Starting phenix.real_space_refine on Sun Mar 17 13:53:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvx_26819/03_2024/7uvx_26819_updated.pdb" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.036 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4357 5.49 5 S 141 5.16 5 C 68580 2.51 5 N 25397 2.21 5 O 37994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 31": "OE1" <-> "OE2" Residue "1 GLU 9": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "K GLU 145": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N GLU 115": "OE1" <-> "OE2" Residue "O GLU 22": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "O TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "T GLU 99": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U GLU 50": "OE1" <-> "OE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U GLU 66": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "X GLU 42": "OE1" <-> "OE2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "b GLU 138": "OE1" <-> "OE2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c GLU 190": "OE1" <-> "OE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d GLU 71": "OE1" <-> "OE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d GLU 181": "OE1" <-> "OE2" Residue "d GLU 204": "OE1" <-> "OE2" Residue "e GLU 12": "OE1" <-> "OE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 161": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f GLU 75": "OE1" <-> "OE2" Residue "f GLU 76": "OE1" <-> "OE2" Residue "f GLU 99": "OE1" <-> "OE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h GLU 50": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "i GLU 108": "OE1" <-> "OE2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "o GLU 76": "OE1" <-> "OE2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "u GLU 10": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 136470 Number of models: 1 Model: "" Number of chains: 53 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: 58247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2715, 58247 Classifications: {'RNA': 2715} Modifications used: {'rna2p': 3, 'rna2p_pur': 260, 'rna2p_pyr': 156, 'rna3p': 9, 'rna3p_pur': 1292, 'rna3p_pyr': 995} Link IDs: {'rna2p': 418, 'rna3p': 2296} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 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': 9, 'rna2p_pyr': 7, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 99} Chain: "C" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2106 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 254} 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: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 865 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 113} 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: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 640 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} 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': 208, 'rna3p': 1319} 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: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 515 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} 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: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'OI9': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 49.100 110.469 140.857 1.00 62.53 S ATOM 1398 SG CYS 3 14 49.812 111.865 137.425 1.00 60.92 S ATOM 1503 SG CYS 3 27 48.280 114.092 140.028 1.00 60.84 S Time building chain proxies: 51.45, per 1000 atoms: 0.38 Number of scatterers: 136470 At special positions: 0 Unit cell: (231.504, 242.528, 274.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 141 16.00 P 4357 15.00 O 37994 8.00 N 25397 7.00 C 68580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 52.10 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " Number of angles added : 3 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10102 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 170 helices and 72 sheets defined 39.5% alpha, 19.8% beta 1465 base pairs and 2268 stacking pairs defined. Time for finding SS restraints: 67.54 Creating SS restraints... Processing helix chain '0' and resid 22 through 27 Proline residue: 0 27 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.179A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.520A 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: 4.770A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 5.568A 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: 4.070A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.593A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.515A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.911A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.592A 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 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.916A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.084A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 5.130A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.528A 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 'C' and resid 197 through 202 removed outlier: 4.461A pdb=" N ASN C 201 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.157A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.711A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'E' and resid 23 through 39 removed outlier: 4.010A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.478A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.599A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.685A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.741A pdb=" N PHE E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 4 through 21 removed outlier: 4.833A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.376A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.827A