Starting phenix.real_space_refine on Thu Dec 14 03:42:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syt_25540/12_2023/7syt_25540.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syt_25540/12_2023/7syt_25540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syt_25540/12_2023/7syt_25540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syt_25540/12_2023/7syt_25540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syt_25540/12_2023/7syt_25540.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syt_25540/12_2023/7syt_25540.pdb" } resolution = 4.4 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 1958 5.49 5 S 180 5.16 5 C 43389 2.51 5 N 14905 2.21 5 O 20529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 35": "OE1" <-> "OE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G ASP 175": "OD1" <-> "OD2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H ASP 103": "OD1" <-> "OD2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 164": "OE1" <-> "OE2" Residue "J GLU 191": "OE1" <-> "OE2" Residue "K PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K ASP 64": "OD1" <-> "OD2" Residue "K ASP 67": "OD1" <-> "OD2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 66": "OE1" <-> "OE2" Residue "O ASP 83": "OD1" <-> "OD2" Residue "O ASP 108": "OD1" <-> "OD2" Residue "O PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 119": "OE1" <-> "OE2" Residue "O TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 142": "OE1" <-> "OE2" Residue "P PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "Q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 43": "OE1" <-> "OE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "R TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S ASP 82": "OD1" <-> "OD2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S ASP 110": "OD1" <-> "OD2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U GLU 32": "OE1" <-> "OE2" Residue "U ASP 35": "OD1" <-> "OD2" Residue "U TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 130": "OD1" <-> "OD2" Residue "V GLU 33": "OE1" <-> "OE2" Residue "V ASP 78": "OD1" <-> "OD2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W ASP 76": "OD1" <-> "OD2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 114": "OE1" <-> "OE2" Residue "X PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 19": "OD1" <-> "OD2" Residue "Y GLU 53": "OE1" <-> "OE2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y ASP 98": "OD1" <-> "OD2" Residue "Y ASP 114": "OD1" <-> "OD2" Residue "Z GLU 42": "OE1" <-> "OE2" Residue "Z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 77": "OD1" <-> "OD2" Residue "Z TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 75": "OE1" <-> "OE2" Residue "a GLU 90": "OE1" <-> "OE2" Residue "a TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b ASP 52": "OD1" <-> "OD2" Residue "b GLU 90": "OE1" <-> "OE2" Residue "b PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "e TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 96": "OE1" <-> "OE2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 91": "OD1" <-> "OD2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 260": "OD1" <-> "OD2" Residue "h GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 80962 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 112, 'rna3p_pur': 754, 'rna3p_pyr': 688} Link IDs: {'rna2p': 254, 'rna3p': 1442} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} bond proxies already assigned to first conformer: 1709 Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "i" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 4017 Classifications: {'RNA': 188} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 80, 'rna3p_pyr': 74} Link IDs: {'rna2p': 34, 'rna3p': 153} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69377 SG CYS b 23 93.680 128.997 133.013 1.00 54.01 S ATOM 69398 SG CYS b 26 97.474 129.456 133.851 1.00 58.37 S ATOM 69781 SG CYS b 74 96.246 126.130 134.517 1.00 47.17 S ATOM 69800 SG CYS b 77 96.211 128.273 137.427 1.00 46.87 S Time building chain proxies: 31.84, per 1000 atoms: 0.39 Number of scatterers: 80962 At special positions: 0 Unit cell: (237.5, 196.65, 261.25, 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 180 16.00 P 1958 15.00 O 20529 8.00 N 14905 7.00 C 43389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 141 " - pdb=" SG CYS g 144 " distance=2.03 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: 30.04 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " Number of angles added : 6 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9076 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 58 sheets defined 34.6% alpha, 17.1% beta 525 base pairs and 1050 stacking pairs defined. Time for finding SS restraints: 24.32 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 51 through 68 removed outlier: 4.125A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.856A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 4.469A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 removed outlier: 3.591A pdb=" N VAL B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.606A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 203 " --> pdb=" O ASP B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 203' Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 26 removed outlier: 3.687A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 57 through 62 removed outlier: 4.052A pdb=" N GLY C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 62' Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.567A pdb=" N GLU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.582A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.513A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 