Starting phenix.real_space_refine (version: dev) on Sun Dec 18 14:21:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/12_2022/5g06_3366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/12_2022/5g06_3366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/12_2022/5g06_3366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/12_2022/5g06_3366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/12_2022/5g06_3366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/12_2022/5g06_3366.pdb" } resolution = 4.2 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= 0.001 sd= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C GLU 339": "OE1" <-> "OE2" Residue "E PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "F ASP 219": "OD1" <-> "OD2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "H ASP 64": "OD1" <-> "OD2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 216": "OD1" <-> "OD2" Residue "I PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 189": "OD1" <-> "OD2" Residue "J PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 668": "OD1" <-> "OD2" Residue "J TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 26794 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2350 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1890 Classifications: {'peptide': 240} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 232} Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2622 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain breaks: 3 Chain: "D" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1707 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain: "E" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2048 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1627 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Chain: "G" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1831 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "H" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2277 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 2 Chain: "I" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1750 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 3 Chain: "J" Number of atoms: 7942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7942 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 941} Chain: "P" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 750 Classifications: {'peptide': 95} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 87} Time building chain proxies: 14.14, per 1000 atoms: 0.53 Number of scatterers: 26794 At special positions: 0 Unit cell: (155.478, 142.413, 138.493, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 5158 8.00 N 4641 7.00 C 16865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS I 3 " - pdb=" SG CYS I 66 " distance=2.04 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 55 " distance=2.02 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: 10.02 Conformation dependent library (CDL) restraints added in 4.0 seconds 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 44 sheets defined 31.5% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.590A pdb=" N LEU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 205 through 211 removed outlier: 4.182A pdb=" N LYS A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 257 through 291 removed outlier: 3.553A pdb=" N GLU A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.583A pdb=" N GLN B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 removed outlier: 3.506A pdb=" N ARG B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 4.189A pdb=" N ILE B 140 " --> pdb=" O MET B 136 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 209 through 239 removed outlier: 3.605A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.245A pdb=" N LEU C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 4.347A pdb=" N ASP C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 145 through 163 removed outlier: 3.511A pdb=" N ILE C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 170 Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.831A pdb=" N TYR C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.530A pdb=" N ASP C 254 " --> pdb=" O ARG C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 336 through 343 removed outlier: 3.522A pdb=" N SER C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 392 removed outlier: 4.150A pdb=" N ILE C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 41 removed outlier: 3.583A pdb=" N GLU D 41 " --> pdb=" O ALA D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 78 removed outlier: 3.503A pdb=" N VAL D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.822A pdb=" N TYR D 83 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 124 Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.578A pdb=" N ILE D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 218 removed outlier: 3.555A pdb=" N SER D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 17 removed outlier: 3.527A pdb=" N SER E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.507A pdb=" N GLU E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 240 through 264 removed outlier: 3.530A pdb=" N LEU E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Proline residue: E 256 - end of helix removed outlier: 3.814A pdb=" N ASN E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 125 removed outlier: 3.746A pdb=" N SER F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 222 through 245 removed outlier: 3.684A pdb=" N GLU F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU F 240 " --> pdb=" O ARG F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 169 Processing helix chain 'G' and resid 173 through 182 removed outlier: 3.869A pdb=" N ALA G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS G 181 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 218 removed outlier: 3.503A pdb=" N LYS G 217 " --> pdb=" O GLU G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 234 removed outlier: 4.057A pdb=" N ASP G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 228 " --> pdb=" O LYS G 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 141 No H-bonds generated for 'chain 'H' and resid 139 through 141' Processing helix chain 'H' and resid 155 through 163 removed outlier: 3.850A pdb=" N PHE H 162 " --> pdb=" O GLN H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 290 through 310 Processing helix chain 'H' and resid 315 through 326 removed outlier: 3.586A pdb=" N ILE H 319 " --> pdb=" O THR H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 329 No H-bonds generated for 'chain 'H' and resid 327 through 329' Processing helix chain 'H' and resid 331 through 335 Processing helix chain 'H' and resid 337 through 356 Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 219 through 223 Processing helix chain 'I' and resid 259 through 263 Processing helix chain 'J' and resid 54 through 59 removed outlier: 3.658A pdb=" N ILE J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 98 removed outlier: 3.536A pdb=" N VAL J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 115 through 125 removed outlier: 3.646A pdb=" N GLU J 120 " --> pdb=" O ILE J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 3.515A pdb=" N TYR J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 185 removed outlier: 3.858A pdb=" N ARG J 169 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE J 174 " --> pdb=" O ASN J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 189 Processing helix chain 'J' and resid 198 through 208 Processing helix chain 'J' and resid 218 through 225 removed outlier: 3.614A pdb=" N LEU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU J 225 " --> pdb=" O TYR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 270 Processing helix chain 'J' and resid 303 through 308 removed outlier: 3.936A pdb=" N ASN J 308 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 381 Processing helix chain 'J' and resid 440 through 446 removed outlier: 4.409A pdb=" N ASP J 446 " --> pdb=" O ALA J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 488 Processing helix chain 'J' and resid 496 through 502 removed outlier: 3.840A pdb=" N GLU J 501 " --> pdb=" O LYS J 497 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS J 502 " --> pdb=" O LYS J 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 525 Processing helix chain 'J' and resid 526 through 531 removed outlier: 4.411A pdb=" N