pdb=" N ILE F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 4.308A 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: 4.002A 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 removed outlier: 3.764A pdb=" N ARG H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.774A pdb=" N GLU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.086A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 removed outlier: 3.563A pdb=" N ALA I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.769A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.711A 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: 3.554A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 removed outlier: 4.339A pdb=" N ILE J 115 " --> pdb=" O PHE J 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.826A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.860A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 4.073A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 4.057A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLU K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 88' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.851A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 4.086A 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: 3.800A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (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: 3.693A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.659A 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: 3.903A pdb=" N GLN N 6 " --> pdb=" O ASN N 2 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 removed outlier: 3.562A pdb=" N LYS N 72 " --> pdb=" O GLU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 4.161A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.786A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.245A 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: 3.644A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.845A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.944A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.021A 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: 3.889A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.534A 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: 4.248A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.903A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 6.177A 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: 3.554A pdb=" N GLN S 8 " --> pdb=" O GLU S 4 " (cutoff:3.500A) removed outlier: 4.557A 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: 4.145A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 5.163A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.797A 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: 3.923A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 35 Processing helix chain 'X' and resid 39 through 61 removed outlier: 4.931A pdb=" N VAL X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.631A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 4.938A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 15 Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.276A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.740A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 78 through 90 Processing helix chain 'b' and resid 105 through 126 removed outlier: 3.970A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 4.709A 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 227 removed outlier: 4.214A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.754A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 4.703A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.015A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.650A 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: 4.111A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 removed outlier: 3.871A pdb=" N TYR d 67 " --> pdb=" O VAL d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.077A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.829A 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: 3.719A pdb=" N ARG d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 153 removed outlier: 5.369A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 3.611A pdb=" N GLN d 166 " --> pdb=" O GLU d 162 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG d 167 " --> pdb=" O LEU d 163 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.655A 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: 4.811A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.326A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.712A 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 19 removed outlier: 4.938A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 33 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 54 removed outlier: 3.537A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.732A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.619A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 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 38 removed outlier: 4.758A pdb=" N GLY i 38 " --> pdb=" O GLU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.523A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.530A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 5.295A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.057A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.920A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 58 through 77 removed outlier: 3.784A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 3.721A pdb=" N LEU k 99 " --> pdb=" O ALA k 95 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY k 100 " --> pdb=" O VAL k 96 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.669A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.401A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.138A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.802A 