Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 09:23:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvy_26820/07_2023/7uvy_26820_updated.pdb" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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 4445 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 69725 2.51 5 N 25849 2.21 5 O 38718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 28": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "R GLU 2": "OE1" <-> "OE2" Residue "R GLU 59": "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 "T GLU 17": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 99": "OE1" <-> "OE2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U GLU 66": "OE1" <-> "OE2" Residue "V GLU 70": "OE1" <-> "OE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "X GLU 12": "OE1" <-> "OE2" Residue "X GLU 13": "OE1" <-> "OE2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "Z PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 138": "OE1" <-> "OE2" Residue "b GLU 144": "OE1" <-> "OE2" Residue "b GLU 171": "OE1" <-> "OE2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d GLU 181": "OE1" <-> "OE2" Residue "d GLU 196": "OE1" <-> "OE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e GLU 150": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f GLU 99": "OE1" <-> "OE2" Residue "g GLU 11": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 67": "OE1" <-> "OE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h GLU 68": "OE1" <-> "OE2" Residue "h GLU 74": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 40": "OE1" <-> "OE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i GLU 110": "OE1" <-> "OE2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "l GLU 17": "OE1" <-> "OE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "n GLU 40": "OE1" <-> "OE2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "q GLU 27": "OE1" <-> "OE2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "t GLU 49": "OE1" <-> "OE2" Residue "u GLU 39": "OE1" <-> "OE2" Residue "u GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 138881 Number of models: 1 Model: "" Number of chains: 60 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: 58438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2724, 58438 Classifications: {'RNA': 2724} Modifications used: {'rna2p': 3, 'rna2p_pur': 265, 'rna2p_pyr': 154, 'rna3p': 11, 'rna3p_pur': 1292, 'rna3p_pyr': 998} Link IDs: {'rna2p': 421, 'rna3p': 2302} 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': 115, 'rna2p_pyr': 92, 'rna3p': 8, 'rna3p_pur': 748, 'rna3p_pyr': 564} Link IDs: {'rna2p': 207, 'rna3p': 1320} 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': 1, 'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p': 3, 'rna3p_pur': 30, 'rna3p_pyr': 26} Link IDs: {'rna2p': 17, 'rna3p': 59} 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: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 273 Unusual residues: {' MG': 1, 'OIY': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'OIY:plan-4': 1, 'OIY:plan-1': 3} Unresolved non-hydrogen planarities: 16 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: 12 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: "W" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'OIY': 1} Classifications: {'undetermined': 1} 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: 24 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 11 179.391 109.802 131.705 1.00 59.98 S ATOM 1398 SG CYS 3 14 177.882 111.040 135.018 1.00 59.19 S ATOM 1503 SG CYS 3 27 179.686 113.375 132.574 1.00 59.02 S Time building chain proxies: 47.81, per 1000 atoms: 0.34 Number of scatterers: 138881 At special positions: 0 Unit cell: (226.8, 244.8, 272.16, 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 4445 15.00 Mg 1 11.99 O 38718 8.00 N 25849 7.00 C 69725 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 53.27 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " 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 forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 171 helices and 70 sheets defined 39.5% alpha, 19.4% beta 1500 base pairs and 2281 stacking pairs defined. Time for finding SS restraints: 56.76 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.210A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 31 through 36 removed outlier: 4.787A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 5.553A 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: 5.671A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.649A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.240A 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: 5.006A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.858A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.416A 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: 3.625A 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: 4.126A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.992A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.364A 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: 4.671A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.294A 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: 5.360A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.528A 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 124 through 129 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.866A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.587A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.554A