 49 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 784 optimal weight: 1.9990 chunk 534 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 701 optimal weight: 7.9990 chunk 388 optimal weight: 40.0000 chunk 804 optimal weight: 3.9990 chunk 651 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 481 optimal weight: 10.0000 chunk 845 optimal weight: 0.1980 chunk 237 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** E 40 GLN E 105 GLN I 63 GLN J 29 HIS 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 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** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 150724 Z= 0.173 Angle : 0.635 14.675 225560 Z= 0.340 Chirality : 0.037 0.409 28819 Planarity : 0.005 0.126 12052 Dihedral : 23.405 179.964 75369 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 3.56 % Allowed : 16.91 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.11), residues: 5432 helix: 1.75 (0.12), residues: 1850 sheet: 0.58 (0.16), residues: 1034 loop : -0.53 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP c 201 HIS 0.006 0.001 HIS M 16 PHE 0.019 0.001 PHE u 37 TYR 0.017 0.002 TYR i 59 ARG 0.009 0.000 ARG c 17 *********************** 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 1192 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1032 time to evaluate : 5.816 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: 0 4 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7965 (mttp) REVERT: D 178 LEU cc_start: 0.8180 (mp) cc_final: 0.7875 (mt) REVERT: E 110 GLU cc_start: 0.6810 (tp30) cc_final: 0.6401 (tp30) REVERT: E 113 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6933 (ttm110) REVERT: E 187 MET cc_start: 0.8040 (ttm) cc_final: 0.7769 (ttm) REVERT: F 33 LYS cc_start: 0.7042 (ptpt) cc_final: 0.6836 (ptmm) REVERT: K 61 ARG cc_start: 0.8276 (mtp180) cc_final: 0.8031 (mtp180) REVERT: M 43 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: M 86 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6044 (ttp-110) REVERT: N 20 ARG cc_start: 0.6568 (tpp-160) cc_final: 0.6191 (tpp-160) REVERT: O 75 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8116 (ttt180) REVERT: T 32 VAL cc_start: 0.8018 (p) cc_final: 0.7818 (t) REVERT: V 53 MET cc_start: 0.7799 (ttt) cc_final: 0.7460 (ttt) REVERT: e 110 MET cc_start: 0.8384 (mtp) cc_final: 0.8115 (mtm) REVERT: e 155 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7427 (ptmm) REVERT: g 22 THR cc_start: 0.7529 (m) cc_final: 0.7237 (t) REVERT: g 38 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7710 (mp) REVERT: g 96 ARG cc_start: 0.6956 (mtm-85) cc_final: 0.6691 (mtm110) REVERT: h 3 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7366 (ttp) REVERT: i 97 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7964 (ttm-80) REVERT: j 16 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7217 (mtm-85) REVERT: m 56 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6710 (mp) REVERT: m 107 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6834 (mmt180) REVERT: p 19 MET cc_start: 0.7421 (ptm) cc_final: 0.7216 (ptp) REVERT: u 46 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6455 (mttt) outliers start: 160 outliers final: 89 residues processed: 1096 average time/residue: 2.2878 time to fit residues: 3481.4520 Evaluate side-chains 1132 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1032 time to evaluate : 5.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 33 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain c residue 211 MET Chi-restraints excluded: chain d residue 34 LYS Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 106 ASP Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 63 THR Chi-restraints excluded: chain h residue 70 LYS Chi-restraints excluded: chain h residue 98 GLN Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 42 MET Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain u residue 34 LYS Chi-restraints excluded: chain u residue 46 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 317 optimal weight: 2.9990 chunk 848 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 553 optimal weight: 0.9980 chunk 232 optimal weight: 10.0000 chunk 943 optimal weight: 2.9990 chunk 783 optimal weight: 0.6980 chunk 436 optimal weight: 0.0570 chunk 78 optimal weight: 8.9990 chunk 312 optimal weight: 10.0000 chunk 495 optimal weight: 6.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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** E 105 GLN I 63 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 R 37 ASN S 36 ASN S 58 ASN U 82 GLN V 17 ASN W 6 GLN c 25 ASN c 139 GLN d 56 GLN d 61 GLN e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS r 31 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 150724 Z= 0.167 Angle : 0.615 14.658 225560 Z= 0.329 Chirality : 0.036 0.416 28819 Planarity : 0.005 0.125 12052 Dihedral : 23.341 179.895 75369 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.11 % Rotamer: Outliers : 3.38 % Allowed : 17.78 % Favored : 78.84 % 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: 0.80 (0.11), residues: 5432 helix: 1.88 (0.12), residues: 1847 sheet: 0.62 (0.16), residues: 1027 loop : -0.48 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 201 HIS 0.005 0.001 HIS M 16 PHE 0.021 0.001 PHE u 37 TYR 0.020 0.002 TYR i 59 ARG 0.008 0.000 ARG c 72 *********************** 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 1195 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1043 time to evaluate : 5.