Starting phenix.real_space_refine (version: dev) on Tue Feb 28 01:32:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2023/6d6r_7809_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2023/6d6r_7809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2023/6d6r_7809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2023/6d6r_7809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2023/6d6r_7809_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2023/6d6r_7809_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 70": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 6": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K ARG 407": "NH1" <-> "NH2" Residue "K ARG 467": "NH1" <-> "NH2" Residue "K ARG 557": "NH1" <-> "NH2" Residue "K PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 624": "NH1" <-> "NH2" Residue "K ARG 638": "NH1" <-> "NH2" Residue "K ARG 741": "NH1" <-> "NH2" Residue "K ARG 781": "NH1" <-> "NH2" Residue "K ARG 829": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "M PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "M ARG 995": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31639 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2264 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "B" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1824 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "C" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2020 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 14, 'TRANS': 250} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1566 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2194 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1859 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 19, 'TRANS': 232} Chain breaks: 1 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 1 Chain: "H" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2263 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Chain: "I" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1407 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 86 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "K" Number of atoms: 6856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6856 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 40, 'TRANS': 812} Chain breaks: 6 Chain: "L" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 573 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 5648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5648 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 683} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 278 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "O" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 966 Classifications: {'DNA': 13, 'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 17, 'rna3p_pyr': 11} Link IDs: {'rna2p': 6, 'rna3p': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' C%rna3p_pyr:plan': 2, ' A%rna3p_pur:plan2': 1, ' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1, ' C%rna3p_pyr:plan2': 2, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17538 SG CYS K 31 45.199 135.961 78.802 1.00 75.54 S ATOM 17564 SG CYS K 36 45.007 136.828 82.641 1.00 92.82 S ATOM 17580 SG CYS K 39 43.986 133.311 81.292 1.00 97.97 S Time building chain proxies: 18.27, per 1000 atoms: 0.58 Number of scatterers: 31639 At special positions: 0 Unit cell: (164.78, 191.53, 174.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 196 16.00 P 61 15.00 Mg 1 11.99 O 6074 8.00 N 5611 7.00 C 19695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.20 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 159 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 31 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 39 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 36 " Number of angles added : 3 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 38 sheets defined 30.3% alpha, 17.4% beta 14 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 10.07 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 244 through 276 removed outlier: 4.055A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 95 through 109 removed outlier: 3.597A pdb=" N ALA B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.857A pdb=" N CYS B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 209 through 242 Processing helix chain 'C' and resid 10 through 20 removed outlier: 4.055A pdb=" N PHE C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 121 through 124 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 245 through 271 removed outlier: 4.169A pdb=" N GLN C 249 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP C 250 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 105 Processing helix chain 'D' and resid 130 through 143 removed outlier: 4.147A pdb=" N ASN D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 203 through 231 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 99 through 111 Processing helix chain 'E' and resid 121 through 124 Processing helix chain 'E' and resid 148 through 161 Processing