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: 3.937A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.417A 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: 5.204A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 52 Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.298A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA o 45 " --> pdb=" O GLY o 41 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS o 47 " --> pdb=" O PHE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.975A 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 removed outlier: 3.537A pdb=" N GLN p 81 " --> pdb=" O HIS p 77 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY p 82 " --> pdb=" O TRP p 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.854A pdb=" N GLN r 31 " --> pdb=" O ASP r 27 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.710A 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 Processing helix chain 's' and resid 70 through 76 removed outlier: 4.626A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.312A 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: 3.602A pdb=" N VAL t 28 " --> pdb=" O LEU t 24 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix removed outlier: 3.779A pdb=" N GLY t 65 " --> pdb=" O MET t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.725A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.072A 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 38 removed outlier: 3.534A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR u 38 " --> pdb=" O LYS u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 21 removed outlier: 5.962A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 6.865A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.869A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 165 through 168 removed outlier: 3.643A pdb=" N GLY C 166 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.055A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.632A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.555A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR D 46 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 9, first strand: chain 'D' and resid 25 through 30 removed outlier: 5.418A pdb=" N SER D 188 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 47 through 52 removed outlier: 4.790A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 1 through 4 Processing sheet with id= 12, first strand: chain 'E' and resid 43 through 46 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.928A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.335A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 40 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 15 through 19 removed outlier: 4.101A pdb=" N GLY G 28 " --> pdb=" O GLY G 31 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 17, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.373A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 19, first strand: chain 'H' and resid 2 through 6 removed outlier: 7.074A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.930A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.226A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.290A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE J 86 " --> pdb=" O ALA J 11 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP J 37 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 68 through 71 removed outlier: 4.036A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 63 through 66 removed outlier: 3.797A pdb=" N LYS J 66 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP J 81 " --> pdb=" O LYS J 66 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 122 through 125 Processing sheet with id= 26, first strand: chain 'L' and resid 38 through 41 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.620A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS L 101 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 74 through 77 removed outlier: 6.878A pdb=" N ILE L 74 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'L' and resid 31 through 37 removed outlier: 8.081A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 33 through 36 Processing sheet with id= 31, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.761A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.889A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.681A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.042A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 17 through 21 removed outlier: 4.239A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 37, first strand: chain 'Q' and resid 71 through 78 removed outlier: 4.253A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 39, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.444A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 80 through 85 removed outlier: 7.477A pdb=" N ARG T 80 " --> pdb=" O LYS T 95 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 42, first strand: chain 'U' and resid 41 through 46 Processing sheet with id= 43, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.525A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 45 through 48 removed outlier: 6.174A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.379A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.585A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 48, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.354A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS Y 5 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'b' and resid 17 through 20 removed outlier: 4.562A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'b' and resid 69 through 73 Processing sheet with id= 51, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.694A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.667A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 142 through 147 removed outlier: 6.833A pdb=" N LEU d 180 " --> pdb=" O VAL d 147 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N TRP d 172 " --> pdb=" O LYS d 185 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 10 through 15 removed outlier: 6.907A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.816A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 32 through 40 removed outlier: 6.477A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.791A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.650A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.512A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.798A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'i' and resid 3 through 9 removed outlier: 4.323A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL i 27 " --> pdb=" O LEU i 61 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 35 through 38 Processing sheet with id= 63, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.754A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'j' and resid 44 through 53 removed outlier: 8.497A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'k' and resid 28 through 35 removed outlier: 4.079A pdb=" N ASN k 28 " --> pdb=" O SER k 25 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'k' and resid 82 through 87 removed outlier: 6.363A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'l' and resid 29 through 34 removed outlier: 4.322A pdb=" N SER l 78 " --> pdb=" O CYS l 34 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'l' and resid 35 through 41 removed outlier: 5.030A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.768A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS p 67 " --> pdb=" O ASN p 58 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 7 through 12 removed outlier: 5.785A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 's' and resid 30 through 34 removed outlier: 4.236A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN s 56 " --> pdb=" O ASN s 53 " (cutoff:3.500A) 1898 hydrogen bonds defined for protein. 5625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3665 hydrogen bonds 5722 hydrogen bond angles 0 basepair planarities 1465 basepair parallelities 2268 stacking parallelities Total time for adding SS restraints: 204.53 Time building geometry restraints manager: 56.81 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: 13101 1.31 - 1.44: 65593 1.44 - 1.56: 60581 1.56 - 1.69: 8709 1.69 - 1.82: 253 Bond restraints: 148237 Sorted by residual: bond pdb=" C22 OI9 W 101 " pdb=" C23 OI9 W 101 " ideal model delta sigma weight residual 2.106 1.525 0.581 2.00e-02 2.50e+03 8.44e+02 bond pdb=" C22 OI9 W 101 " pdb=" C24 OI9 W 101 " ideal model delta sigma weight residual 1.022 1.501 -0.479 2.00e-02 2.50e+03 5.73e+02 bond pdb=" C25 OI9 W 101 " pdb=" N12 OI9 W 101 " ideal model delta sigma weight residual 1.748 1.330 0.418 2.00e-02 2.50e+03 4.37e+02 bond pdb=" C27 OI9 W 101 " pdb=" N13 OI9 W 101 " ideal model delta sigma weight residual 1.906 1.492 0.414 2.00e-02 2.50e+03 4.29e+02 bond pdb=" C4 5MU A1935 " pdb=" C5 5MU A1935 " ideal model delta sigma weight residual 1.802 1.446 0.356 2.00e-02 2.50e+03 3.16e+02 ... (remaining 148232 not shown) Histogram of bond angle deviations from ideal: 96.59 - 106.69: 26538 106.69 - 116.79: 106417 116.79 - 126.89: 77434 126.89 - 136.98: 11320 136.98 - 147.08: 4 Bond angle restraints: 221713 Sorted by residual: angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 147.08 -20.85 3.00e+00 1.11e-01 4.83e+01 angle pdb=" C1' OMG A2247 " pdb=" N9 OMG A2247 " pdb=" C4 OMG A2247 " ideal model delta sigma weight residual 108.29 127.61 -19.32 3.00e+00 1.11e-01 4.15e+01 angle pdb=" C1' 2MG a1204 " pdb=" N9 2MG a1204 " pdb=" C8 2MG a1204 " ideal model delta sigma weight residual 110.07 128.56 -18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" C1' 2MG a 963 " pdb=" N9 2MG a 963 " pdb=" C8 2MG a 963 " ideal model delta sigma weight residual 110.07 128.23 -18.16 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C1' 2MG A2441 " pdb=" N9 2MG A2441 " pdb=" C8 2MG A2441 " ideal model delta sigma weight residual 110.07 127.68 -17.61 3.00e+00 1.11e-01 3.45e+01 ... (remaining 221708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 83883 35.97 - 71.94: 9662 71.94 - 107.91: 1072 107.91 - 143.88: 23 143.88 - 179.85: 58 Dihedral angle restraints: 94698 sinusoidal: 79015 harmonic: 15683 Sorted by residual: dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual -160.00 14.02 -174.02 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U A2473 " pdb=" C1' U A2473 " pdb=" N1 U A2473 " pdb=" C2 U A2473 " ideal model delta sinusoidal sigma weight residual -160.00 6.21 -166.21 1 1.50e+01 4.44e-03 8.41e+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 6.06 -166.06 1 1.50e+01 4.44e-03 8.41e+01 ... (remaining 94695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 28195 0.148 - 0.296: 131 0.296 - 0.445: 4 0.445 - 0.593: 0 0.593 - 0.741: 1 Chirality restraints: 28331 Sorted by residual: chirality pdb=" C24 OI9 W 101 " pdb=" C22 OI9 W 101 " pdb=" C27 OI9 W 101 " pdb=" O04 OI9 W 101 " both_signs ideal model delta sigma weight residual False -1.93 -2.67 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CG LEU F 59 " pdb=" CB LEU F 59 " pdb=" CD1 LEU F 59 " pdb=" CD2 LEU F 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C1' U a 838 " pdb=" O4' U a 838 " pdb=" C2' U a 838 " pdb=" N1 U a 838 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 28328 not shown) Planarity restraints: 11923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " -0.063 2.00e-02 2.50e+03 6.18e-01 8.59e+03 