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7997 (mttp) REVERT: C 17 GLU cc_start: 0.5478 (OUTLIER) cc_final: 0.5204 (mp0) REVERT: D 178 LEU cc_start: 0.8216 (mp) cc_final: 0.7893 (mt) REVERT: E 110 GLU cc_start: 0.6796 (tp30) cc_final: 0.6417 (tp30) REVERT: E 113 ARG cc_start: 0.7182 (mtm110) cc_final: 0.6924 (ttm110) REVERT: E 187 MET cc_start: 0.8013 (ttm) cc_final: 0.7726 (ttm) REVERT: F 13 LYS cc_start: 0.4375 (mptt) cc_final: 0.3969 (tttp) REVERT: M 43 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: M 86 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.6035 (ttp-110) REVERT: N 16 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7611 (mtt180) REVERT: N 20 ARG cc_start: 0.6551 (tpp-160) cc_final: 0.6173 (tpp-160) REVERT: O 75 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8107 (ttt180) REVERT: R 86 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6913 (ttm) REVERT: e 110 MET cc_start: 0.8382 (mtp) cc_final: 0.8115 (mtm) REVERT: e 155 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7445 (ptmm) REVERT: g 22 THR cc_start: 0.7481 (m) cc_final: 0.7216 (t) REVERT: g 38 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7707 (mp) REVERT: g 96 ARG cc_start: 0.6949 (mtm-85) cc_final: 0.6681 (mtm110) REVERT: i 97 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7966 (ttm-80) REVERT: j 16 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7230 (mtm-85) REVERT: m 56 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6696 (mt) REVERT: p 19 MET cc_start: 0.7420 (ptm) cc_final: 0.7212 (ptp) REVERT: t 3 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8191 (m-40) REVERT: u 46 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6408 (mttt) REVERT: u 47 ARG cc_start: 0.7383 (ttp-110) cc_final: 0.7132 (ttp80) outliers start: 152 outliers final: 87 residues processed: 1107 average time/residue: 2.3032 time to fit residues: 3540.7523 Evaluate side-chains 1130 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1030 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 223 ILE Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 126 LYS Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain c residue 211 MET Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 106 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 63 THR Chi-restraints excluded: chain h residue 98 GLN Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 41 THR Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 42 MET Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain t residue 80 ASN Chi-restraints excluded: chain u residue 34 LYS Chi-restraints excluded: chain u residue 46 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 909 optimal weight: 0.8980 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: 5.9990 chunk 526 optimal weight: 0.9990 chunk 939 optimal weight: 5.9990 chunk 588 optimal weight: 6.9990 chunk 572 optimal weight: 40.0000 chunk 433 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN O 44 GLN Q 11 GLN Q 86 GLN R 34 ASN ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN S 36 ASN S 58 ASN U 82 GLN V 17 ASN c 25 ASN c 139 GLN 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** h 38 ASN h 41 GLN i 30 ASN ** k 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 71 ASN o 75 HIS r 31 GLN t 80 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2117 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= 0.396 Angle : 0.829 14.617 225560 Z= 0.422 Chirality : 0.046 0.462 28819 Planarity : 0.007 0.134 12052 Dihedral : 23.525 179.914 75369 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.67 % Rotamer: Outliers : 4.38 % Allowed : 17.53 % Favored : 78.08 % 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: 0.40 (0.11), residues: 5432 helix: 1.43 (0.12), residues: 1844 sheet: 0.40 (0.16), residues: 1033 loop : -0.63 (0.11), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP c 201 HIS 0.009 0.002 HIS M 16 PHE 0.030 0.003 PHE g 26 TYR 0.028 0.003 TYR d 78 ARG 0.010 0.001 ARG o 63 *********************** 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 1230 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1033 time to evaluate : 5.