pdb=" N ILE E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 3.677A 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 'E' and resid 15 through 20 Processing helix chain 'F' and resid 4 through 11 removed outlier: 4.782A 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: 4.461A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 4.216A pdb=" N GLY F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.018A 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: 3.846A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.021A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.099A 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: 3.728A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.555A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.526A 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: 3.905A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.623A 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: 3.722A 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: 3.982A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 87 removed outlier: 3.905A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 87' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 4.122A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.834A 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: 3.796A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU M 49 " --> pdb=" O ARG M 45 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.612A 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: 5.269A 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: 3.852A pdb=" N GLN N 6 " --> pdb=" O ASN N 2 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG N 8 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.598A pdb=" N SER N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 removed outlier: 3.561A pdb=" N ALA N 70 " --> pdb=" O ASN N 66 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 3.795A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.659A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.246A 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: 3.706A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.722A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.712A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.913A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.791A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.137A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.997A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.296A 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: 4.165A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.572A 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: 3.523A pdb=" N GLN U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 5.470A 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 58 removed outlier: 3.915A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN U 58 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 2 through 9 removed outlier: 3.788A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 removed outlier: 3.511A pdb=" N ALA X 16 " --> pdb=" O GLU X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 61 removed outlier: 4.935A pdb=" N VAL X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.706A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Y 50 " --> pdb=" O MET Y 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 5.005A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 6.866A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 3.959A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.846A 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 75 through 90 removed outlier: 5.096A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 126 removed outlier: 3.634A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 4.930A pdb=" N THR b 132 " --> pdb=" O PHE b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 150 Processing helix chain 'b' and resid 167 through 172 Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 226 removed outlier: 4.243A pdb=" N GLY b 226 " --> pdb=" O ALA b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.889A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 4.808A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.534A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 Processing helix chain 'c' and resid 108 through 113 removed outlier: 3.964A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.696A 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 removed outlier: 3.665A pdb=" N TYR d 67 " --> pdb=" O VAL d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.206A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.512A 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 removed outlier: 3.839A pdb=" N ARG d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 153 removed outlier: 5.025A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 3.933A pdb=" N GLN d 166 " --> pdb=" O GLU d 162 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG d 167 " --> pdb=" O LEU d 163 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.986A pdb=" N LEU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) Proline residue: d 194 - end of helix No H-bonds generated for 'chain 'd' and resid 189 through 194' Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.363A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.228A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.599A 