pdb=" C4' 7MG A2065 " -0.452 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " -0.700 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " 0.649 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " 0.184 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " -0.976 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " -0.203 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " 0.967 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 5.87e-01 7.76e+03 pdb=" C4' 2MG a1204 " 0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.625 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.598 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.609 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.190 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.954 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.225 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.893 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2441 " 0.021 2.00e-02 2.50e+03 5.81e-01 7.60e+03 pdb=" C4' 2MG A2441 " 0.443 2.00e-02 2.50e+03 pdb=" O4' 2MG A2441 " 0.711 2.00e-02 2.50e+03 pdb=" C3' 2MG A2441 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG A2441 " -0.555 2.00e-02 2.50e+03 pdb=" C2' 2MG A2441 " -0.230 2.00e-02 2.50e+03 pdb=" O2' 2MG A2441 " 0.886 2.00e-02 2.50e+03 pdb=" C1' 2MG A2441 " 0.209 2.00e-02 2.50e+03 pdb=" N9 2MG A2441 " -0.895 2.00e-02 2.50e+03 ... (remaining 11920 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 7832 2.70 - 3.25: 113651 3.25 - 3.80: 265470 3.80 - 4.35: 357166 4.35 - 4.90: 469022 Nonbonded interactions: 1213141 Sorted by model distance: nonbonded pdb=" O2' U A 533 " pdb=" OD2 ASP P 49 " model vdw 2.144 2.440 nonbonded pdb=" O2' G a 207 " pdb=" O4' G a 208 " model vdw 2.160 2.440 nonbonded pdb=" O MET W 1 " pdb=" OG SER W 2 " model vdw 2.163 2.440 nonbonded pdb=" O2 U A2093 " pdb=" N2 G A2188 " model vdw 2.165 2.496 nonbonded pdb=" O2' C a1144 " pdb=" OH TYR i 5 " model vdw 2.166 2.440 ... (remaining 1213136 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: 8.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.610 Construct map_model_manager: 0.130 Extract box with map and model: 29.750 Check model and map are aligned: 1.370 Set scattering table: 0.840 Process input model: 489.980 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.300 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:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 542.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 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 : 0.005 0.581 148237 Z= 0.316 Angle : 0.614 20.853 221713 Z= 0.325 Chirality : 0.036 0.741 28331 Planarity : 0.015 0.618 11923 Dihedral : 23.014 179.852 84596 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.33 % Favored : 97.47 % Rotamer: Outliers : 2.57 % Allowed : 25.38 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.11), residues: 5412 helix: 1.65 (0.12), residues: 1864 sheet: 0.60 (0.16), residues: 1013 loop : -0.48 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 83 HIS 0.006 0.001 HIS j 15 PHE 0.029 0.001 PHE F 77 TYR 0.021 0.001 TYR b 93 ARG 0.015 0.001 ARG J 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 986 time to evaluate : 5.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 141 ASN cc_start: 0.8316 (t0) cc_final: 0.8029 (t0) REVERT: F 48 LYS cc_start: 0.7226 (mmtm) cc_final: 0.7000 (mmpt) REVERT: G 114 ASP cc_start: 0.8555 (m-30) cc_final: 0.8239 (m-30) REVERT: Y 44 ARG cc_start: 0.8400 (mmt180) cc_final: 0.8080 (mmt180) REVERT: b 45 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7788 (mt) REVERT: d 17 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8211 (p) REVERT: f 73 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: g 68 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8252 (mtmm) REVERT: t 49 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7307 (mp0) outliers start: 115 outliers final: 78 residues processed: 1080 average time/residue: 2.0876 time to fit residues: 3175.2837 Evaluate side-chains 1045 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 963 time to evaluate : 5.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 87 GLN Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain T residue 9 GLN Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain X residue 4 LYS Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 45 LEU Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 179 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 163 ILE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 128 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 45 LEU Chi-restraints excluded: chain q residue 53 VAL Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 49 GLU Chi-restraints excluded: chain t residue 77 SER Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 814 optimal weight: 20.0000 chunk 731 optimal weight: 10.0000 chunk 405 optimal weight: 0.0470 chunk 249 optimal weight: 7.9990 chunk 493 optimal weight: 6.9990 chunk 390 optimal weight: 20.0000 chunk 756 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 459 optimal weight: 0.6980 chunk 562 optimal weight: 0.9990 chunk 876 optimal weight: 6.9990 overall best weight: 3.