Starting phenix.real_space_refine on Mon Nov 20 19:56:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvz_26821/11_2023/7uvz_26821_updated.pdb" } resolution = 2.21 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= 0.003 sd= 0.024 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4451 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 69742 2.51 5 N 25855 2.21 5 O 38751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 31": "OE1" <-> "OE2" Residue "0 GLU 47": "OE1" <-> "OE2" Residue "1 GLU 9": "OE1" <-> "OE2" Residue "3 GLU 30": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N GLU 115": "OE1" <-> "OE2" Residue "O GLU 22": "OE1" <-> "OE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 62": "OE1" <-> "OE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U GLU 66": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "W GLU 43": "OE1" <-> "OE2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "X GLU 8": "OE1" <-> "OE2" Residue "X GLU 12": "OE1" <-> "OE2" Residue "X GLU 20": "OE1" <-> "OE2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "b GLU 135": "OE1" <-> "OE2" Residue "b GLU 138": "OE1" <-> "OE2" Residue "b GLU 144": "OE1" <-> "OE2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c GLU 190": "OE1" <-> "OE2" Residue "d GLU 15": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 115": "OE1" <-> "OE2" Residue "d GLU 174": "OE1" <-> "OE2" Residue "d GLU 196": "OE1" <-> "OE2" Residue "d GLU 204": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 150": "OE1" <-> "OE2" Residue "e GLU 161": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f GLU 75": "OE1" <-> "OE2" Residue "f GLU 76": "OE1" <-> "OE2" Residue "f GLU 93": "OE1" <-> "OE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "f GLU 99": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h GLU 68": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m GLU 72": "OE1" <-> "OE2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "n GLU 14": "OE1" <-> "OE2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "q GLU 27": "OE1" <-> "OE2" Residue "q GLU 64": "OE1" <-> "OE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "s GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 138943 Number of models: 1 Model: "" Number of chains: 59 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} 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': 262, 'rna2p_pyr': 154, 'rna3p': 11, 'rna3p_pur': 1298, 'rna3p_pyr': 1001} Link IDs: {'rna2p': 418, 'rna3p': 2311} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 101} 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: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} 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: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 873 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "O" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} 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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 455 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "Z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} 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': 114, 'rna2p_pyr': 91, 'rna3p': 8, 'rna3p_pur': 749, 'rna3p_pyr': 565} Link IDs: {'rna2p': 205, 'rna3p': 1322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 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: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} 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': 2, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 2, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 66} 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: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 260 Unusual residues: {' MG': 1, 'OIY': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'OIY:plan-4': 2, 'OIY:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "N" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'OIY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'OIY:plan-4': 1, 'OIY:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {'OIY': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'OIY:plan-4': 2, 'OIY:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 178.225 122.297 133.937 1.00 60.75 S ATOM 1398 SG CYS 3 14 177.252 123.840 137.291 1.00 59.44 S ATOM 1503 SG CYS 3 27 178.645 126.053 134.495 1.00 59.41 S Time building chain proxies: 55.13, per 1000 atoms: 0.40 Number of scatterers: 138943 At special positions: 0 Unit cell: (224.64, 247.68, 272.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 142 16.00 P 4451 15.00 Mg 1 11.99 O 38751 8.00 N 25855 7.00 C 69742 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: 57.78 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10106 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: 170 helices and 69 sheets defined 39.3% alpha, 18.9% beta 1503 base pairs and 2245 stacking pairs defined. Time for finding SS restraints: 69.30 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.165A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.502A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 36 removed outlier: 4.858A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER 2 36 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 31 through 36' Processing helix chain '2' and resid 37 through 45 removed outlier: 3.814A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.513A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.300A 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: 4.824A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.730A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.640A pdb=" N MET C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.889A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.002A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 4.999A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.558A 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: 5.214A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.547A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.642A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 