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7953 (mttp) REVERT: 0 6 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7091 (mtp85) REVERT: C 174 ILE cc_start: 0.5726 (OUTLIER) cc_final: 0.5458 (pp) REVERT: E 110 GLU cc_start: 0.6844 (tp30) cc_final: 0.6366 (tp30) REVERT: E 187 MET cc_start: 0.8102 (ttm) cc_final: 0.7775 (ttm) REVERT: F 13 LYS cc_start: 0.4553 (OUTLIER) cc_final: 0.3939 (tttp) REVERT: F 31 ILE cc_start: 0.4315 (OUTLIER) cc_final: 0.4050 (tp) REVERT: L 1 MET cc_start: 0.6424 (mmm) cc_final: 0.6142 (mtt) REVERT: M 43 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: M 86 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.6869 (ttp-170) REVERT: N 16 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7698 (mtt180) REVERT: N 20 ARG cc_start: 0.6589 (tpp-160) cc_final: 0.6210 (tpp-160) REVERT: O 75 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8136 (ttt180) REVERT: R 75 TYR cc_start: 0.8471 (p90) cc_final: 0.8234 (p90) REVERT: R 86 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7025 (ttm) REVERT: S 44 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7330 (ptpt) REVERT: V 53 MET cc_start: 0.7896 (ttt) cc_final: 0.7560 (ttt) REVERT: e 110 MET cc_start: 0.8418 (mtp) cc_final: 0.8176 (mtm) REVERT: e 155 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7542 (ptmm) REVERT: g 22 THR cc_start: 0.7658 (m) cc_final: 0.7361 (t) REVERT: g 38 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7805 (mp) REVERT: g 96 ARG cc_start: 0.6945 (mtm-85) cc_final: 0.6653 (mtm110) REVERT: h 3 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7485 (ttp) REVERT: i 97 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.8072 (ttm-80) REVERT: j 16 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7360 (mtm-85) REVERT: j 72 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7271 (mmt180) REVERT: l 121 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7355 (ttp80) REVERT: m 56 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6844 (mp) REVERT: m 107 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7166 (mmt180) REVERT: t 34 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6671 (mtt90) REVERT: u 46 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6580 (mttm) outliers start: 197 outliers final: 113 residues processed: 1116 average time/residue: 2.2850 time to fit residues: 3540.6785 Evaluate side-chains 1146 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1012 time to evaluate : 5.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 114 LYS Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 44 LYS Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 223 ILE Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain c residue 211 MET Chi-restraints excluded: chain d residue 34 LYS Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 106 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 63 THR Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 98 GLN Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 41 THR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 42 MET Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 121 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain u residue 34 LYS Chi-restraints excluded: chain u residue 46 LYS Chi-restraints excluded: chain u residue 49 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 581 optimal weight: 10.0000 chunk 375 optimal weight: 30.0000 chunk 561 optimal weight: 7.9990 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: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 c 25 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 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS r 31 GLN t 80 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.137 150724 Z= 0.545 Angle : 0.998 15.951 225560 Z= 0.495 Chirality : 0.055 0.493 28819 Planarity : 0.008 0.141 12052 Dihedral : 23.710 179.904 75369 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.57 % Favored : 96.28 % Rotamer: Outliers : 4.25 % Allowed : 18.56 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 5432 helix: 0.87 (0.12), residues: 1854 sheet: 0.17 (0.15), residues: 1049 loop : -0.84 (0.11), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP c 201 HIS 0.012 0.002 HIS M 16 PHE 0.028 0.003 PHE g 26 TYR 0.035 0.004 TYR d 78 ARG 0.016 0.001 ARG c 17 *********************** 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 1199 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1008 time to evaluate : 5.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7941 (mttp) REVERT: C 174 ILE cc_start: 0.5726 (OUTLIER) cc_final: 0.5464 (pp) REVERT: E 110 GLU cc_start: 0.6874 (tp30) cc_final: 0.6312 (tp30) REVERT: E 187 MET cc_start: 0.8151 (ttm) cc_final: 0.7869 (ttm) REVERT: F 13 LYS cc_start: 0.4676 (OUTLIER) cc_final: 0.3900 (tttp) REVERT: F 23 LYS cc_start: 0.6144 (tptp) cc_final: 0.5598 (tptt) REVERT: F 130 MET cc_start: 0.3875 (OUTLIER) cc_final: 0.2619 (mmt) REVERT: F 136 ILE cc_start: 0.3621 (tp) cc_final: 0.3387 (tt) REVERT: M 43 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: M 86 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6898 (ttp-170) REVERT: N 16 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7838 (mtt180) REVERT: e 110 MET cc_start: 0.8429 (mtp) cc_final: 0.8152 (mtm) REVERT: g 38 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7858 (mt) REVERT: g 96 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.6736 (mtm110) REVERT: h 3 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7521 (ttp) REVERT: h 19 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6153 (tpp) REVERT: j 16 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7377 (mtm-85) REVERT: j 72 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7348 (mmt180) REVERT: l 121 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7291 (ttp80) REVERT: m 56 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6802 (mp) REVERT: m 107 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7194 (mmt180) REVERT: u 46 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6647 (mttm) REVERT: u 47 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.7189 (ttp80) outliers start: 191 outliers final: 115 residues processed: 1088 average time/residue: 2.2735 time to fit residues: 3437.0095 Evaluate side-chains 1127 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 996 time to evaluate : 5.