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 3 20 ASN C 163 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 ASN K 125 GLN N 2 ASN N 39 GLN O 9 GLN O 13 ASN O 44 GLN S 29 GLN S 36 ASN T 38 ASN T 59 GLN X 22 GLN ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 GLN c 88 GLN ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 128 ASN e 96 GLN f 28 GLN h 41 GLN h 86 GLN i 98 GLN k 27 ASN l 111 ASN m 76 ASN o 20 ASN r 54 GLN r 61 GLN t 82 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 148237 Z= 0.246 Angle : 0.616 14.181 221713 Z= 0.333 Chirality : 0.038 0.347 28331 Planarity : 0.006 0.131 11923 Dihedral : 22.916 179.837 73983 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.94 % Favored : 96.86 % Rotamer: Outliers : 5.24 % Allowed : 21.95 % Favored : 72.81 % 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: 0.88 (0.11), residues: 5412 helix: 1.86 (0.12), residues: 1869 sheet: 0.67 (0.16), residues: 1024 loop : -0.40 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 201 HIS 0.006 0.001 HIS j 15 PHE 0.017 0.002 PHE D 121 TYR 0.017 0.002 TYR F 8 ARG 0.010 0.000 ARG b 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 988 time to evaluate : 5.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: 2 59 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8170 (mtp180) REVERT: E 141 ASN cc_start: 0.8325 (t0) cc_final: 0.7913 (t0) REVERT: F 30 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8212 (mtp-110) REVERT: F 38 MET cc_start: 0.6670 (mtm) cc_final: 0.6253 (pmm) REVERT: F 48 LYS cc_start: 0.7325 (mmtm) cc_final: 0.7116 (mmpt) REVERT: F 79 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7045 (pt) REVERT: G 81 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6962 (tm-30) REVERT: K 19 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7485 (ttp-170) REVERT: S 20 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: T 45 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8127 (tptt) REVERT: Z 52 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6776 (tt0) REVERT: e 64 GLU cc_start: 0.7733 (tp30) cc_final: 0.7461 (tp30) REVERT: e 158 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8316 (mptm) REVERT: f 76 GLU cc_start: 0.7521 (pp20) cc_final: 0.7266 (pp20) REVERT: g 53 LYS cc_start: 0.8272 (tptp) cc_final: 0.7901 (tmmt) REVERT: g 68 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8255 (mtmm) REVERT: g 144 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6776 (tmt) REVERT: h 50 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: j 19 ASP cc_start: 0.8030 (m-30) cc_final: 0.7779 (m-30) REVERT: o 64 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8341 (tpm170) REVERT: q 20 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8895 (mttm) REVERT: r 25 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7398 (t0) REVERT: s 20 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7193 (mp0) outliers start: 235 outliers final: 106 residues processed: 1119 average time/residue: 2.1349 time to fit residues: 3352.4787 Evaluate side-chains 1088 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 966 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 GLU Chi-restraints excluded: chain 2 residue 59 ARG Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 28 SER Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 12 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain T residue 9 GLN Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain X residue 39 LYS Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 52 GLN Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 199 ASP Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 227 LYS Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 143 LEU Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 163 ILE Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 68 LYS Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 53 LEU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 112 VAL Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain p residue 95 GLN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 20 LYS Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 38 SER Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 30 LYS Chi-restraints excluded: chain r residue 36 ASN Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 487 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 729 optimal weight: 10.0000 chunk 596 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 877 optimal weight: 5.9990 chunk 948 optimal weight: 7.9990 chunk 781 optimal weight: 20.0000 chunk 870 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 704 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 3 20 ASN C 163 GLN C 243 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 73 ASN G 106 ASN J 110 GLN K 125 GLN N 2 ASN N 39 GLN O 9 GLN O 13 ASN O 44 GLN Q 43 ASN S 29 GLN S 36 ASN T 21 GLN T 38 ASN T 59 GLN U 58 ASN V 50 ASN W 74 GLN X 22 GLN ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 GLN c 88 GLN ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 102 ASN e 96 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN h 41 GLN h 86 GLN i 48 GLN i 98 GLN k 27 ASN l 111 ASN m 76 ASN o 20 ASN o 40 GLN p 62 GLN r 54 GLN r 61 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 148237 Z= 0.516 Angle : 0.774 16.812 221713 Z= 0.403 Chirality : 0.047 0.460 28331 Planarity : 0.007 0.146 11923 Dihedral : 22.962 179.943 73919 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.20 % Favored : 96.56 % Rotamer: Outliers : 5.87 % Allowed : 21.46 % Favored : 72.67 % 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: 0.62 (0.11), residues: 5412 helix: 1.64 (0.12), residues: 1864 sheet: 0.54 (0.16), residues: 1009 loop : -0.55 (0.11), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 201 HIS 0.011 0.002 HIS W 34 PHE 0.027 0.002 PHE D 121 TYR 0.022 0.002 TYR P 32 ARG 0.009 0.001 ARG b 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 971 time to evaluate : 5.