123 through 129 removed outlier: 4.400A pdb=" N TRP D 128 " --> pdb=" O GLY D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.831A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.605A 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: 3.610A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.587A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Proline residue: E 164 - end of helix Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.744A pdb=" N PHE E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 4 through 11 removed outlier: 4.430A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 21 Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.402A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.659A 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 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: 3.860A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 3.757A 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 49 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.016A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.202A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.716A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.584A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.630A 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: 3.859A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.586A 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: 3.860A 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: 4.263A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 85 removed outlier: 3.971A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 85' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 removed outlier: 3.702A pdb=" N GLY K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.768A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.949A 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 37 through 57 removed outlier: 3.829A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 3.524A pdb=" N LYS M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 4.861A 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: 3.753A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 2 through 23 removed outlier: 4.389A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.552A 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: 3.699A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.633A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.297A 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: 3.669A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.750A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.823A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.933A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.963A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.224A 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: 4.195A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.642A 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: 4.176A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.539A 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: 3.662A pdb=" N GLN U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 12 through 17' Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 57 removed outlier: 4.211A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 removed outlier: 4.103A pdb=" N GLU U 62 " --> pdb=" O ASN U 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 removed outlier: 3.597A pdb=" N GLY W 75 " --> pdb=" O LEU W 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 10 removed outlier: 3.901A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 removed outlier: 3.505A pdb=" N ASP X 19 " --> pdb=" O LYS X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 61 removed outlier: 4.347A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA X 51 " --> pdb=" O ARG X 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.624A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 4.896A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 6.779A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 34 removed outlier: 4.321A pdb=" N ARG b 30 " --> pdb=" O ASN b 26 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLN b 31 " --> pdb=" O PRO b 27 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N TYR b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.853A 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: 4.094A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 150 removed outlier: 3.713A pdb=" N SER b 149 " --> pdb=" O LYS b 145 " (cutoff:3.500A) 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: 4.709A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 156 removed outlier: 4.099A pdb=" N LYS b 154 " --> pdb=" O GLY b 151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN b 155 " --> pdb=" O GLY b 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.715A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 4.559A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.742A 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: 3.537A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.832A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 3.948A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.762A 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 removed outlier: 3.685A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.533A pdb=" N GLY c 145 " --> pdb=" O THR c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.536A 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: 4.976A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.677A 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: 5.348A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 4.645A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 Proline residue: d 194 - end of helix Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.041A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS d 208 " --> pdb=" O GLU d 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.152A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.612A 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: 