helix chain 'E' and resid 216 through 219 No H-bonds generated for 'chain 'E' and resid 216 through 219' Processing helix chain 'E' and resid 251 through 280 Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 119 through 130 Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 234 through 269 Proline residue: F 253 - end of helix Processing helix chain 'G' and resid 204 through 210 Processing helix chain 'G' and resid 217 through 224 removed outlier: 3.981A pdb=" N GLY G 222 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 256 Processing helix chain 'G' and resid 262 through 274 Processing helix chain 'H' and resid 13 through 15 No H-bonds generated for 'chain 'H' and resid 13 through 15' Processing helix chain 'H' and resid 125 through 133 removed outlier: 4.975A pdb=" N ARG H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 228 through 247 removed outlier: 4.690A pdb=" N VAL H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 262 Processing helix chain 'H' and resid 274 through 292 Processing helix chain 'I' and resid 17 through 19 No H-bonds generated for 'chain 'I' and resid 17 through 19' Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 118 through 121 No H-bonds generated for 'chain 'I' and resid 118 through 121' Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 77 through 81 Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 103 through 113 Processing helix chain 'K' and resid 141 through 163 Processing helix chain 'K' and resid 178 through 187 Processing helix chain 'K' and resid 194 through 200 Processing helix chain 'K' and resid 206 through 209 No H-bonds generated for 'chain 'K' and resid 206 through 209' Processing helix chain 'K' and resid 234 through 243 removed outlier: 3.882A pdb=" N LYS K 242 " --> pdb=" O GLN K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 436 removed outlier: 4.640A pdb=" N GLU K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 446 through 451 Processing helix chain 'K' and resid 463 through 465 No H-bonds generated for 'chain 'K' and resid 463 through 465' Processing helix chain 'K' and resid 509 through 512 No H-bonds generated for 'chain 'K' and resid 509 through 512' Processing helix chain 'K' and resid 518 through 525 Processing helix chain 'K' and resid 542 through 546 Processing helix chain 'K' and resid 590 through 598 Processing helix chain 'K' and resid 607 through 626 removed outlier: 3.909A pdb=" N LEU K 616 " --> pdb=" O GLY K 612 " (cutoff:3.500A) Processing helix chain 'K' and resid 658 through 681 Processing helix chain 'K' and resid 700 through 708 Processing helix chain 'K' and resid 718 through 725 Processing helix chain 'K' and resid 731 through 733 No H-bonds generated for 'chain 'K' and resid 731 through 733' Processing helix chain 'K' and resid 737 through 745 Processing helix chain 'K' and resid 783 through 795 Processing helix chain 'K' and resid 802 through 804 No H-bonds generated for 'chain 'K' and resid 802 through 804' Processing helix chain 'K' and resid 807 through 842 Processing helix chain 'L' and resid 11 through 14 No H-bonds generated for 'chain 'L' and resid 11 through 14' Processing helix chain 'L' and resid 17 through 20 No H-bonds generated for 'chain 'L' and resid 17 through 20' Processing helix chain 'L' and resid 64 through 67 No H-bonds generated for 'chain 'L' and resid 64 through 67' Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'M' and resid 142 through 152 Processing helix chain 'M' and resid 169 through 180 Processing helix chain 'M' and resid 193 through 206 Processing helix chain 'M' and resid 230 through 238 Processing helix chain 'M' and resid 255 through 258 Processing helix chain 'M' and resid 263 through 272 removed outlier: 4.122A pdb=" N GLU M 267 " --> pdb=" O GLY M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 300 Processing helix chain 'M' and resid 340 through 353 Processing helix chain 'M' and resid 374 through 383 Processing helix chain 'M' and resid 397 through 408 removed outlier: 5.028A pdb=" N LYS M 408 " --> pdb=" O LEU M 404 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 430 removed outlier: 5.006A pdb=" N CYS M 430 " --> pdb=" O ASN M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 450 Proline residue: M 446 - end of helix Processing helix chain 'M' and resid 461 through 473 Processing helix chain 'M' and resid 484 through 487 No H-bonds generated for 'chain 'M' and resid 484 through 487' Processing helix chain 'M' and resid 514 through 523 removed outlier: 4.547A pdb=" N ARG M 523 " --> pdb=" O GLN M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 552 Processing helix chain 'M' and resid 567 through 574 Processing helix chain 'M' and resid 581 through 587 Processing helix chain 'M' and resid 589 through 594 removed outlier: 4.199A pdb=" N HIS M 594 " --> pdb=" O TYR M 590 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 608 Processing helix chain 'M' and resid 832 through 839 Processing helix chain 'M' and resid 848 through 861 Processing helix chain 'M' and resid 872 through 