90 through 98 removed outlier: 4.436A pdb=" N ILE D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 264 through 277 removed outlier: 5.547A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 55 through 60 removed outlier: 4.081A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 60' Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 110 removed outlier: 3.599A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.710A pdb=" N VAL E 164 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.937A pdb=" N VAL F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.605A pdb=" N LEU G 35 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.683A pdb=" N GLN G 65 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 77 removed outlier: 3.937A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.903A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR G 104 " --> pdb=" O ILE G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.767A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.505A pdb=" N LEU G 173 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'H' and resid 21 through 25 Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.665A pdb=" N GLN H 155 " --> pdb=" O ASP H 152 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR H 156 " --> pdb=" O VAL H 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 152 through 156' Processing helix chain 'H' and resid 181 through 236 removed outlier: 3.556A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 33 Processing helix chain 'I' and resid 35 through 40 removed outlier: 4.150A pdb=" N ALA I 38 " --> pdb=" O ASP I 35 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU I 40 " --> pdb=" O LYS I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 68 through 75 removed outlier: 3.551A pdb=" N PHE I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 3.607A pdb=" N VAL I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 132 Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.705A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 117 removed outlier: 3.519A pdb=" N ARG J 110 " --> pdb=" O SER J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 192 through 207 removed outlier: 3.681A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY J 207 " --> pdb=" O LYS J 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.292A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 Processing helix chain 'K' and resid 94 through 98 removed outlier: 3.540A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 107 removed outlier: 3.670A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 removed outlier: 3.632A pdb=" N GLN K 132 " --> pdb=" O VAL K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 171 through 185 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.801A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 4.101A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'N' and resid 15 through 28 Processing helix chain 'N' and resid 35 through 44 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.841A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 129 Processing helix chain 'O' and resid 29 through 44 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.812A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 3.890A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'O' and resid 142 through 147 removed outlier: 3.572A pdb=" N ALA O 146 " --> pdb=" O GLU O 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 142 through 147' Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 111 through 122 Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.941A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 46 Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 Processing helix chain 'Q' and resid 108 through 112 removed outlier: 4.377A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 119 removed outlier: 3.506A pdb=" N GLU Q 118 " --> pdb=" O TYR Q 115 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE Q 119 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 115 through 119' Processing helix chain 'R' and resid 38 through 42 removed outlier: 3.999A pdb=" N MET R 41 " --> pdb=" O PRO R 38 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE R 42 " --> pdb=" O LEU R 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 38 through 42' Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 52 through 59 Processing helix chain 'R' and resid 77 through 100 removed outlier: 4.239A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.770A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 38 Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 76 through 83 Processing helix chain 'S' and resid 99 through 109 Processing helix chain 'T' and resid 29 through 33 removed outlier: 3.869A pdb=" N ALA T 32 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 48 removed outlier: 4.059A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG T 46 " --> pdb=" O HIS T 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS T 47 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.624A pdb=" N TYR T 77 " --> pdb=" O PRO T 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 74 through 78' Processing helix chain 'T' and resid 80 through 84 Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.576A pdb=" N PHE U 14 " --> pdb=" O ASN U 10 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY U 26 " --> pdb=" O LEU U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 removed outlier: 3.874A pdb=" N VAL U 34 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 31 through 35' Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.747A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 97 through 110 Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.544A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 Processing helix chain 'W' and resid 64 through 77 removed outlier: 3.738A pdb=" N SER W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 21 removed outlier: 3.719A pdb=" N ASP X 9 " --> pdb=" O ASN X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 45 removed outlier: 3.650A pdb=" N VAL X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 93 removed outlier: 3.602A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 30 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 3.799A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 94 removed outlier: 3.671A pdb=" N ASN Y 92 " --> pdb=" O GLY Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.725A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.517A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 94 removed outlier: 3.765A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.861A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 118 through 120 No H-bonds generated for 'chain 'Z' and resid 118 through 120' Processing helix chain 'Z' and resid 121 through 126 removed outlier: 3.764A pdb=" N GLY Z 126 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.607A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 Processing helix chain 'b' and resid 49 through 55 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.757A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 32 through 36 removed outlier: 4.124A pdb=" N GLY e 35 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'e' and resid 46 through 51 Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 104 through 116 removed outlier: 3.542A pdb=" N ARG f 108 " --> pdb=" O ARG f 104 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 104 Processing helix chain 'n' and resid 2 through 23 removed outlier: 3.648A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.644A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.503A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER B 75 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 159 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.858A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL C 33 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 49 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU C 97 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 89 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS C 85 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET C 103 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS C 83 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG C 65 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 128 removed outlier: 3.730A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE C 142 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL C 210 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 102 through 115 removed outlier: 5.909A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 137 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.833A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 205 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 42 removed outlier: 7.304A pdb=" N LEU E 51 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE E 49 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL E 39 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU E 47 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL E 41 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 147 through 155 removed outlier: 3.541A pdb=" N GLY E 140 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E 187 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER E 139 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS E 141 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL E 181 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 173 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 186 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 209 through 210 removed outlier: 3.527A pdb=" N SER E 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 224 through 226 removed outlier: 3.573A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS h 183 " --> pdb=" O ASN h 178 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL h 176 " --> pdb=" O LYS h 185 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN h 187 " --> pdb=" O VAL h 174 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL h 174 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU h 173 " --> pdb=" O GLY h 169 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY h 169 " --> pdb=" O LEU h 173 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS h 153 " --> pdb=" O CYS h 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'F' and resid 70 through 72 removed outlier: 3.548A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.137A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.800A pdb=" N ILE F 147 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL F 140 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR F 159 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.531A pdb=" N PHE F 218 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.515A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS F 233 " --> pdb=" O LYS F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'G' and resid 123 through 127 removed outlier: 3.588A pdb=" N ASP G 124 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 18.740A pdb=" N ARG G 136 " --> pdb=" O ILE d 43 " (cutoff:3.500A) removed