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 11 through 16 removed outlier: 3.672A pdb=" N SER f 15 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 11 through 16' Processing helix chain 'f' and resid 17 through 33 removed outlier: 3.560A pdb=" N MET f 21 " --> pdb=" O GLN f 17 " (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 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.654A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.684A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 4.061A 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 Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 Processing helix chain 'i' and resid 91 through 100 removed outlier: 4.974A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.589A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.997A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.567A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 77 removed outlier: 4.013A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 3.849A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.744A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.050A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.873A 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: 3.926A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.625A 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: 3.914A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.500A 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 33 removed outlier: 5.199A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.559A pdb=" N ARG n 41 " --> pdb=" O SER n 37 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.739A pdb=" N GLN n 90 " --> pdb=" O ASP n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.548A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.478A 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) removed outlier: 3.809A pdb=" N LYS o 47 " --> pdb=" O PHE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.224A 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: 3.888A pdb=" N GLN r 31 " --> pdb=" O ASP r 27 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 3.762A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.453A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.228A 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 removed outlier: 3.809A pdb=" N LYS t 16 " --> pdb=" O ARG t 12 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix removed outlier: 3.555A pdb=" N GLY t 65 " --> pdb=" O MET t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.896A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 3.854A 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: 4.801A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 21 removed outlier: 6.123A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.115A 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 removed outlier: 5.684A pdb=" N PHE 2 21 " --> pdb=" O VAL 2 49 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 6.810A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER 3 28 " --> pdb=" O SER 3 13 " (cutoff:3.500A) removed outlier: 8.417A 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: 3.665A pdb=" N GLN C 4 " --> pdb=" O LYS C 18 " (cutoff:3.500A) removed outlier: 5.376A 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: 3.734A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.757A 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: 4.082A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.257A 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: 5.276A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.333A 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: 4.166A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.157A 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: 4.900A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 11, first strand: chain 'D' and resid 25 through 29 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.879A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.921A pdb=" N ARG E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA E 86 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.845A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 65 through 69 removed outlier: 6.554A pdb=" N VAL F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS F 87 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 17, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 18, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.159A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 20, first strand: chain 'H' and resid 17 through 20 removed outlier: 4.409A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.729A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.438A 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: 4.205A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.899A 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: 3.731A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 3.868A 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: 6.919A 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: 7.909A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.613A 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 Processing sheet with id= 28, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.676A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.616A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.835A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 