877 Processing helix chain 'M' and resid 885 through 894 Processing helix chain 'M' and resid 902 through 913 removed outlier: 3.876A pdb=" N THR M 906 " --> pdb=" O ALA M 902 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE M 912 " --> pdb=" O LEU M 908 " (cutoff:3.500A) Processing helix chain 'M' and resid 926 through 948 Proline residue: M 931 - end of helix removed outlier: 3.555A pdb=" N GLN M 934 " --> pdb=" O GLY M 930 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 960 Processing helix chain 'M' and resid 967 through 974 Processing helix chain 'M' and resid 979 through 981 No H-bonds generated for 'chain 'M' and resid 979 through 981' Processing helix chain 'M' and resid 990 through 1014 Processing helix chain 'M' and resid 1018 through 1030 Processing sheet with id= A, first strand: chain 'A' and resid 284 through 286 Processing sheet with id= B, first strand: chain 'A' and resid 165 through 168 Processing sheet with id= C, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.781A pdb=" N MET A 225 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 219 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A 233 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 24 through 27 removed outlier: 3.700A pdb=" N GLN B 128 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 48 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL B 126 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 50 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL B 124 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 52 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE B 122 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 70 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE B 122 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN B 72 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL B 124 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN B 74 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL B 126 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 167 through 170 removed outlier: 6.174A pdb=" N LEU B 189 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE B 195 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 35 through 39 removed outlier: 3.867A pdb=" N ASP C 143 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 59 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N CYS C 141 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 61 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU C 139 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS C 63 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N CYS C 137 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU C 65 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU C 135 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA C 67 " --> pdb=" O TRP C 133 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP C 133 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR C 78 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N CYS C 137 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 80 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU C 139 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASN C 82 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N CYS C 141 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP C 84 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP C 143 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 206 through 208 removed outlier: 3.862A pdb=" N VAL C 194 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS C 234 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP C 227 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU C 232 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 164 through 171 removed outlier: 3.963A pdb=" N GLU C 167 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS C 183 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 12.524A pdb=" N THR C 169 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N LEU C 181 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N ASN C 171 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 11.168A pdb=" N VAL C 179 " --> pdb=" O ASN C 171 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 31 through 35 removed outlier: 3.752A pdb=" N SER D 53 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU D 55 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL D 122 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLY D 57 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU D 120 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR D 59 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL D 118 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR D 75 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 118 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU D 77 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU D 120 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 79 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL D 122 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG D 81 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N SER D 124 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.874A pdb=" N ASP D 186 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU D 192 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 35 through 39 removed outlier: 6.891A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 168 through 171 Processing sheet with id= M, first strand: chain 'E' and resid 209 through 211 removed outlier: 4.384A pdb=" N ALA E 224 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.814A pdb=" N GLY F 51 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 63 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU F 150 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA F 65 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA F 148 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER F 67 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL F 146 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG F 95 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL F 146 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU F 97 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA F 148 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP F 99 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU F 150 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 195 through 197 removed outlier: 4.454A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 71 through 74 Processing sheet with id= Q, first strand: chain 'G' and resid 86 through 89 Processing sheet with id= R, first strand: chain 'G' and resid 128 through 132 removed outlier: 5.817A pdb=" N ASP G 132 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL G 121 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU G 177 " --> pdb=" O VAL G 168 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 198 through 201 Processing sheet with id= T, first strand: chain 'H' and resid 45 through 47 Processing sheet with id= U, first strand: chain 'H' and resid 58 through 62 removed outlier: 3.911A pdb=" N SER H 59 " --> pdb=" O LYS H 70 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 106 through 109 removed outlier: 5.682A pdb=" N GLU H 99 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE H 88 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER H 155 " --> pdb=" O GLN H 146 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 170 through 173 removed outlier: 3.894A pdb=" N ALA H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 26 through 29 Processing sheet with id= Y, first strand: chain 'I' and resid 40 through 45 removed outlier: 5.777A pdb=" N SER I 21 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL I 55 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY I 23 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 131 through 134 removed outlier: 6.589A pdb=" N LEU I 143 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER I 77 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS I 86 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL I 75 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 127 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL I 155 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU I 129 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL I 153 " --> pdb=" O LEU I 129 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 2 through 10 Processing sheet with id= AB, first strand: chain 'K' and resid 87 through 90 removed outlier: 5.915A pdb=" N HIS K 119 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL K 90 " --> pdb=" O HIS K 119 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR K 121 " --> pdb=" O VAL K 90 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'K' and resid 274 through 277 Processing sheet with id= AD, first strand: chain 'K' and resid 383 through 385 Processing sheet with id= AE, first strand: chain 'K' and resid 489 through 494 removed outlier: 3.964A pdb=" N LYS K 574 " --> pdb=" O GLU K 565 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 688 through 691 Processing sheet with id= AG, first strand: chain 'K' and resid 862 through 864 Processing sheet with id= AH, first strand: chain 'K' and resid 886 through 888 Processing sheet with id= AI, first strand: chain 'K' and resid 908 through 911 Processing sheet with id= AJ, first strand: chain 'K' and resid 396 through 399 removed outlier: 3.931A pdb=" N GLY K 421 " --> pdb=" O ARG K 397 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE K 399 " --> pdb=" O ASN K 419 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN K 419 " --> pdb=" O ILE K 399 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 99 through 103 removed outlier: 7.162A pdb=" N SER M 156 " --> pdb=" O HIS M 305 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ILE M 307 " --> pdb=" O SER M 156 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU M 158 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N THR M 309 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER M 160 " --> pdb=" O THR M 