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 114 LYS Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 223 ILE Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 150 LYS Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain c residue 211 MET Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 126 CYS Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 77 LEU Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 106 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 63 THR Chi-restraints excluded: chain h residue 92 LYS Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 41 THR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 42 MET Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 121 ARG Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 66 ARG Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain u residue 46 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 854 optimal weight: 0.5980 chunk 900 optimal weight: 0.5980 chunk 821 optimal weight: 7.9990 chunk 875 optimal weight: 2.9990 chunk 527 optimal weight: 4.9990 chunk 381 optimal weight: 0.0370 chunk 687 optimal weight: 50.0000 chunk 268 optimal weight: 7.9990 chunk 791 optimal weight: 0.9990 chunk 828 optimal weight: 2.9990 chunk 872 optimal weight: 0.5980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 HIS 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 e 96 GLN f 58 HIS f 63 ASN h 38 ASN h 41 GLN i 30 ASN o 37 ASN o 71 ASN o 75 HIS r 31 GLN t 80 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 150724 Z= 0.129 Angle : 0.611 16.426 225560 Z= 0.329 Chirality : 0.036 0.428 28819 Planarity : 0.005 0.121 12052 Dihedral : 23.350 179.733 75369 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.20 % Rotamer: Outliers : 2.63 % Allowed : 20.47 % 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: 0.60 (0.11), residues: 5432 helix: 1.70 (0.12), residues: 1836 sheet: 0.47 (0.16), residues: 1046 loop : -0.57 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 201 HIS 0.006 0.001 HIS s 83 PHE 0.031 0.001 PHE u 37 TYR 0.019 0.001 TYR i 59 ARG 0.009 0.001 ARG c 72 *********************** 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 1140 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1022 time to evaluate : 5.195 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: 0 4 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7988 (mttp) REVERT: 2 53 ASP cc_start: 0.7197 (m-30) cc_final: 0.6815 (m-30) REVERT: C 115 LYS cc_start: 0.6950 (mppt) cc_final: 0.6155 (mmmt) REVERT: E 104 MET cc_start: 0.7892 (mmt) cc_final: 0.7562 (mmt) REVERT: E 110 GLU cc_start: 0.6727 (tp30) cc_final: 0.6372 (tp30) REVERT: E 113 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6925 (ttm110) REVERT: E 187 MET cc_start: 0.8027 (ttm) cc_final: 0.7764 (ttm) REVERT: F 13 LYS cc_start: 0.4545 (OUTLIER) cc_final: 0.3894 (tttp) REVERT: F 23 LYS cc_start: 0.6039 (tptp) cc_final: 0.5623 (tptt) REVERT: F 136 ILE cc_start: 0.3592 (tp) cc_final: 0.3376 (tt) REVERT: I 88 ASN cc_start: 0.8286 (p0) cc_final: 0.8030 (p0) REVERT: M 69 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.7237 (mtm-85) REVERT: M 86 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7908 (ttp-170) REVERT: N 16 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7597 (mtt180) REVERT: O 75 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7124 (ttt180) REVERT: e 67 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6767 (mtt90) REVERT: g 22 THR cc_start: 0.7524 (m) cc_final: 0.7193 (t) REVERT: g 96 ARG cc_start: 0.6971 (mtm-85) cc_final: 0.6699 (mtm110) REVERT: h 3 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7361 (ttp) REVERT: j 16 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7148 (mtm-85) REVERT: l 121 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7201 (ttp80) REVERT: m 107 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6729 (mmt180) outliers start: 118 outliers final: 61 residues processed: 1077 average time/residue: 2.3190 time to fit residues: 3460.7433 Evaluate side-chains 1076 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1006 time to evaluate : 5.