2 through 6 Processing sheet with id= 32, first strand: chain 'Q' and resid 18 through 21 removed outlier: 4.147A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.434A 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: 3.840A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 71 through 78 removed outlier: 4.076A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 37, first strand: chain 'S' and resid 28 through 32 removed outlier: 3.592A pdb=" N LYS S 67 " --> pdb=" O GLY S 74 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 38 through 43 removed outlier: 5.504A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'T' and resid 81 through 85 Processing sheet with id= 40, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 41, first strand: chain 'U' and resid 41 through 46 Processing sheet with id= 42, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.456A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 45 through 48 removed outlier: 6.065A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 50 through 54 removed outlier: 7.027A pdb=" N ASN V 50 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.276A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 47, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.160A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 17 through 20 removed outlier: 5.023A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'b' and resid 92 through 95 Processing sheet with id= 50, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.782A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 164 through 170 removed outlier: 6.485A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 142 through 147 removed outlier: 3.677A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU d 180 " --> pdb=" O VAL d 147 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TRP d 172 " --> pdb=" O LYS d 185 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.766A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.818A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 32 through 39 Processing sheet with id= 56, first strand: chain 'f' and resid 38 through 42 removed outlier: 5.543A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.850A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.395A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.418A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'i' and resid 3 through 9 removed outlier: 3.980A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 35 through 38 Processing sheet with id= 62, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.607A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 44 through 53 removed outlier: 8.489A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'k' and resid 41 through 44 removed outlier: 7.231A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.237A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 36 through 41 removed outlier: 5.002A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE l 67 " --> pdb=" O LYS l 51 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.683A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 7 through 12 removed outlier: 5.587A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 30 through 34 removed outlier: 4.717A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN s 56 " --> pdb=" O ASN s 53 " (cutoff:3.500A) 1888 hydrogen bonds defined for protein. 5589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3750 hydrogen bonds 5840 hydrogen bond angles 0 basepair planarities 1500 basepair parallelities 2281 stacking parallelities Total time for adding SS restraints: 235.55 Time building geometry restraints manager: 57.75 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: 13634 1.31 - 1.44: 66521 1.44 - 1.57: 61593 1.57 - 1.70: 8888 1.70 - 1.84: 253 Bond restraints: 150889 Sorted by residual: 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 7.99e+02 bond pdb=" C03 OIY A3002 " pdb=" C04 OIY A3002 " 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 W 101 " pdb=" C04 OIY W 101 " 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 a1604 " pdb=" C04 OIY a1604 " ideal model delta sigma weight residual 2.080 1.517 0.563 2.00e-02 2.50e+03 7.93e+02 bond pdb=" C03 OIY A3001 " pdb=" C04 OIY A3001 " ideal model delta sigma weight residual 2.080 1.518 0.562 2.00e-02 2.50e+03 7.91e+02 ... (remaining 150884 not shown) Histogram of bond angle deviations from ideal: 95.74 - 105.94: 24237 105.94 - 116.15: 107549 116.15 - 126.35: 79940 126.35 - 136.56: 14007 136.56 - 146.76: 4 Bond angle restraints: 225737 Sorted by residual: angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 146.76 -20.53 3.00e+00 1.11e-01 4.68e+01 angle pdb=" CA PRO g 14 " pdb=" N PRO g 14 " pdb=" CD PRO g 14 " ideal model delta sigma weight residual 112.00 103.04 8.96 1.40e+00 5.10e-01 4.10e+01 angle pdb=" C1' OMG A2247 " pdb=" N9 OMG A2247 " pdb=" C4 OMG A2247 " ideal model delta sigma weight residual 108.29 127.23 -18.94 3.00e+00 1.11e-01 3.98e+01 angle pdb=" C1' 2MG a1204 " pdb=" N9 2MG a1204 " pdb=" C8 2MG a1204 " ideal model delta sigma weight residual 110.07 128.70 -18.63 3.00e+00 1.11e-01 3.86e+01 angle pdb=" C1' 2MG a 963 " pdb=" N9 2MG a 963 " pdb=" C8 2MG a 963 " ideal model delta sigma weight residual 110.07 128.57 -18.50 3.00e+00 1.11e-01 3.80e+01 ... (remaining 225732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 77016 