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 161 " --> pdb=" O SER M 283 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG M 184 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL M 249 " --> pdb=" O ARG M 184 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE M 186 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE M 251 " --> pdb=" O ILE M 186 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR M 188 " --> pdb=" O PHE M 251 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY M 210 " --> pdb=" O VAL M 226 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 452 through 455 removed outlier: 6.460A pdb=" N ALA M 478 " --> pdb=" O GLY M 453 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS M 455 " --> pdb=" O ALA M 478 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE M 480 " --> pdb=" O HIS M 455 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL M 389 " --> pdb=" O LEU M 479 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA M 481 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE M 391 " --> pdb=" O ALA M 481 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR M 495 " --> pdb=" O ILE M 390 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE M 392 " --> pdb=" O THR M 495 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU M 497 " --> pdb=" O PHE M 392 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE M 534 " --> pdb=" O VAL M 496 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE M 498 " --> pdb=" O ILE M 534 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE M 536 " --> pdb=" O PHE M 498 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS M 318 " --> pdb=" O VAL M 332 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL M 332 " --> pdb=" O HIS M 318 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE M 320 " --> pdb=" O LEU M 330 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU M 330 " --> pdb=" O ILE M 320 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 11.57 Time building geometry restraints manager: 14.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10430 1.34 - 1.46: 5378 1.46 - 1.58: 16070 1.58 - 1.69: 120 1.69 - 1.81: 291 Bond restraints: 32289 Sorted by residual: bond pdb=" O3A ANP M2001 " pdb=" PB ANP M2001 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" P C O 17 " pdb=" O5' C O 17 " ideal model delta sigma weight residual 1.593 1.681 -0.088 1.50e-02 4.44e+03 3.41e+01 bond pdb=" P C O 17 " pdb=" OP1 C O 17 " ideal model delta sigma weight residual 1.485 1.568 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O5' ANP M2001 " pdb=" PA ANP M2001 " ideal model delta sigma weight residual 1.655 1.585 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.22e+01 ... (remaining 32284 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.30: 851 105.30 - 112.48: 17002 112.48 - 119.66: 10396 119.66 - 126.85: 15165 126.85 - 134.03: 461 Bond angle restraints: 43875 Sorted by residual: angle pdb=" CA PRO K 648 " pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 112.00 99.55 12.45 1.40e+00 5.10e-01 7.90e+01 angle pdb=" O3' DT O 16 " pdb=" P C O 17 " pdb=" O5' C O 17 " ideal model delta sigma weight residual 104.00 115.00 -11.00 1.50e+00 4.44e-01 5.38e+01 angle pdb=" O1B ANP M2001 " pdb=" PB ANP M2001 " pdb=" O2B ANP M2001 " ideal model delta sigma weight residual 120.08 109.31 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C HIS M 278 " pdb=" N TYR M 279 " pdb=" CA TYR M 279 " ideal model delta sigma weight residual 122.09 116.39 5.70 1.86e+00 2.89e-01 9.38e+00 angle pdb=" N ALA K 600 " pdb=" CA ALA K 600 " pdb=" CB ALA K 600 " ideal model delta sigma weight residual 114.17 110.90 3.27 1.14e+00 7.69e-01 8.25e+00 ... (remaining 43870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.55: 19472 33.55 - 67.10: 167 67.10 - 100.65: 15 100.65 - 134.20: 1 134.20 - 167.76: 2 Dihedral angle restraints: 19657 sinusoidal: 8432 harmonic: 11225 Sorted by residual: dihedral pdb=" CA MET K 455 " pdb=" C MET K 455 " pdb=" N PRO K 456 " pdb=" CA PRO K 456 " ideal model delta harmonic sigma weight residual 180.00 131.40 48.60 0 5.00e+00 4.00e-02 9.45e+01 dihedral pdb=" O4' C O 49 " pdb=" C1' C O 49 " pdb=" N1 C O 49 " pdb=" C2 C O 49 " ideal model delta sinusoidal sigma weight residual -128.00 32.68 -160.68 1 1.70e+01 3.46e-03 6.46e+01 dihedral pdb=" CA ASP B 201 " pdb=" C ASP B 201 " pdb=" N ALA B 202 " pdb=" CA ALA B 202 " ideal model delta harmonic sigma weight residual 180.00 149.16 30.84 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 19654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5007 0.119 - 0.238: 45 0.238 - 0.357: 1 0.357 - 0.476: 0 0.476 - 0.595: 1 Chirality restraints: 5054 Sorted by residual: chirality pdb=" P C O 17 " pdb=" OP1 C O 17 " pdb=" OP2 C O 17 " pdb=" O5' C O 17 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" C3' ANP M2001 " pdb=" C2' ANP M2001 " pdb=" C4' ANP M2001 " pdb=" O3' ANP M2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1' A O 58 " pdb=" O4' A O 58 " pdb=" C2' A O 58 " pdb=" N9 A O 58 