outlier: 13.900A pdb=" N ASN d 45 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N CYS d 27 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG d 20 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN d 29 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLU d 33 " --> pdb=" O VAL d 14 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL d 14 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 13 through 17 removed outlier: 6.887A pdb=" N LYS H 2 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER H 6 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN H 56 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU H 109 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLY H 54 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU H 111 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE H 52 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE H 113 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL H 50 " --> pdb=" O ILE H 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.593A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 160 through 162 Processing sheet with id=AC4, first strand: chain 'I' and resid 47 through 52 removed outlier: 3.509A pdb=" N ALA I 47 " --> pdb=" O PHE I 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS I 49 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE I 61 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS I 58 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL I 93 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE I 60 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE I 95 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE I 62 " --> pdb=" O ILE I 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 185 through 188 removed outlier: 4.169A pdb=" N LEU I 158 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP X 54 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL X 62 " --> pdb=" O GLU X 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.766A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 42 through 47 removed outlier: 7.105A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.578A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS J 72 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG J 77 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP J 105 " --> pdb=" O ARG J 77 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE J 175 " --> pdb=" O CYS J 100 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY J 187 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 141 through 142 removed outlier: 4.883A pdb=" N ILE K 135 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 24 removed outlier: 4.042A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP L 69 " --> pdb=" O MET L 21 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 72 through 79 removed outlier: 7.634A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN M 141 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 91 through 96 removed outlier: 3.788A pdb=" N ILE M 96 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 31 through 34 removed outlier: 4.152A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY N 34 " --> pdb=" O CYS N 108 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS N 108 " --> pdb=" O GLY N 34 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL N 79 " --> pdb=" O CYS N 50 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.305A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.305A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 76 through 78 removed outlier: 5.977A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR Q 78 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL Q 105 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL Q 96 " --> pdb=" O ASN Q 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN Q 103 " --> pdb=" O VAL Q 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'R' and resid 9 through 12 removed outlier: 3.582A pdb=" N LYS R 26 " --> pdb=" O ASP R 67 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU R 31 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL R 70 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL R 72 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 97 through 98 Processing sheet with id=AE1, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.558A pdb=" N VAL T 15 " --> pdb=" O THR T 18 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 81 through 83 removed outlier: 3.559A pdb=" N HIS U 91 " --> pdb=" O GLN U 83 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.611A pdb=" N ILE V 89 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU V 91 " --> pdb=" O ILE V 20 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG V 21 " --> pdb=" O THR V 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 32 through 39 removed outlier: 3.543A pdb=" N ILE W 32 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE W 55 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL W 36 " --> pdb=" O LYS W 51 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.873A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.873A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY X 127 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 128 through 129 removed outlier: 6.673A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE Y 120 " --> pdb=" O THR Y 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 6 through 15 removed outlier: 3.988A pdb=" N THR Z 6 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU Z 28 " --> pdb=" O THR Z 6 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG Z 8 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP Z 26 " --> pdb=" O ARG Z 8 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL Z 27 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR Z 69 " --> pdb=" O VAL Z 27 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 98 through 101 removed outlier: 3.627A pdb=" N VAL a 100 " --> pdb=" O ILE a 108 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'b' and resid 20 through 21 Processing sheet with id=AF2, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.990A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 32 through 35 removed outlier: 3.543A pdb=" N VAL c 35 " --> pdb=" O THR c 44 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 106 through 108 Processing sheet with id=AF5, first strand: chain 'g' and resid 138 through 139 Processing sheet with id=AF6, first strand: chain 'h' and resid 5 through 6 removed outlier: 3.641A pdb=" N GLN h 311 " --> pdb=" O THR h 6 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 10 through 11 removed outlier: 3.867A pdb=" N ARG h 308 " --> pdb=" O ALA h 300 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA h 300 " --> pdb=" O ARG h 308 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER h 288 " --> pdb=" O GLY h 301 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 18 through 22 removed outlier: 3.725A pdb=" N GLN h 20 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU h 32 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 66 through 71 removed outlier: 6.511A pdb=" N GLY h 81 " --> pdb=" O SER h 67 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL h 69 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU h 79 " --> pdb=" O VAL h 69 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE h 71 " --> pdb=" O PHE h 77 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE h 77 " --> pdb=" O ILE h 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 108 through 110 removed outlier: 6.531A pdb=" N GLY h 123 " --> pdb=" O LEU h 109 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 129 through 130 Processing sheet with id=AG3, first strand: chain 'h' and resid 195 through 197 removed outlier: 7.098A pdb=" N GLY h 210 " --> pdb=" O ASN h 196 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU h 230 " --> pdb=" O ALA h 216 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 247 through 251 removed outlier: 4.103A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP h 259 " --> pdb=" O LEU h 248 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) 1381 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1327 hydrogen bonds 2226 hydrogen bond angles 0 basepair planarities 525 basepair parallelities 1050 stacking parallelities Total time for adding SS restraints: 59.71 Time building geometry restraints manager: 32.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.35: 22283 1.35 - 1.51: 38005 1.51 - 1.67: 26002 1.67 - 1.82: 275 Bond restraints: 86566 Sorted by residual: bond pdb=" CG PRO L 4 " pdb=" CD PRO L 4 " ideal model delta sigma weight residual 1.503 1.041 0.462 3.40e-02 8.65e+02 1.84e+02 bond pdb=" CG PRO b 97 " pdb=" CD PRO b 97 " ideal model delta sigma weight residual 1.503 1.244 0.259 3.40e-02 8.65e+02 5.81e+01 bond pdb=" C PHE I 135 " pdb=" N PRO I 136 " ideal model delta sigma weight residual 1.337 1.387 -0.051 1.11e-02 8.12e+03 2.11e+01 bond pdb=" C VAL S 98 " pdb=" N ASP S 99 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.83e-02 1.25e+03 1.90e+01 bond pdb=" CB PRO h 25 " pdb=" CG PRO h 25 " ideal model delta sigma weight residual 1.492 1.681 -0.189 5.00e-02 4.00e+02 1.43e+01 ... (remaining 86561 not shown) Histogram of bond angle deviations from ideal: 76.42 - 89.81: 3 89.81 - 103.21: 4127 103.21 - 116.60: 69390 116.60 - 129.99: 51547 129.99 - 143.38: 1208 Bond angle restraints: 126275 Sorted by residual: angle pdb=" N PRO L 4 " pdb=" CD PRO L 4 " pdb=" CG PRO L 4 " ideal model delta sigma weight residual 103.20 76.42 26.78 1.50e+00 4.44e-01 3.19e+02 angle pdb=" CA PRO L 4 " pdb=" CB PRO L 4 " pdb=" CG PRO L 4 " ideal model delta sigma weight residual 104.50 82.64 21.86 1.90e+00 2.77e-01 1.32e+02 angle pdb=" N PRO b 97 " pdb=" CD PRO b 97 " pdb=" CG PRO b 97 " ideal model delta sigma weight residual 103.20 87.41 15.79 1.50e+00 4.44e-01 1.11e+02 angle pdb=" CA PRO h 25 " pdb=" N PRO h 25 " pdb=" CD PRO h 25 " ideal model delta sigma weight residual 112.00 97.75 14.25 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CB PRO L 4 " pdb=" CG PRO L 4 " pdb=" CD PRO L 4 " ideal model delta sigma weight residual 106.10 134.95 -28.85 3.20e+00 9.77e-02 8.13e+01 ... (remaining 126270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 48884 35.80 - 71.60: 4069 71.60 - 107.39: 608 107.39 - 143.19: 12 143.19 - 178.99: 29 Dihedral angle restraints: 53602 sinusoidal: 39529 harmonic: 14073 Sorted by residual: dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 25.82 174.18 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 4.03 -164.03 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual -160.00 -4.21 -155.79 1 1.50e+01 4.44e-03 8.16e+01 ... (remaining 53599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 14264 0.068 - 0.136: 1250 0.136 - 0.204: 154 0.204 - 0.272: 21 0.272 - 0.340: 14 Chirality restraints: 15703 Sorted by residual: chirality pdb=" CB ILE D 88 " pdb=" CA ILE D 88 " pdb=" CG1 ILE D 88 " pdb=" CG2 ILE D 88 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' G 2 383 " pdb=" C4' G 2 383 " pdb=" O3' G 2 383 " pdb=" C2' G 2 383 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C3' G 2 874 " pdb=" C4' G 2 874 " pdb=" O3' G 2 874 " pdb=" C2' G 2 874 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 15700 