35.99 - 71.99: 3016 71.99 - 107.98: 218 107.98 - 143.97: 24 143.97 - 179.97: 60 Dihedral angle restraints: 80334 sinusoidal: 64645 harmonic: 15689 Sorted by residual: dihedral pdb=" O4' C a1375 " pdb=" C1' C a1375 " pdb=" N1 C a1375 " pdb=" C2 C a1375 " ideal model delta sinusoidal sigma weight residual -160.00 18.08 -178.08 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 16.66 -176.66 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 434 " pdb=" C1' C A 434 " pdb=" N1 C A 434 " pdb=" C2 C A 434 " ideal model delta sinusoidal sigma weight residual -160.00 12.76 -172.76 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 80331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 28850 0.383 - 0.765: 20 0.765 - 1.148: 3 1.148 - 1.530: 0 1.530 - 1.913: 1 Chirality restraints: 28874 Sorted by residual: chirality pdb=" C04 OIY A3001 " pdb=" C03 OIY A3001 " pdb=" C05 OIY A3001 " pdb=" N08 OIY A3001 " both_signs ideal model delta sigma weight residual False -2.62 -0.71 -1.91 2.00e-01 2.50e+01 9.15e+01 chirality pdb=" C04 OIY a1604 " pdb=" C03 OIY a1604 " pdb=" C05 OIY a1604 " pdb=" N08 OIY a1604 " both_signs ideal model delta sigma weight residual False -2.62 -1.57 -1.06 2.00e-01 2.50e+01 2.79e+01 chirality pdb=" C04 OIY W 101 " pdb=" C03 OIY W 101 " pdb=" C05 OIY W 101 " pdb=" N08 OIY W 101 " both_signs ideal model delta sigma weight residual False -2.62 -1.76 -0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 28871 not shown) Planarity restraints: 12073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.077 2.00e-02 2.50e+03 6.33e-01 9.01e+03 pdb=" C4' 7MG A2065 " 0.458 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.700 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.684 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.166 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 1.009 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.198 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.998 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 524 " 0.040 2.00e-02 2.50e+03 5.95e-01 7.96e+03 pdb=" C4' 7MG a 524 " 0.447 2.00e-02 2.50e+03 pdb=" O4' 7MG a 524 " 0.691 2.00e-02 2.50e+03 pdb=" C3' 7MG a 524 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 7MG a 524 " -0.600 2.00e-02 2.50e+03 pdb=" C2' 7MG a 524 " -0.206 2.00e-02 2.50e+03 pdb=" O2' 7MG a 524 " 0.927 2.00e-02 2.50e+03 pdb=" C1' 7MG a 524 " 0.213 2.00e-02 2.50e+03 pdb=" N9 7MG a 524 " -0.923 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 5.86e-01 7.71e+03 pdb=" C4' 2MG a1204 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.616 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.609 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.954 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.227 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.891 2.00e-02 2.50e+03 ... (remaining 12070 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 395 2.52 - 3.12: 91823 3.12 - 3.71: 259854 3.71 - 4.31: 390766 4.31 - 4.90: 516293 Nonbonded interactions: 1259131 Sorted by model distance: nonbonded pdb="MG MG A3007 " pdb=" O HOH A3102 " model vdw 1.926 2.170 nonbonded pdb="MG MG A3007 " pdb=" O HOH A3104 " model vdw 1.937 2.170 nonbonded pdb="MG MG A3007 " pdb=" O HOH A3103 " model vdw 1.938 2.170 nonbonded pdb="MG MG A3007 " pdb=" O HOH A3101 " model vdw 1.956 2.170 nonbonded pdb=" OP1 A A1612 " pdb="MG MG A3007 " model vdw 2.039 2.170 ... (remaining 1259126 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: 11.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.630 Construct map_model_manager: 0.140 Extract box with map and model: 56.220 Check model and map are aligned: 1.470 Set scattering table: 0.980 Process input model: 507.960 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 592.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 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 : 0.011 0.565 150889 Z= 0.725 Angle : 0.699 20.530 225737 Z= 0.354 Chirality : 0.044 1.913 28874 Planarity : 0.017 0.633 12073 Dihedral : 15.794 179.968 70228 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.25 % Rotamer Outliers : 2.41 % 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: 0.67 (0.11), residues: 5414 helix: 1.70 (0.12), residues: 1860 sheet: 0.41 (0.15), residues: 1076 loop : -0.46 (0.12), residues: 2478 *********************** 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 985 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 877 time to evaluate : 6.149 Fit side-chains outliers start: 108 outliers final: 80 residues processed: 968 average time/residue: 2.0870 time to fit residues: 2896.1491 Evaluate side-chains 948 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 868 time to evaluate : 6.266 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 74 residues processed: 8 average time/residue: 1.3937 time to fit residues: 24.5343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 821 optimal weight: 2.9990 chunk 737 optimal weight: 7.9990 chunk 409 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 497 optimal weight: 6.9990 chunk 394 optimal weight: 6.9990 chunk 762 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 567 optimal weight: 6.9990 chunk 883 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN D 129 ASN E 141 ASN F 24 ASN I 67 ASN J 89 ASN O 9 GLN S 8 GLN T 38 ASN T 59 GLN W 74 GLN X 44 GLN Y 38 GLN b 91 GLN c 28 GLN c 104 ASN d 159 ASN e 42 ASN f 35 GLN i 35 GLN m 32 ASN p 62 GLN q 31 