4.000A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 5.325A 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: 3.575A pdb=" N LYS g 55 " --> pdb=" O GLN g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.714A pdb=" N ASP g 106 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA g 107 " --> pdb=" O TRP g 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA g 108 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N SER g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.728A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 4.652A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) 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 removed outlier: 3.869A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.637A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 100 Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.128A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.686A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.335A 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 58 through 77 removed outlier: 3.689A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.013A 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: 4.769A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.322A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.531A 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 44 through 49 removed outlier: 4.025A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASP m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.792A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.131A 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 21 Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.517A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.527A pdb=" N GLN n 90 " --> pdb=" O ASP n 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY n 91 " --> pdb=" O THR n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 57 Proline residue: n 57 - end of helix Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 4.416A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.903A 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: 3.751A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.636A 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 Processing helix chain 's' and resid 70 through 76 removed outlier: 4.581A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.255A 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 42 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: 3.809A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.039A 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: 4.762A 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: 5.938A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.067A 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 1 through 5 removed outlier: 6.545A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.280A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.874A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.011A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.305A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.184A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.491A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.789A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.037A 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: 4.978A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.647A 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 'D' and resid 108 through 111 removed outlier: 4.519A pdb=" N GLN D 108 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 1 through 4 Processing sheet with id= 14, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.938A pdb=" N ARG E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA E 86 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.613A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.482A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ARG F 150 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 18, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 19, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.383A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 21, first strand: chain 'H' and resid 17 through 20 removed outlier: 4.336A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.466A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.200A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.610A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS L 101 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 74 through 77 removed outlier: 6.862A pdb=" N ILE L 74 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 31 through 37 removed outlier: 7.942A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 33 through 36 removed outlier: 4.863A pdb=" N ARG M 103 " --> pdb=" O ALA M 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL M 113 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL M 97 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU M 115 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 50 through 53 Processing sheet with id= 29, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.812A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.853A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 11 through 15 removed outlier: 3.933A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN Q 46 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.097A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'Q' and resid 65 through 69 removed outlier: 3.710A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 36, first strand: chain 'S' and resid 27 through 32 removed outlier: 6.472A pdb=" N GLY S 27 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 81 through 85 Processing sheet with id= 38, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 39, first strand: chain 'U' and resid 41 through 46 removed outlier: 3.504A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.486A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 29 through 32 removed outlier: 4.670A pdb=" N GLN V 29 " --> pdb=" O VAL V 67 