not shown) Planarity restraints: 8745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR b 96 " 0.085 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO b 97 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO b 97 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO b 97 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Y 85 " 0.058 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO Y 86 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO Y 86 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO Y 86 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 15 " -0.297 9.50e-02 1.11e+02 1.33e-01 1.12e+01 pdb=" NE ARG b 15 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG b 15 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG b 15 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG b 15 " -0.007 2.00e-02 2.50e+03 ... (remaining 8742 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 18168 2.80 - 3.32: 65633 3.32 - 3.85: 153662 3.85 - 4.37: 176610 4.37 - 4.90: 257288 Nonbonded interactions: 671361 Sorted by model distance: nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.271 2.440 nonbonded pdb=" OP1 G 21345 " pdb=" O2' C 21688 " model vdw 2.273 2.440 nonbonded pdb=" O2' G 21528 " pdb=" OP1 C 21666 " model vdw 2.277 2.440 nonbonded pdb=" OD2 ASP G 32 " pdb=" OG SER G 34 " model vdw 2.282 2.440 nonbonded pdb=" O HIS D 272 " pdb=" OG1 THR D 276 " model vdw 2.287 2.440 ... (remaining 671356 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 16.510 Check model and map are aligned: 0.930 Set scattering table: 0.600 Process input model: 217.910 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 244.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 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 : 0.004 0.462 86566 Z= 0.251 Angle : 0.854 28.853 126275 Z= 0.426 Chirality : 0.041 0.340 15703 Planarity : 0.007 0.133 8745 Dihedral : 21.338 178.990 44523 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.10), residues: 4827 helix: -1.79 (0.11), residues: 1512 sheet: -0.24 (0.20), residues: 703 loop : -2.13 (0.10), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 256 HIS 0.012 0.001 HIS I 157 PHE 0.033 0.002 PHE X 101 TYR 0.048 0.002 TYR B 204 ARG 0.019 0.001 ARG V 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 836 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 838 average time/residue: 0.7741 time to fit residues: 1106.2951 Evaluate side-chains 583 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 4.554 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 564 optimal weight: 0.0020 chunk 507 optimal weight: 40.0000 chunk 281 optimal weight: 0.1980 chunk 173 optimal weight: 20.0000 chunk 342 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 524 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 318 optimal weight: 20.0000 chunk 390 optimal weight: 0.2980 chunk 607 optimal weight: 7.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN G 149 GLN H 13 GLN H 110 ASN J 99 ASN J 165 GLN K 132 GLN K 177 ASN M 83 GLN O 101 HIS Q 32 GLN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN T 73 ASN V 81 GLN X 44 HIS X 56 HIS Y 63 ASN Z 94 HIS ** c 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 GLN f 112 ASN h 119 GLN h 191 HIS h 226 HIS h 311 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 86566 Z= 0.120 Angle : 0.521 10.989 126275 Z= 0.264 Chirality : 0.033 0.220 15703 Planarity : 0.005 0.112 8745 Dihedral : 22.230 179.395 34396 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.11), residues: 4827 helix: -0.30 (0.13), residues: 1532 sheet: -0.15 (0.19), residues: 743 loop : -1.85 (0.11), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 52 HIS 0.005 0.000 HIS c 9 PHE 0.024 0.001 PHE Q 119 TYR 0.014 0.001 TYR h 302 ARG 0.006 0.000 ARG V 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 753 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 755 average time/residue: 0.7603 time to fit residues: 996.0955 Evaluate side-chains 570 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 4.461 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 337 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 505 optimal weight: 1.9990 chunk 413 optimal weight: 40.0000 chunk 167 optimal weight: 10.0000 chunk 608 optimal weight: 20.0000 chunk 657 optimal weight: 30.0000 chunk 542 optimal weight: 30.0000 chunk 603 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 488 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 70 ASN C 92 GLN C 163 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN K 177 ASN P 94 HIS Q 32 GLN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN U 12 GLN V 81 GLN X 44 HIS Y 20 GLN Y 63 ASN Z 94 HIS c 19 HIS g 135 HIS h 311 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 86566 Z= 0.138 Angle : 0.507 11.055 126275 Z= 0.256 Chirality : 0.032 0.212 15703 Planarity : 0.004 0.068 8745 Dihedral : 22.156 179.881 34396 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.12 % Allowed : 4.29 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4827 helix: 0.32 (0.13), residues: 1536 sheet: -0.00 (0.19), residues: 754 loop : -1.70 (0.11), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 64 HIS 0.015 0.001 HIS b 72 PHE 0.017 0.001 PHE Q 119 TYR 0.014 0.001 TYR h 246 ARG 0.008 0.000 ARG V 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 731 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 736 average time/residue: 0.7720 time to fit residues: 976.7274 Evaluate side-chains 548 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 4.