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.0432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 150889 Z= 0.449 Angle : 0.707 14.746 225737 Z= 0.376 Chirality : 0.045 0.531 28874 Planarity : 0.007 0.143 12073 Dihedral : 14.616 179.792 59489 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.96 % Favored : 96.84 % Rotamer Outliers : 5.71 % 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: 0.61 (0.11), residues: 5414 helix: 1.67 (0.12), residues: 1873 sheet: 0.29 (0.15), residues: 1094 loop : -0.49 (0.12), residues: 2447 *********************** 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 1123 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 867 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 256 outliers final: 137 residues processed: 1017 average time/residue: 2.1100 time to fit residues: 3059.7035 Evaluate side-chains 1002 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 865 time to evaluate : 6.076 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 84 residues processed: 55 average time/residue: 1.2547 time to fit residues: 125.3848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 491 optimal weight: 0.9990 chunk 274 optimal weight: 8.9990 chunk 735 optimal weight: 7.9990 chunk 601 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 885 optimal weight: 6.9990 chunk 956 optimal weight: 6.9990 chunk 788 optimal weight: 1.9990 chunk 877 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 710 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN F 24 ASN H 57 GLN I 67 ASN J 89 ASN O 9 GLN S 8 GLN T 38 ASN T 59 GLN W 74 GLN Y 38 GLN b 91 GLN ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 ASN d 159 ASN e 42 ASN f 35 GLN f 68 GLN i 35 GLN k 49 GLN m 32 ASN p 62 GLN q 31 GLN u 57 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.0498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 150889 Z= 0.366 Angle : 0.662 14.112 225737 Z= 0.356 Chirality : 0.042 0.402 28874 Planarity : 0.006 0.139 12073 Dihedral : 14.517 179.890 59489 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.81 % Favored : 96.99 % Rotamer Outliers : 5.11 % 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: 0.66 (0.11), residues: 5414 helix: 1.75 (0.12), residues: 1873 sheet: 0.31 (0.15), residues: 1094 loop : -0.50 (0.12), residues: 2447 *********************** 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 1120 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 891 time to evaluate : 6.215 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 229 outliers final: 141 residues processed: 1036 average time/residue: 2.1215 time to fit residues: 3141.5038 Evaluate side-chains 1003 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 862 time to evaluate : 6.186 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 98 residues processed: 45 average time/residue: 1.1757 time to fit residues: 101.2405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 874 optimal weight: 6.9990 chunk 665 optimal weight: 7.9990 chunk 459 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 422 optimal weight: 3.9990 chunk 594 optimal weight: 7.9990 chunk 888 optimal weight: 8.9990 chunk 940 optimal weight: 5.9990 chunk 464 optimal weight: 3.9990 chunk 841 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN E 141 ASN F 24 ASN H 57 GLN I 67 ASN J 89 ASN O 9 GLN S 8 GLN T 38 ASN T 59 GLN W 74 GLN Y 38 GLN b 91 GLN b 170 HIS c 28 GLN c 104 ASN ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 ASN e 42 ASN f 35 GLN f 68 GLN i 35 GLN k 49 GLN m 32 ASN p 62 GLN q 31 GLN u 57 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 150889 Z= 0.379 Angle : 0.667 13.951 225737 Z= 0.358 Chirality : 0.042 0.405 28874 Planarity : 0.006 0.139 12073 Dihedral : 14.486 179.829 59489 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.94 % Favored : 96.86 % Rotamer Outliers : 5.64 % 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: 0.66 (0.11), residues: 5414 helix: 1.80 (0.12), residues: 1869 sheet: 0.28 (0.15), residues: 1098 loop : -0.52 (0.12), residues: 2447 *********************** 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 1137 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 884 time to evaluate : 6.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 253 outliers final: 160 residues processed: 1035 average time/residue: 2.1880 time to fit residues: 3236.7344 Evaluate side-chains 1031 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 871 time to evaluate : 6.240 Switching outliers to nearest non-outliers outliers start: 160 outliers final: 104 residues processed: 59 average time/residue: 1.2699 time to fit residues: 135.6576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 783 optimal weight: 0.7980 chunk 533 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 700 optimal weight: 30.0000 chunk 388 optimal weight: 20.0000 chunk 802 optimal weight: 5.9990 chunk 650 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 480 optimal weight: 3.9990 chunk 844 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN F 24 ASN I 67 ASN J 89 ASN O 9 GLN S 8 GLN T 38 ASN T 59 GLN W 74 GLN Y 38 GLN b 91 GLN b 170 HIS c 28 GLN c 104 ASN ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 ASN e 42 ASN f 35 GLN i 35 GLN k 49 GLN m 32 ASN o 40 GLN p 62 GLN u 57 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 150889 Z= 0.319 Angle : 0.646 13.772 225737 Z= 0.349 Chirality : 0.040 0.369 28874 Planarity : 0.006 0.137 12073 Dihedral : 14.473 179.897 59489 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.83 % Favored : 96.97 % Rotamer Outliers : 4.73 % 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: 0.70 (0.11), residues: 5414 helix: 1.85 (0.12), residues: 1869 sheet: 0.28 (0.15), residues: 1098 loop : -0.50 (0.12), residues: 2447 *********************** 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 1092 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 880 time to evaluate : 6.