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.428A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.293A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 45, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.198A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 28 through 31 removed outlier: 3.971A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 17 through 20 removed outlier: 4.740A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 69 through 73 Processing sheet with id= 49, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.693A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 164 through 170 removed outlier: 6.112A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'd' and resid 142 through 146 removed outlier: 3.640A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N TRP d 172 " --> pdb=" O LYS d 185 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.736A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.842A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 32 through 39 Processing sheet with id= 55, first strand: chain 'f' and resid 38 through 42 removed outlier: 6.193A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.817A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.411A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.568A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 3 through 9 removed outlier: 3.719A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 35 through 38 removed outlier: 3.563A pdb=" N GLN j 35 " --> pdb=" O VAL j 77 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.666A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 63, first strand: chain 'k' and resid 28 through 35 removed outlier: 3.864A pdb=" N ASN k 28 " --> pdb=" O SER k 25 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.205A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 36 through 41 removed outlier: 5.030A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.640A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 7 through 12 removed outlier: 5.770A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 's' and resid 47 through 52 removed outlier: 4.284A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1864 hydrogen bonds defined for protein. 5508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3754 hydrogen bonds 5870 hydrogen bond angles 0 basepair planarities 1503 basepair parallelities 2245 stacking parallelities Total time for adding SS restraints: 210.97 Time building geometry restraints manager: 62.15 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: 13135 1.31 - 1.43: 67026 1.43 - 1.56: 61645 1.56 - 1.69: 8905 1.69 - 1.82: 253 Bond restraints: 150964 Sorted by residual: bond pdb=" C03 OIY A3003 " pdb=" C04 OIY A3003 " ideal model delta sigma weight residual 2.080 1.514 0.566 2.00e-02 2.50e+03 8.01e+02 bond pdb=" C03 OIY a1601 " pdb=" C04 OIY a1601 " ideal model delta sigma weight residual 2.080 1.515 0.565 2.00e-02 2.50e+03 7.97e+02 bond pdb=" C03 OIY A3004 " pdb=" C04 OIY A3004 " ideal model delta sigma weight residual 2.080 1.516 0.564 2.00e-02 2.50e+03 7.96e+02 bond pdb=" C03 OIY a1602 " pdb=" C04 OIY a1602 " ideal model delta sigma weight residual 2.080 1.518 0.562 2.00e-02 2.50e+03 7.89e+02 bond pdb=" C03 OIY A3002 " pdb=" C04 OIY A3002 " ideal model delta sigma weight residual 2.080 1.519 0.561 2.00e-02 2.50e+03 7.87e+02 ... (remaining 150959 not shown) Histogram of bond angle deviations from ideal: 95.49 - 105.72: 22879 105.72 - 115.94: 107877 115.94 - 126.16: 80257 126.16 - 136.38: 14853 136.38 - 146.60: 4 Bond angle restraints: 225870 Sorted by residual: angle pdb=" O3' C a1051 " pdb=" C3' C a1051 " pdb=" C2' C a1051 " ideal model delta sigma weight residual 109.50 121.02 -11.52 1.50e+00 4.44e-01 5.90e+01 angle pdb=" CG ARG b 115 " pdb=" CD ARG b 115 " pdb=" NE ARG b 115 " ideal model delta sigma weight residual 112.00 95.49 16.51 2.20e+00 2.07e-01 5.63e+01 angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 146.60 -20.37 3.00e+00 1.11e-01 4.61e+01 angle pdb=" C1' OMG A2247 " pdb=" N9 OMG A2247 " pdb=" C4 OMG A2247 " ideal model delta sigma weight residual 108.29 126.87 -18.58 3.00e+00 1.11e-01 3.84e+01 angle pdb=" N LYS u 20 " pdb=" CA LYS u 20 " pdb=" CB LYS u 20 " ideal model delta sigma weight residual 110.30 119.82 -9.52 1.54e+00 4.22e-01 3.82e+01 ... (remaining 225865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 77399 35.98 - 71.96: 2909 71.96 - 107.94: 217 107.94 - 143.91: 37 143.91 - 179.89: 64 Dihedral angle restraints: 80626 sinusoidal: 64937 harmonic: 15689 Sorted by residual: dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual -160.00 19.14 -179.14 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 17.88 -177.88 1 1.50e+01 4.44e-03 8.53e+01 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 -160.00 17.12 -177.12 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 80623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 28857 0.252 - 0.503: 19 0.503 - 0.755: 13 0.755 - 1.007: 1 1.007 - 1.258: 1 Chirality restraints: 28891 Sorted by residual: chirality pdb=" C04 OIY A3003 " pdb=" C03 OIY A3003 " pdb=" C05 OIY A3003 " pdb=" N08 OIY A3003 " both_signs ideal model delta sigma weight residual False -2.62 -1.37 -1.26 2.00e-01 2.50e+01 3.96e+01 chirality pdb=" C04 OIY A3004 " pdb=" C03 OIY A3004 " pdb=" C05 OIY A3004 " pdb=" N08 OIY A3004 " both_signs ideal model delta sigma weight residual False -2.62 -1.80 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C04 OIY a1601 " pdb=" C03 OIY a1601 " pdb=" C05 OIY a1601 " pdb=" N08 OIY a1601 " both_signs ideal model delta sigma weight residual False -2.62 -1.88 -0.75 2.00e-01 2.50e+01 1.40e+01 ... (remaining 28888 not shown) Planarity restraints: 12072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.064 2.00e-02 2.50e+03 6.19e-01 8.63e+03 pdb=" C4' 7MG A2065 " 0.455 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.705 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.649 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.184 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 0.973 