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5051 not shown) Planarity restraints: 5456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C O 42 " 0.040 2.00e-02 2.50e+03 2.04e-02 9.39e+00 pdb=" N1 C O 42 " -0.043 2.00e-02 2.50e+03 pdb=" C2 C O 42 " -0.010 2.00e-02 2.50e+03 pdb=" O2 C O 42 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C O 42 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C O 42 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C O 42 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C O 42 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C O 42 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 60 " 0.035 2.00e-02 2.50e+03 1.59e-02 6.92e+00 pdb=" N9 A O 60 " -0.036 2.00e-02 2.50e+03 pdb=" C8 A O 60 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A O 60 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A O 60 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A O 60 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A O 60 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A O 60 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A O 60 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 41 " 0.034 2.00e-02 2.50e+03 1.48e-02 6.05e+00 pdb=" N9 A O 41 " -0.031 2.00e-02 2.50e+03 pdb=" C8 A O 41 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A O 41 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A O 41 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A O 41 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A O 41 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A O 41 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A O 41 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A O 41 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A O 41 " -0.005 2.00e-02 2.50e+03 ... (remaining 5453 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 157 2.43 - 3.05: 22069 3.05 - 3.67: 44805 3.67 - 4.28: 67541 4.28 - 4.90: 113573 Nonbonded interactions: 248145 Sorted by model distance: nonbonded pdb=" O2' C O 42 " pdb=" O5' A O 43 " model vdw 1.816 2.440 nonbonded pdb=" OG SER B 7 " pdb=" OE1 GLN B 9 " model vdw 1.944 2.440 nonbonded pdb=" OG SER M 189 " pdb=" OG SER M 195 " model vdw 1.956 2.440 nonbonded pdb=" OD1 ASP C 111 " pdb=" ND2 ASN C 115 " model vdw 1.959 2.520 nonbonded pdb=" OE2 GLU M 267 " pdb=" OG SER M 561 " model vdw 1.979 2.440 ... (remaining 248140 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 196 5.16 5 C 19695 2.51 5 N 5611 2.21 5 O 6074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.190 Check model and map are aligned: 0.500 Process input model: 92.700 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.290 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.008 0.142 32289 Z= 0.520 Angle : 0.680 12.446 43875 Z= 0.376 Chirality : 0.045 0.595 5054 Planarity : 0.004 0.051 5456 Dihedral : 10.123 167.755 12393 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.03 % 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: -4.48 (0.11), residues: 3839 helix: -1.97 (0.12), residues: 1234 sheet: -2.38 (0.17), residues: 762 loop : -4.04 (0.10), residues: 1843 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 769 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 770 average time/residue: 0.5295 time to fit residues: 609.5379 Evaluate side-chains 383 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 4.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 0.0770 chunk 293 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 351 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 188 HIS B 33 GLN E 19 GLN E 114 ASN E 131 HIS F 15 GLN G 116 HIS ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN L 20 GLN L 92 ASN M 300 HIS ** M 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 981 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 32289 Z= 0.200 Angle : 0.627 10.321 43875 Z= 0.319 Chirality : 0.044 0.252 5054 Planarity : 0.004 0.055 5456 Dihedral : 9.181 171.267 4917 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.45 (0.13), residues: 3839 helix: 0.03 (0.15), residues: 1239 sheet: -1.67 (0.18), residues: 758 loop : -2.84 (0.13), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 448 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 32 residues processed: 488 average time/residue: 0.4925 time to fit residues: 380.2073 Evaluate side-chains 383 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 351 time to evaluate : 4.051 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3399 time to fit residues: 25.1121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 0.2980 chunk 292 optimal weight: 0.9980 chunk 239 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 352 optimal weight: 2.9990 chunk 380 optimal weight: 2.9990 chunk 313 optimal weight: 0.8980 chunk 349 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN H 93 GLN H 101 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN K 919 GLN M 300 HIS M 317 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 32289 Z= 0.217 Angle : 0.578 8.719 43875 Z= 0.294 Chirality : 0.042 0.288 5054 Planarity : 0.004 0.058 5456 Dihedral : 9.070 174.996 4917 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -1.61 (0.13), residues: 3839 helix: 0.64 (0.15), residues: 1253 sheet: -1.15 (0.18), residues: 761 loop : -2.31 (0.13), residues: 1825 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 393 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 22 residues processed: 430 average time/residue: 0.4663 time to fit residues: 315.7452 Evaluate side-chains 353 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 331 time to evaluate : 3.747 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2790 time to fit residues: 16.