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 141 ASN cc_start: 0.8411 (t0) cc_final: 0.7923 (t0) REVERT: F 30 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (mtp-110) REVERT: F 38 MET cc_start: 0.6852 (mtm) cc_final: 0.6137 (pmm) REVERT: F 48 LYS cc_start: 0.7349 (mmtm) cc_final: 0.7113 (mmpt) REVERT: F 127 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7361 (m-40) REVERT: G 81 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7106 (tm-30) REVERT: J 104 ARG cc_start: 0.7134 (mmp80) cc_final: 0.6821 (mmp80) REVERT: K 19 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7563 (ttp-170) REVERT: M 119 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5311 (pp20) REVERT: S 20 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: T 45 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8191 (tptt) REVERT: Z 52 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6868 (tt0) REVERT: b 45 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (mt) REVERT: b 135 GLU cc_start: 0.2943 (OUTLIER) cc_final: 0.2670 (pm20) REVERT: d 17 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8266 (p) REVERT: d 133 ASN cc_start: 0.9099 (p0) cc_final: 0.8895 (p0) REVERT: e 64 GLU cc_start: 0.7730 (tp30) cc_final: 0.7471 (tp30) REVERT: e 158 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8300 (mptm) REVERT: g 68 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8168 (mtmm) REVERT: h 50 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: j 19 ASP cc_start: 0.8170 (m-30) cc_final: 0.7900 (m-30) REVERT: j 88 MET cc_start: 0.8513 (mpp) cc_final: 0.8209 (mmm) REVERT: l 36 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7617 (ttt180) REVERT: l 54 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8170 (ttm110) REVERT: n 51 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8873 (mp) REVERT: o 64 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8288 (tpm170) REVERT: p 81 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8498 (mt0) REVERT: p 97 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8583 (ttmm) outliers start: 263 outliers final: 136 residues processed: 1120 average time/residue: 2.1851 time to fit residues: 3413.2794 Evaluate side-chains 1123 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 968 time to evaluate : 5.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 28 SER Chi-restraints excluded: chain 3 residue 30 GLU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 12 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain T residue 9 GLN Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 39 LYS Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Z residue 23 THR Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 52 GLN Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 10 ASP Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 45 LEU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 135 GLU Chi-restraints excluded: chain b residue 138 GLU Chi-restraints excluded: chain b residue 142 GLU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 199 ASP Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 227 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 143 LEU Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 68 LYS Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 53 LEU Chi-restraints excluded: chain j residue 42 MET Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 112 VAL Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 54 ARG Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain p residue 81 GLN Chi-restraints excluded: chain p residue 95 GLN Chi-restraints excluded: chain p residue 97 LYS Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 12 LYS Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 38 SER Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain r residue 36 ASN Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 37 SER Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.7357 > 50: distance: 68 - 77: 34.060 distance: 77 - 78: 22.979 distance: 77 - 83: 40.750 distance: 78 - 79: 47.090 distance: 78 - 81: 26.195 distance: 79 - 80: 41.009 distance: 79 - 84: 40.455 distance: 81 - 82: 26.176 distance: 82 - 83: 42.532 distance: 85 - 86: 56.418 distance: 85 - 88: 42.137 distance: 86 - 87: 56.491 distance: 88 - 89: 47.389 distance: 89 - 90: 17.473 distance: 89 - 91: 39.999 distance: 92 - 93: 41.628 distance: 93 - 94: 31.341 distance: 93 - 96: 41.713 distance: 94 - 95: 49.526 distance: 94 - 101: 43.074 distance: 96 - 97: 10.728 distance: 97 - 98: 57.192 distance: 98 - 99: 40.384 distance: 99 - 100: 27.853 distance: 101 - 102: 56.472 distance: 101 - 107: 3.072 distance: 102 - 103: 68.598 distance: 102 - 105: 38.972 distance: 103 - 104: 53.549 distance: 103 - 108: 54.151 distance: 105 - 106: 53.055 distance: 106 - 107: 37.201 distance: 108 - 109: 39.116 distance: 109 - 110: 48.867 distance: 109 - 112: 40.036 distance: 110 - 111: 45.750 distance: 110 - 116: 42.401 distance: 111 - 202: 30.197 distance: 112 - 113: 39.156 distance: 113 - 115: 44.916 distance: 116 - 117: 56.978 distance: 117 - 118: 41.449 distance: 118 - 119: 57.516 distance: 118 - 123: 55.599 distance: 120 - 121: 68.791 distance: 120 - 122: 42.649 distance: 123 - 124: 40.228 distance: 123 - 191: 35.086 distance: 124 - 125: 55.528 distance: 124 - 127: 55.520 distance: 125 - 126: 40.881 distance: 125 - 132: 58.005 distance: 126 - 188: 32.108 distance: 127 - 128: 57.864 distance: 128 - 129: 57.606 distance: 129 - 130: 57.785 distance: 129 - 131: 45.459 distance: 132 - 133: 56.182 distance: 133 - 134: 39.966 distance: 133 - 136: 69.155 distance: 134 - 135: 56.575 distance: 134 - 141: 70.290 distance: 136 - 137: 58.044 distance: 137 - 138: 38.835 distance: 138 - 139: 50.852 distance: 139 - 140: 27.338 distance: 141 - 142: 40.017 distance: 141 - 147: 57.328 distance: 142 - 143: 57.211 distance: 142 - 145: 40.434 distance: 143 - 144: 41.075 distance: 143 - 148: 36.026 distance: 145 - 146: 17.233 distance: 146 - 147: 59.868 distance: 148 - 149: 54.309 distance: 149 - 150: 60.566 distance: 149 - 152: 44.036 distance: 150 - 151: 69.681 distance: 150 - 156: 34.426 distance: 152 - 153: 55.780 distance: 153 - 154: 43.638 distance: 153 - 155: 50.038