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.203 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.974 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2441 " -0.040 2.00e-02 2.50e+03 5.85e-01 7.69e+03 pdb=" C4' 2MG A2441 " -0.440 2.00e-02 2.50e+03 pdb=" O4' 2MG A2441 " -0.664 2.00e-02 2.50e+03 pdb=" C3' 2MG A2441 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG A2441 " 0.588 2.00e-02 2.50e+03 pdb=" C2' 2MG A2441 " 0.208 2.00e-02 2.50e+03 pdb=" O2' 2MG A2441 " -0.923 2.00e-02 2.50e+03 pdb=" C1' 2MG A2441 " -0.218 2.00e-02 2.50e+03 pdb=" N9 2MG A2441 " 0.896 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.054 2.00e-02 2.50e+03 5.85e-01 7.69e+03 pdb=" C4' 2MG a1204 " 0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.616 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.597 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.608 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.189 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.953 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.227 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.887 2.00e-02 2.50e+03 ... (remaining 12069 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 286 2.48 - 3.09: 84652 3.09 - 3.69: 256749 3.69 - 4.30: 395165 4.30 - 4.90: 524382 Nonbonded interactions: 1261234 Sorted by model distance: nonbonded pdb=" O GLN b 111 " pdb=" NH1 ARG b 115 " model vdw 1.876 2.520 nonbonded pdb="MG MG A3007 " pdb=" O HOH A3103 " model vdw 1.939 2.170 nonbonded pdb="MG MG A3007 " pdb=" O HOH A3102 " model vdw 1.973 2.170 nonbonded pdb="MG MG A3007 " pdb=" O HOH A3101 " model vdw 2.032 2.170 nonbonded pdb="MG MG A3007 " pdb=" O HOH A3104 " model vdw 2.045 2.170 ... (remaining 1261229 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: 17.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.660 Construct map_model_manager: 0.140 Extract box with map and model: 53.730 Check model and map are aligned: 1.640 Set scattering table: 1.000 Process input model: 515.930 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.390 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 608.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 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 : 0.010 0.566 150964 Z= 0.664 Angle : 0.650 20.370 225870 Z= 0.328 Chirality : 0.041 1.258 28891 Planarity : 0.017 0.619 12072 Dihedral : 15.677 179.893 70520 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.14 % Favored : 97.69 % Rotamer: Outliers : 2.03 % Allowed : 22.54 % Favored : 75.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.11), residues: 5414 helix: 1.82 (0.12), residues: 1864 sheet: 0.46 (0.16), residues: 1021 loop : -0.17 (0.12), residues: 2529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 866 time to evaluate : 6.139 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 66 residues processed: 945 average time/residue: 2.2015 time to fit residues: 2942.3573 Evaluate side-chains 913 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 847 time to evaluate : 6.200 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 64 residues processed: 3 average time/residue: 1.0437 time to fit residues: 12.4455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 822 optimal weight: 2.9990 chunk 738 optimal weight: 30.0000 chunk 409 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 497 optimal weight: 6.9990 chunk 394 optimal weight: 6.9990 chunk 763 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 464 optimal weight: 8.9990 chunk 568 optimal weight: 2.9990 chunk 884 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 1 29 GLN C 163 GLN G 137 ASN N 39 GLN O 13 ASN S 29 GLN T 59 GLN X 22 GLN Z 52 GLN c 3 GLN c 104 ASN e 96 GLN e 137 ASN h 23 GLN h 41 GLN i 48 GLN k 39 ASN l 73 ASN o 62 GLN q 31 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 150964 Z= 0.351 Angle : 0.664 15.548 225870 Z= 0.358 Chirality : 0.041 0.419 28891 Planarity : 0.006 0.136 12072 Dihedral : 14.510 179.884 59781 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.64 % Favored : 97.17 % Rotamer: Outliers : 4.44 % Allowed : 19.64 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.98 (0.11), residues: 5414 helix: 1.87 (0.12), residues: 1874 sheet: 0.48 (0.16), residues: 1036 loop : -0.14 (0.12), residues: 2504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 836 time to evaluate : 6.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 199 outliers final: 115 residues processed: 965 average time/residue: 2.2002 time to fit residues: 3013.0294 Evaluate side-chains 945 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 830 time to evaluate : 5.594 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 82 residues processed: 34 average time/residue: 1.1973 time to fit residues: 74.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 491 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 736 optimal weight: 7.9990 chunk 602 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 886 optimal weight: 0.9990 chunk 957 optimal weight: 9.9990 chunk 789 optimal weight: 7.9990 chunk 878 optimal weight: 8.9990 chunk 302 optimal weight: 0.6980 chunk 710 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 163 GLN C 198 GLN D 129 ASN E 138 ASN G 137 ASN G 143 GLN O 13 ASN S 29 GLN T 59 GLN X 22 GLN Z 52 GLN d 61 GLN e 42 ASN e 96 GLN h 23 GLN h 41 GLN i 48 GLN k 39 ASN l 73 ASN o 62 GLN q 31 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 150964 Z= 0.316 Angle : 0.642 15.722 225870 Z= 0.348 Chirality : 0.040 0.402 28891 Planarity : 0.006 0.138 12072 Dihedral : 14.494 179.970 59781 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.41 % Rotamer: Outliers : 4.15 % Allowed : 19.84 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 1.04 (0.11), residues: 5414 helix: 1.94 (0.12), residues: 1874 sheet: 0.49 (0.16), residues: 1041 loop : -0.13 (0.12), residues: 2499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 844 time to evaluate : 6.