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 601 optimal weight: 0.8980 chunk 457 optimal weight: 0.8980 chunk 315 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 290 optimal weight: 0.3980 chunk 408 optimal weight: 10.0000 chunk 610 optimal weight: 8.9990 chunk 646 optimal weight: 30.0000 chunk 319 optimal weight: 20.0000 chunk 578 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 70 ASN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN Q 32 GLN Q 54 HIS R 11 GLN S 118 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS X 113 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 86566 Z= 0.163 Angle : 0.535 11.034 126275 Z= 0.270 Chirality : 0.033 0.236 15703 Planarity : 0.004 0.066 8745 Dihedral : 22.154 179.478 34396 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 4827 helix: 0.53 (0.13), residues: 1545 sheet: -0.05 (0.19), residues: 777 loop : -1.65 (0.11), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP h 291 HIS 0.014 0.001 HIS F 201 PHE 0.036 0.002 PHE I 173 TYR 0.022 0.001 TYR B 204 ARG 0.006 0.001 ARG S 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 724 time to evaluate : 5.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 726 average time/residue: 0.7710 time to fit residues: 967.5468 Evaluate side-chains 560 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 559 time to evaluate : 4.507 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6834 time to fit residues: 6.6924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 538 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 481 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 551 optimal weight: 4.9990 chunk 446 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 330 optimal weight: 1.9990 chunk 580 optimal weight: 0.0470 chunk 163 optimal weight: 30.0000 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN C 43 ASN C 163 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN J 35 ASN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN Q 32 GLN Q 54 HIS R 11 GLN S 118 GLN V 81 GLN X 91 ASN Y 20 GLN b 72 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 86566 Z= 0.121 Angle : 0.498 10.893 126275 Z= 0.251 Chirality : 0.032 0.239 15703 Planarity : 0.004 0.057 8745 Dihedral : 22.111 179.542 34396 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 4827 helix: 0.72 (0.13), residues: 1545 sheet: 0.06 (0.19), residues: 772 loop : -1.56 (0.11), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 64 HIS 0.006 0.001 HIS Z 94 PHE 0.015 0.001 PHE X 101 TYR 0.026 0.001 TYR Q 37 ARG 0.024 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 749 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 750 average time/residue: 0.7794 time to fit residues: 1003.4270 Evaluate side-chains 556 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 4.522 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 217 optimal weight: 7.9990 chunk 582 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 379 optimal weight: 4.9990 chunk 159 optimal weight: 30.0000 chunk 647 optimal weight: 40.0000 chunk 537 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 214 optimal weight: 0.9990 chunk 339 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN Q 54 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 GLN V 81 GLN Y 20 GLN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 86566 Z= 0.209 Angle : 0.584 11.174 126275 Z= 0.294 Chirality : 0.035 0.264 15703 Planarity : 0.005 0.072 8745 Dihedral : 22.206 179.959 34396 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4827 helix: 0.67 (0.13), residues: 1537 sheet: -0.13 (0.19), residues: 774 loop : -1.56 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP h 247 HIS 0.009 0.001 HIS F 201 PHE 0.018 0.002 PHE Z 12 TYR 0.021 0.002 TYR h 246 ARG 0.022 0.001 ARG h 245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 703 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 703 average time/residue: 0.8342 time to fit residues: 1013.5358 Evaluate side-chains 553 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 4.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 624 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 chunk 368 optimal weight: 10.0000 chunk 472 optimal weight: 1.9990 chunk 366 optimal weight: 8.9990 chunk 544 optimal weight: 5.9990 chunk 361 optimal weight: 5.9990 chunk 644 optimal weight: 20.0000 chunk 403 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 113 GLN C 118 GLN C 163 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN F 201 HIS ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN M 83 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN Q 54 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 44 HIS ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 94 HIS b 72 HIS h 4 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 86566 Z= 0.206 Angle : 0.608 13.395 126275 Z= 0.306 Chirality : 0.036 0.287 15703 Planarity : 0.005 0.089 8745 Dihedral : 22.297 179.303 34396 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 4827 helix: 0.53 (0.13), residues: 1532 sheet: -0.25 (0.19), residues: 762 loop : -1.60 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP h 247 HIS 0.011 0.001 HIS F 201 PHE 0.033 0.002 PHE B 32 TYR 0.031 0.002 TYR O 141 ARG 0.011 0.001 ARG h 245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 703 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 705 average time/residue: 0.7953 time to fit residues: 959.9124 Evaluate side-chains 555 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 555 time to evaluate : 4.644 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 398 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 chunk 385 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 