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 353 optimal weight: 6.9990 chunk 374 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS F 249 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN M 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 32289 Z= 0.328 Angle : 0.638 9.588 43875 Z= 0.322 Chirality : 0.044 0.294 5054 Planarity : 0.004 0.059 5456 Dihedral : 9.138 175.886 4917 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3839 helix: 0.77 (0.15), residues: 1247 sheet: -0.91 (0.18), residues: 751 loop : -2.07 (0.14), residues: 1841 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 363 time to evaluate : 4.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 38 residues processed: 415 average time/residue: 0.4695 time to fit residues: 312.7487 Evaluate side-chains 365 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 327 time to evaluate : 4.155 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3126 time to fit residues: 27.9827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 278 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 319 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 335 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 HIS G 88 HIS G 105 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 GLN J 632 GLN M 898 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 32289 Z= 0.230 Angle : 0.572 8.892 43875 Z= 0.289 Chirality : 0.042 0.303 5054 Planarity : 0.004 0.057 5456 Dihedral : 9.021 174.968 4917 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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 (0.13), residues: 3839 helix: 1.01 (0.15), residues: 1248 sheet: -0.66 (0.19), residues: 740 loop : -1.91 (0.14), residues: 1851 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 355 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 21 residues processed: 392 average time/residue: 0.4644 time to fit residues: 293.5094 Evaluate side-chains 347 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 326 time to evaluate : 4.132 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2869 time to fit residues: 16.8255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9705 > 50: distance: 86 - 93: 34.319 distance: 94 - 95: 8.337 distance: 94 - 97: 46.026 distance: 95 - 96: 29.673 distance: 95 - 99: 10.234 distance: 97 - 98: 26.001 distance: 101 - 102: 41.086 distance: 106 - 107: 24.966 distance: 107 - 108: 32.243 distance: 107 - 110: 43.656 distance: 108 - 109: 20.825 distance: 108 - 115: 19.757 distance: 110 - 111: 50.835 distance: 111 - 112: 18.495 distance: 112 - 113: 23.129 distance: 113 - 114: 30.279 distance: 115 - 116: 15.179 distance: 116 - 117: 40.660 distance: 116 - 119: 11.942 distance: 117 - 118: 34.105 distance: 117 - 122: 22.281 distance: 119 - 120: 9.640 distance: 119 - 121: 36.374 distance: 122 - 123: 13.235 distance: 123 - 124: 59.522 distance: 123 - 126: 43.264 distance: 124 - 125: 3.094 distance: 124 - 132: 21.453 distance: 126 - 127: 15.486 distance: 127 - 128: 40.018 distance: 127 - 129: 8.322 distance: 128 - 130: 40.604 distance: 129 - 131: 6.782 distance: 132 - 133: 3.268 distance: 133 - 134: 21.466 distance: 133 - 136: 48.490 distance: 134 - 135: 21.263 distance: 134 - 139: 12.900 distance: 136 - 138: 40.257 distance: 139 - 140: 35.838 distance: 140 - 141: 33.367 distance: 140 - 143: 29.026 distance: 141 - 142: 40.007 distance: 141 - 148: 32.699 distance: 143 - 144: 34.653 distance: 144 - 145: 35.814 distance: 145 - 146: 30.454 distance: 146 - 147: 32.934 distance: 148 - 149: 6.954 distance: 149 - 150: 21.744 distance: 149 - 152: 17.039 distance: 150 - 151: 16.894 distance: 150 - 157: 26.919 distance: 152 - 153: 12.439 distance: 153 - 154: 36.987 distance: 154 - 155: 28.898 distance: 154 - 156: 45.984 distance: 157 - 158: 38.317 distance: 158 - 159: 7.738 distance: 158 - 161: 35.267 distance: 159 - 160: 33.025 distance: 159 - 168: 18.342 distance: 161 - 162: 12.303 distance: 162 - 163: 24.407 distance: 162 - 164: 11.599 distance: 163 - 165: 12.613 distance: 164 - 166: 10.565 distance: 165 - 167: 14.705 distance: 166 - 167: 8.997 distance: 168 - 169: 22.816 distance: 169 - 170: 7.022 distance: 169 - 172: 25.149 distance: 170 - 171: 26.555 distance: 170 - 179: 11.870 distance: 172 - 173: 16.569 distance: 173 - 174: 43.800 distance: 174 - 175: 12.291 distance: 175 - 176: 13.885 distance: 176 - 177: 36.826 distance: 176 - 178: 7.652