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 116 residues processed: 966 average time/residue: 2.1832 time to fit residues: 2991.5322 Evaluate side-chains 945 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 829 time to evaluate : 6.145 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 83 residues processed: 33 average time/residue: 1.2972 time to fit residues: 79.1489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 875 optimal weight: 10.0000 chunk 666 optimal weight: 7.9990 chunk 459 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 422 optimal weight: 6.9990 chunk 595 optimal weight: 6.9990 chunk 889 optimal weight: 10.0000 chunk 941 optimal weight: 0.2980 chunk 464 optimal weight: 6.9990 chunk 842 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 163 GLN E 138 ASN G 137 ASN O 13 ASN S 29 GLN T 59 GLN X 22 GLN Z 52 GLN c 19 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 ASN d 118 GLN e 96 GLN h 23 GLN h 41 GLN k 39 ASN l 73 ASN o 62 GLN q 31 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 150964 Z= 0.415 Angle : 0.690 16.382 225870 Z= 0.371 Chirality : 0.043 0.435 28891 Planarity : 0.006 0.142 12072 Dihedral : 14.551 179.794 59781 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.70 % Favored : 97.12 % Rotamer: Outliers : 4.10 % Allowed : 19.84 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.97 (0.11), residues: 5414 helix: 1.88 (0.12), residues: 1863 sheet: 0.47 (0.16), residues: 1058 loop : -0.16 (0.12), residues: 2493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 838 time to evaluate : 6.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 184 outliers final: 122 residues processed: 958 average time/residue: 2.1606 time to fit residues: 2948.6873 Evaluate side-chains 946 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 824 time to evaluate : 6.182 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 89 residues processed: 33 average time/residue: 1.1601 time to fit residues: 74.8994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 784 optimal weight: 0.0470 chunk 534 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 700 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 803 optimal weight: 10.0000 chunk 650 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 480 optimal weight: 9.9990 chunk 845 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 163 GLN E 138 ASN G 137 ASN O 13 ASN S 2 ASN S 29 GLN T 59 GLN X 22 GLN Z 52 GLN c 28 GLN d 41 GLN e 96 GLN h 23 GLN h 41 GLN i 48 GLN k 39 ASN l 73 ASN o 62 GLN q 31 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 150964 Z= 0.350 Angle : 0.658 16.628 225870 Z= 0.356 Chirality : 0.041 0.413 28891 Planarity : 0.006 0.139 12072 Dihedral : 14.517 179.974 59781 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.48 % Favored : 97.32 % Rotamer: Outliers : 4.08 % Allowed : 20.02 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.11), residues: 5414 helix: 1.92 (0.12), residues: 1871 sheet: 0.50 (0.16), residues: 1047 loop : -0.14 (0.12), residues: 2496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 846 time to evaluate : 6.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 183 outliers final: 118 residues processed: 969 average time/residue: 2.2493 time to fit residues: 3091.1613 Evaluate side-chains 947 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 829 time to evaluate : 6.122 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 90 residues processed: 29 average time/residue: 1.1222 time to fit residues: 65.1743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 316 optimal weight: 5.9990 chunk 847 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 552 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 942 optimal weight: 0.0270 chunk 782 optimal weight: 8.9990 chunk 436 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 494 optimal weight: 3.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 163 GLN G 137 ASN K 125 GLN O 13 ASN S 2 ASN T 59 GLN X 22 GLN X 41 HIS Z 52 GLN c 21 ASN d 41 GLN e 96 GLN h 23 GLN h 41 GLN i 48 GLN k 39 ASN l 73 ASN o 62 GLN q 31 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 150964 Z= 0.308 Angle : 0.644 16.662 225870 Z= 0.350 Chirality : 0.040 0.399 28891 Planarity : 0.006 0.137 12072 Dihedral : 14.507 179.883 59781 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 3.84 % Allowed : 20.69 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.11), residues: 5414 helix: 1.92 (0.12), residues: 1870 sheet: 0.51 (0.16), residues: 1030 loop : -0.14 (0.12), residues: 2514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 835 time to evaluate : 6.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 126 residues processed: 952 average time/residue: 2.2719 time to fit residues: 3068.1391 Evaluate side-chains 951 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 825 time to evaluate : 6.181 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 97 residues processed: 30 average time/residue: 1.1740 time to fit residues: 67.2518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 908 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 536 optimal weight: 2.9990 chunk 688 optimal weight: 20.0000 chunk 533 optimal weight: 10.0000 chunk 793 optimal weight: 0.1980 chunk 526 optimal weight: 2.9990 chunk 938 optimal weight: 7.9990 chunk 587 optimal weight: 7.9990 chunk 572 optimal weight: 0.9990 chunk 433 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 163 GLN F 95 GLN G 137 ASN K 125 GLN O 13 ASN S 2 ASN T 59 GLN X 22 GLN Z 52 GLN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 23 GLN h 41 GLN i 48 GLN k 39 ASN l 73 ASN o 62 GLN q 31 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 150964 Z= 0.190 Angle : 0.613 16.675 225870 Z= 0.335 Chirality : 0.037 0.425 28891 Planarity : 0.006 0.132 12072 Dihedral : 14.500 179.798 59781 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer: Outliers : 3.08 % Allowed : 21.40 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.11), residues: 5414 helix: 2.02 (0.12), residues: 1872 sheet: 0.51 (0.16), residues: 1042 loop : -0.11 (0.12), residues: 2500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 837 time to evaluate : 6.