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 223 ILE Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain c residue 211 MET Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 106 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 41 THR Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 121 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain q residue 53 VAL Chi-restraints excluded: chain u residue 34 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 575 optimal weight: 8.9990 chunk 926 optimal weight: 5.9990 chunk 565 optimal weight: 10.0000 chunk 439 optimal weight: 7.9990 chunk 643 optimal weight: 5.9990 chunk 971 optimal weight: 4.9990 chunk 894 optimal weight: 6.9990 chunk 773 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 597 optimal weight: 6.9990 chunk 474 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 GLN L 17 ASN M 23 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN O 55 ASN Q 86 GLN R 34 ASN ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN S 58 ASN U 79 GLN U 82 GLN V 17 ASN Y 43 ASN c 139 GLN d 56 GLN d 61 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 58 HIS h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS r 31 GLN t 13 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 150724 Z= 0.415 Angle : 0.853 14.673 225560 Z= 0.432 Chirality : 0.047 0.547 28819 Planarity : 0.007 0.136 12052 Dihedral : 23.483 179.841 75369 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.39 % Rotamer: Outliers : 2.25 % Allowed : 20.89 % Favored : 76.86 % 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: 0.24 (0.11), residues: 5432 helix: 1.30 (0.12), residues: 1836 sheet: 0.31 (0.16), residues: 1051 loop : -0.73 (0.11), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP c 201 HIS 0.011 0.002 HIS M 16 PHE 0.051 0.003 PHE n 42 TYR 0.035 0.003 TYR o 78 ARG 0.013 0.001 ARG C 189 ********************** 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 1100 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 999 time to evaluate : 5.803 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: 0 4 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7956 (mttp) REVERT: C 174 ILE cc_start: 0.5690 (OUTLIER) cc_final: 0.5440 (pp) REVERT: C 187 GLU cc_start: 0.5982 (tm-30) cc_final: 0.5688 (tm-30) REVERT: E 110 GLU cc_start: 0.6774 (tp30) cc_final: 0.6349 (tp30) REVERT: E 187 MET cc_start: 0.8109 (ttm) cc_final: 0.7787 (ttm) REVERT: F 13 LYS cc_start: 0.4618 (OUTLIER) cc_final: 0.3793 (tttp) REVERT: F 23 LYS cc_start: 0.5866 (tptp) cc_final: 0.5633 (tptt) REVERT: M 43 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: M 86 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.6891 (ttp-170) REVERT: N 16 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7803 (mtt180) REVERT: e 110 MET cc_start: 0.8461 (mtp) cc_final: 0.8226 (mtm) REVERT: g 22 THR cc_start: 0.7632 (m) cc_final: 0.7325 (t) REVERT: g 38 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7818 (mp) REVERT: g 96 ARG cc_start: 0.6957 (mtm-85) cc_final: 0.6694 (mtm110) REVERT: h 3 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7487 (ttp) REVERT: j 16 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7396 (mtm-85) REVERT: l 121 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7355 (ttp80) outliers start: 101 outliers final: 73 residues processed: 1049 average time/residue: 2.3232 time to fit residues: 3374.2533 Evaluate side-chains 1070 residues out of total 4494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 987 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 75 ARG Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain V residue 72 LYS Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 223 ILE Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain c residue 211 MET Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 106 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 41 THR Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 121 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 94 SER Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain q residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 614 optimal weight: 4.9990 chunk 823 optimal weight: 0.9980 chunk 236 optimal weight: 8.9990 chunk 713 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 774 optimal weight: 0.7980 chunk 324 optimal weight: 0.1980 chunk 795 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN 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 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 58 HIS h 38 ASN h 41 GLN i 30 ASN k 49 GLN o 37 ASN o 71 ASN o 75 HIS r 31 GLN t 13 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.148027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136573 restraints weight = 183739.195| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 0.39 r_work: 0.3452 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 150724 Z= 0.162 Angle : 0.627 14.726 225560 Z= 0.335 Chirality : 0.037 0.436 28819 Planarity : 0.005 0.124 12052 Dihedral : 23.309 179.930 75369 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.05 % Rotamer: Outliers : 2.29 % Allowed : 21.18 % Favored : 76.52 % 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: 0.56 (0.11), residues: 5432 helix: 1.65 (0.12), residues: 1844 sheet: 0.49 (0.16), residues: 1029 loop : -0.61 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 201 HIS 0.006 0.001 HIS s 83 PHE 0.024 0.002 PHE u 37 TYR 0.024 0.002 TYR o 78 ARG 0.011 0.000 ARG C 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47483.40 seconds wall clock time: 821 minutes 16.83 seconds (49276.83 seconds total)