409 optimal weight: 3.9990 chunk 439 optimal weight: 8.9990 chunk 318 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 506 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 163 GLN C 232 HIS ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN F 201 HIS F 209 HIS ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN Q 54 HIS X 44 HIS Y 20 GLN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 272 GLN h 296 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 86566 Z= 0.269 Angle : 0.686 12.772 126275 Z= 0.346 Chirality : 0.039 0.324 15703 Planarity : 0.006 0.084 8745 Dihedral : 22.509 179.069 34396 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.02 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.12), residues: 4827 helix: 0.26 (0.13), residues: 1523 sheet: -0.60 (0.19), residues: 776 loop : -1.74 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 69 HIS 0.009 0.002 HIS D 136 PHE 0.022 0.002 PHE G 97 TYR 0.024 0.002 TYR h 302 ARG 0.009 0.001 ARG I 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 4.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.8453 time to fit residues: 998.5915 Evaluate side-chains 545 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 4.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 586 optimal weight: 0.0980 chunk 617 optimal weight: 7.9990 chunk 563 optimal weight: 8.9990 chunk 600 optimal weight: 0.0980 chunk 361 optimal weight: 9.9990 chunk 261 optimal weight: 0.2980 chunk 471 optimal weight: 1.9990 chunk 184 optimal weight: 0.0770 chunk 542 optimal weight: 8.9990 chunk 568 optimal weight: 7.9990 chunk 598 optimal weight: 6.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN C 118 GLN C 163 GLN C 177 GLN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS F 188 ASN F 201 HIS ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN M 83 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 HIS R 11 GLN U 83 GLN X 15 ASN c 9 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 86566 Z= 0.131 Angle : 0.545 11.478 126275 Z= 0.275 Chirality : 0.033 0.285 15703 Planarity : 0.004 0.063 8745 Dihedral : 22.282 179.314 34396 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4827 helix: 0.64 (0.13), residues: 1532 sheet: -0.19 (0.19), residues: 746 loop : -1.55 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP h 247 HIS 0.007 0.001 HIS c 9 PHE 0.027 0.001 PHE B 32 TYR 0.019 0.001 TYR a 65 ARG 0.043 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 727 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 727 average time/residue: 0.7993 time to fit residues: 993.6236 Evaluate side-chains 558 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 4.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 394 optimal weight: 0.3980 chunk 635 optimal weight: 3.9990 chunk 387 optimal weight: 20.0000 chunk 301 optimal weight: 3.9990 chunk 441 optimal weight: 0.0870 chunk 666 optimal weight: 40.0000 chunk 613 optimal weight: 20.0000 chunk 530 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 409 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 overall best weight: 3.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 163 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS F 138 HIS ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN F 201 HIS ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN Q 54 HIS R 11 GLN V 81 GLN ** X 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 86566 Z= 0.177 Angle : 0.575 12.718 126275 Z= 0.289 Chirality : 0.035 0.292 15703 Planarity : 0.005 0.065 8745 Dihedral : 22.275 179.346 34396 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.02 % Allowed : 0.43 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.12), residues: 4827 helix: 0.64 (0.13), residues: 1533 sheet: -0.26 (0.19), residues: 768 loop : -1.58 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 291 HIS 0.006 0.001 HIS X 44 PHE 0.018 0.002 PHE L 16 TYR 0.021 0.002 TYR P 72 ARG 0.011 0.001 ARG Z 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 652 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 652 average time/residue: 0.7729 time to fit residues: 874.4702 Evaluate side-chains 543 residues out of total 4221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 4.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 669 random chunks: chunk 421 optimal weight: 6.9990 chunk 565 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 489 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 531 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 545 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN Q 32 GLN W 33 GLN ** X 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.091775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.075159 restraints weight = 403203.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.076857 restraints weight = 218041.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.077151 restraints weight = 118980.186| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 86566 Z= 0.308 Angle : 0.751 14.020 126275 Z= 0.375 Chirality : 0.042 0.334 15703 Planarity : 0.006 0.082 8745 Dihedral : 22.607 179.835 34396 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.02 % Allowed : 0.59 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4827 helix: 0.08 (0.13), residues: 1528 sheet: -0.60 (0.19), residues: 754 loop : -1.83 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP h 291 HIS 0.009 0.002 HIS c 9 PHE 0.026 0.002 PHE L 16 TYR 0.029 0.003 TYR h 246 ARG 0.023 0.001 ARG S 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15351.01 seconds wall clock time: 273 minutes 14.67 seconds (16394.67 seconds total)