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 110 residues processed: 945 average time/residue: 2.2560 time to fit residues: 3042.7835 Evaluate side-chains 946 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 836 time to evaluate : 6.072 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 95 residues processed: 17 average time/residue: 1.1175 time to fit residues: 39.2709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 580 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 596 optimal weight: 8.9990 chunk 639 optimal weight: 10.0000 chunk 464 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 737 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 163 GLN E 138 ASN G 73 ASN G 137 ASN O 13 ASN S 2 ASN T 59 GLN X 22 GLN Z 52 GLN e 96 GLN h 23 GLN h 41 GLN h 86 GLN i 48 GLN k 39 ASN k 118 ASN l 73 ASN o 62 GLN q 31 GLN t 3 ASN t 20 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.111 150964 Z= 0.636 Angle : 0.802 16.871 225870 Z= 0.419 Chirality : 0.051 0.515 28891 Planarity : 0.007 0.149 12072 Dihedral : 14.653 179.760 59781 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 3.86 % Allowed : 20.67 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 5414 helix: 1.67 (0.12), residues: 1875 sheet: 0.42 (0.16), residues: 1064 loop : -0.24 (0.12), residues: 2475 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 847 time to evaluate : 6.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 119 residues processed: 963 average time/residue: 2.2258 time to fit residues: 3034.7893 Evaluate side-chains 948 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 829 time to evaluate : 6.149 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 94 residues processed: 27 average time/residue: 1.2706 time to fit residues: 65.6050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 853 optimal weight: 3.9990 chunk 899 optimal weight: 8.9990 chunk 820 optimal weight: 0.0980 chunk 874 optimal weight: 1.9990 chunk 526 optimal weight: 4.9990 chunk 381 optimal weight: 9.9990 chunk 686 optimal weight: 10.0000 chunk 268 optimal weight: 0.9990 chunk 790 optimal weight: 7.9990 chunk 827 optimal weight: 0.9990 chunk 871 optimal weight: 10.0000 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 163 GLN E 138 ASN G 137 ASN O 13 ASN S 2 ASN T 59 GLN X 22 GLN Z 52 GLN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN i 48 GLN k 39 ASN k 118 ASN l 73 ASN o 62 GLN t 3 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 150964 Z= 0.169 Angle : 0.598 16.919 225870 Z= 0.326 Chirality : 0.036 0.347 28891 Planarity : 0.005 0.127 12072 Dihedral : 14.448 179.731 59781 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.62 % Rotamer: Outliers : 2.47 % Allowed : 22.21 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.11), residues: 5414 helix: 2.03 (0.12), residues: 1882 sheet: 0.55 (0.16), residues: 1046 loop : -0.11 (0.12), residues: 2486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 862 time to evaluate : 6.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 92 residues processed: 962 average time/residue: 2.2922 time to fit residues: 3140.7638 Evaluate side-chains 925 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 833 time to evaluate : 6.359 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 88 residues processed: 5 average time/residue: 1.3455 time to fit residues: 18.2704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 574 optimal weight: 8.9990 chunk 925 optimal weight: 5.9990 chunk 564 optimal weight: 1.9990 chunk 438 optimal weight: 7.9990 chunk 643 optimal weight: 10.0000 chunk 970 optimal weight: 20.0000 chunk 893 optimal weight: 10.0000 chunk 772 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 596 optimal weight: 8.9990 chunk 473 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 1 29 GLN C 163 GLN G 104 ASN G 137 ASN O 13 ASN S 2 ASN T 59 GLN X 22 GLN Y 38 GLN Z 52 GLN c 21 ASN c 104 ASN h 23 GLN h 41 GLN i 48 GLN k 21 HIS l 73 ASN o 40 GLN o 62 GLN r 36 ASN t 3 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 150964 Z= 0.501 Angle : 0.736 16.867 225870 Z= 0.390 Chirality : 0.046 0.462 28891 Planarity : 0.007 0.145 12072 Dihedral : 14.539 179.947 59781 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 2.54 % Allowed : 22.61 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.11), residues: 5414 helix: 1.80 (0.12), residues: 1882 sheet: 0.49 (0.16), residues: 1058 loop : -0.19 (0.12), residues: 2474 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 832 time to evaluate : 6.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 99 residues processed: 931 average time/residue: 2.3639 time to fit residues: 3130.7907 Evaluate side-chains 923 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 824 time to evaluate : 6.284 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 90 residues processed: 10 average time/residue: 1.2658 time to fit residues: 28.0753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 613 optimal weight: 6.9990 chunk 823 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 712 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 773 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 794 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 163 GLN E 138 ASN G 137 ASN O 13 ASN S 2 ASN T 59 GLN X 22 GLN Z 52 GLN h 23 GLN h 41 GLN i 48 GLN k 21 HIS k 39 ASN l 73 ASN o 62 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.046862 restraints weight = 252632.699| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 0.86 r_work: 0.2474 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9232 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 150964 Z= 0.354 Angle : 0.678 16.884 225870 Z= 0.366 Chirality : 0.041 0.418 28891 Planarity : 0.006 0.140 12072 Dihedral : 14.532 179.931 59781 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.21 % Rotamer: Outliers : 2.45 % Allowed : 22.74 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.11), residues: 5414 helix: 1.81 (0.12), residues: 1881 sheet: 0.51 (0.16), residues: 1047 loop : -0.19 (0.12), residues: 2486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48272.27 seconds wall clock time: 835 minutes 50.76 seconds (50150.76 seconds total)