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 153 residues processed: 1025 average time/residue: 2.1939 time to fit residues: 3234.2408 Evaluate side-chains 1026 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 873 time to evaluate : 6.139 Switching outliers to nearest non-outliers outliers start: 153 outliers final: 110 residues processed: 46 average time/residue: 1.2826 time to fit residues: 108.1719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 316 optimal weight: 7.9990 chunk 846 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 552 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 941 optimal weight: 4.9990 chunk 781 optimal weight: 0.2980 chunk 435 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 311 optimal weight: 3.9990 chunk 494 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 4 GLN E 141 ASN F 24 ASN I 67 ASN J 89 ASN O 9 GLN S 8 GLN T 38 ASN W 74 GLN Y 38 GLN b 91 GLN b 170 HIS c 28 GLN c 104 ASN ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 ASN f 35 GLN i 35 GLN m 32 ASN p 62 GLN u 57 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 150889 Z= 0.234 Angle : 0.623 13.504 225737 Z= 0.337 Chirality : 0.038 0.330 28874 Planarity : 0.006 0.133 12073 Dihedral : 14.459 179.923 59489 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.88 % Favored : 96.93 % Rotamer Outliers : 4.50 % 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: 0.77 (0.11), residues: 5414 helix: 1.93 (0.12), residues: 1867 sheet: 0.30 (0.15), residues: 1095 loop : -0.47 (0.12), residues: 2452 *********************** 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 1092 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 890 time to evaluate : 6.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 202 outliers final: 153 residues processed: 1024 average time/residue: 2.1650 time to fit residues: 3216.9439 Evaluate side-chains 1016 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 863 time to evaluate : 6.171 Switching outliers to nearest non-outliers outliers start: 153 outliers final: 113 residues processed: 45 average time/residue: 1.2973 time to fit residues: 105.8045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 907 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 536 optimal weight: 7.9990 chunk 687 optimal weight: 20.0000 chunk 532 optimal weight: 8.9990 chunk 792 optimal weight: 10.0000 chunk 525 optimal weight: 0.9990 chunk 937 optimal weight: 6.9990 chunk 586 optimal weight: 8.9990 chunk 571 optimal weight: 10.0000 chunk 432 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 90 HIS E 141 ASN F 24 ASN I 67 ASN J 89 ASN O 9 GLN P 101 HIS Q 43 ASN S 8 GLN T 38 ASN W 74 GLN Y 38 GLN b 91 GLN b 170 HIS c 28 GLN c 104 ASN c 139 GLN d 159 ASN f 35 GLN f 68 GLN i 35 GLN m 32 ASN p 62 GLN u 57 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.081 150889 Z= 0.407 Angle : 0.682 13.879 225737 Z= 0.364 Chirality : 0.043 0.425 28874 Planarity : 0.006 0.141 12073 Dihedral : 14.466 179.766 59489 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.84 % Rotamer Outliers : 4.46 % 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: 0.65 (0.11), residues: 5414 helix: 1.79 (0.12), residues: 1875 sheet: 0.27 (0.15), residues: 1084 loop : -0.53 (0.12), residues: 2455 *********************** 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 1072 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 872 time to evaluate : 6.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 200 outliers final: 151 residues processed: 1006 average time/residue: 2.1872 time to fit residues: 3145.8368 Evaluate side-chains 1019 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 868 time to evaluate : 6.093 Switching outliers to nearest non-outliers outliers start: 151 outliers final: 112 residues processed: 44 average time/residue: 1.2492 time to fit residues: 101.4334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 580 optimal weight: 0.9980 chunk 374 optimal weight: 6.9990 chunk 560 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 596 optimal weight: 9.9990 chunk 638 optimal weight: 10.0000 chunk 463 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 737 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 4 GLN E 141 ASN F 24 ASN I 67 ASN J 89 ASN O 9 GLN S 8 GLN T 38 ASN T 59 GLN W 74 GLN Y 38 GLN b 91 GLN b 170 HIS c 28 GLN c 104 ASN c 139 GLN d 159 ASN e 42 ASN f 35 GLN f 68 GLN i 35 GLN k 49 GLN m 32 ASN o 40 GLN p 62 GLN u 57 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 150889 Z= 0.380 Angle : 0.671 13.759 225737 Z= 0.360 Chirality : 0.042 0.398 28874 Planarity : 0.006 0.139 12073 Dihedral : 14.457 179.663 59489 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.88 % Favored : 96.92 % Rotamer Outliers : 3.88 % 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: 0.65 (0.11), residues: 5414 helix: 1.78 (0.12), residues: 1875 sheet: 0.27 (0.15), residues: 1085 loop : -0.53 (0.12), residues: 2454 *********************** 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 1045 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 871 time to evaluate : 6.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 174 outliers final: 140 residues processed: 997 average time/residue: 2.1439 time to fit residues: 3065.4371 Evaluate side-chains 998 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 858 time to evaluate : 6.207 Switching outliers to nearest non-outliers outliers start: 140 outliers final: 115 residues processed: 28 average time/residue: 1.3660 time to fit residues: 70.3665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 853 optimal weight: 0.0010 chunk 898 optimal weight: 6.9990 chunk 819 optimal weight: 8.9990 chunk 873 optimal weight: 3.9990 chunk 526 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 686 optimal weight: 50.0000 chunk 268 optimal weight: 6.9990 chunk 789 optimal weight: 0.9990 chunk 826 optimal weight: 0.1980 chunk 870 optimal weight: 5.9990 overall best weight: 2.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN E 141 ASN F 24 ASN I 67 ASN J 89 ASN O 9 GLN Q 43 ASN S 8 GLN T 38 ASN T 59 GLN W 74 GLN Y 38 GLN b 91 GLN b 170 HIS c 28 GLN c 104 ASN ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 ASN e 42 ASN f 35 GLN i 35 GLN m 32 ASN o 40 GLN p 62 GLN u 57 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 150889 Z= 0.196 Angle : 0.612 13.517 225737 Z= 0.333 Chirality : 0.037 0.354 28874 Planarity : 0.006 0.129 12073 Dihedral : 14.429 179.834 59489 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.70 % Favored : 97.10 % Rotamer Outliers : 3.28 % 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: 0.81 (0.11), residues: 5414 helix: 1.96 (0.12), residues: 1869 sheet: 0.34 (0.15), residues: 1074 loop : -0.44 (0.12), residues: 2471 *********************** 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 1035 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 888 time to evaluate : 6.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 126 residues processed: 1004 average time/residue: 2.1438 time to fit residues: 3100.3959 Evaluate side-chains 999 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 873 time to evaluate : 6.200 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 107 residues processed: 21 average time/residue: 1.3471 time to fit residues: 54.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 573 optimal weight: 5.9990 chunk 924 optimal weight: 8.9990 chunk 564 optimal weight: 7.9990 chunk 438 optimal weight: 0.9990 chunk 642 optimal weight: 10.0000 chunk 969 optimal weight: 10.0000 chunk 892 optimal weight: 6.9990 chunk 771 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 596 optimal weight: 10.0000 chunk 473 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN E 141 ASN F 24 ASN I 67 ASN O 9 GLN S 8 GLN T 38 ASN T 59 GLN W 74 GLN Y 38 GLN b 91 GLN b 170 HIS c 28 GLN c 104 ASN d 159 ASN e 42 ASN f 35 GLN f 68 GLN i 35 GLN m 32 ASN p 62 GLN u 57 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 150889 Z= 0.275 Angle : 0.623 13.513 225737 Z= 0.337 Chirality : 0.039 0.334 28874 Planarity : 0.006 0.133 12073 Dihedral : 14.360 179.844 59489 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.92 % Rotamer Outliers : 2.94 % 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: 0.81 (0.11), residues: 5414 helix: 1.98 (0.12), residues: 1861 sheet: 0.30 (0.15), residues: 1099 loop : -0.44 (0.12), residues: 2454 ********************** 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 1006 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 874 time to evaluate : 6.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 120 residues processed: 987 average time/residue: 2.2090 time to fit residues: 3133.1595 Evaluate side-chains 983 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 863 time to evaluate : 6.245 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 107 residues processed: 17 average time/residue: 1.2364 time to fit residues: 43.5138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 613 optimal weight: 7.9990 chunk 822 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 711 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 214 optimal weight: 7.9990 chunk 773 optimal weight: 8.9990 chunk 323 optimal weight: 0.6980 chunk 793 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN E 141 ASN F 24 ASN I 67 ASN J 89 ASN O 9 GLN Q 43 ASN S 8 GLN T 38 ASN T 59 GLN W 74 GLN b 91 GLN b 170 HIS c 28 GLN c 104 ASN d 159 ASN e 42 ASN f 35 GLN f 68 GLN i 35 GLN m 32 ASN o 40 GLN p 62 GLN u 57 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.044957 restraints weight = 295915.983| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 0.93 r_work: 0.2495 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9236 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 150889 Z= 0.375 Angle : 0.665 14.011 225737 Z= 0.357 Chirality : 0.042 0.397 28874 Planarity : 0.006 0.139 12073 Dihedral : 14.384 179.490 59489 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.99 % Favored : 96.79 % Rotamer Outliers : 2.97 % 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: 0.70 (0.11), residues: 5414 helix: 1.86 (0.12), residues: 1872 sheet: 0.28 (0.15), residues: 1089 loop : -0.51 (0.12), residues: 2453 =============================================================================== Job complete usr+sys time: 45716.61 seconds wall clock time: 792 minutes 28.26 seconds (47548.26 seconds total)