THR J 529 " --> pdb=" O PRO J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 591 Processing helix chain 'J' and resid 605 through 611 Processing helix chain 'J' and resid 654 through 663 Processing helix chain 'J' and resid 668 through 693 removed outlier: 3.899A pdb=" N VAL J 682 " --> pdb=" O LEU J 678 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS J 683 " --> pdb=" O LYS J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 698 through 703 Processing helix chain 'J' and resid 721 through 746 removed outlier: 3.523A pdb=" N VAL J 727 " --> pdb=" O THR J 723 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU J 728 " --> pdb=" O ASN J 724 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU J 729 " --> pdb=" O SER J 725 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE J 730 " --> pdb=" O LEU J 726 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET J 731 " --> pdb=" O VAL J 727 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 775 Processing helix chain 'J' and resid 782 through 792 Processing helix chain 'J' and resid 800 through 813 Processing helix chain 'J' and resid 825 through 829 removed outlier: 3.503A pdb=" N PHE J 829 " --> pdb=" O TYR J 826 " (cutoff:3.500A) Processing helix chain 'J' and resid 848 through 862 removed outlier: 3.624A pdb=" N VAL J 852 " --> pdb=" O ARG J 848 " (cutoff:3.500A) Processing helix chain 'J' and resid 868 through 872 Processing helix chain 'J' and resid 873 through 911 removed outlier: 3.632A pdb=" N MET J 877 " --> pdb=" O ASP J 873 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE J 880 " --> pdb=" O LYS J 876 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE J 899 " --> pdb=" O GLY J 895 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR J 902 " --> pdb=" O SER J 898 " (cutoff:3.500A) Processing helix chain 'J' and resid 940 through 944 Processing helix chain 'P' and resid 2 through 20 removed outlier: 3.766A pdb=" N SER P 19 " --> pdb=" O LYS P 15 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR P 20 " --> pdb=" O ASN P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 37 removed outlier: 3.784A pdb=" N LYS P 35 " --> pdb=" O PHE P 31 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS P 37 " --> pdb=" O SER P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.821A pdb=" N VAL P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA P 58 " --> pdb=" O THR P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 72 removed outlier: 4.589A pdb=" N ASP P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE P 71 " --> pdb=" O PRO P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 95 removed outlier: 3.515A pdb=" N ASN P 85 " --> pdb=" O GLU P 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS P 89 " --> pdb=" O ASN P 85 " (cutoff:3.500A) Proline residue: P 92 - end of helix Processing sheet with id= AA, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.231A pdb=" N LYS A 55 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N TRP A 132 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.231A pdb=" N LYS A 55 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 76 " --> pdb=" O TRP A 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 124 through 126 removed outlier: 7.460A pdb=" N LYS A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TRP A 132 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 163 through 164 Processing sheet with id= AE, first strand: chain 'A' and resid 167 through 170 Processing sheet with id= AF, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.520A pdb=" N LEU A 239 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR A 236 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 248 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR A 238 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 301 through 302 Processing sheet with id= BA, first strand: chain 'B' and resid 25 through 29 removed outlier: 7.365A pdb=" N ILE B 49 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 129 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR B 51 " --> pdb=" O HIS B 127 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS B 127 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL B 53 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU B 125 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY B 55 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 123 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'B' and resid 169 through 172 removed outlier: 8.374A pdb=" N THR B 184 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL B 201 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 199 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 188 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.663A pdb=" N GLY C 76 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 86 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 96 through 97 Processing sheet with id= CC, first strand: chain 'C' and resid 185 through 188 removed outlier: 3.575A pdb=" N GLY C 175 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 248 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N LEU C 243 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR C 279 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'C' and resid 255 through 257 removed outlier: 3.901A pdb=" N LEU C 255 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'C' and resid 329 through 332 removed outlier: 3.812A pdb=" N ILE C 349 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 347 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER C 345 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR C 346 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU C 362 " --> pdb=" O THR C 346 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER C 348 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU C 360 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU C 350 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS C 358 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY D 184 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU D 178 " --> pdb=" O GLY C 364 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS D 175 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL D 168 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 177 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU D 166 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP D 185 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU D 158 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 159 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 163 " --> pdb=" O ILE D 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 134 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 165 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA D 132 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'D' and resid 3 through 7 removed outlier: 7.051A pdb=" N VAL D 26 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU D 95 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N CYS D 28 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN D 93 " --> pdb=" O CYS D 28 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL D 30 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR D 91 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY D 32 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLN D 89 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 49 " --> pdb=" O CYS D 88 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'E' and resid 76 through 82 Processing sheet with id= EB, first strand: chain 'E' and resid 115 through 117 removed outlier: 9.337A pdb=" N PHE E 122 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id= HA, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.665A pdb=" N ILE E 36 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU E 57 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE E 122 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id= HB, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.665A pdb=" N ILE E 36 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU E 57 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id= EC, first strand: chain 'E' and resid 153 through 157 removed outlier: 8.698A pdb=" N LEU E 154 " --> pdb=" O TYR E 175 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N TYR E 175 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS E 156 " --> pdb=" O HIS E 173 " (cutoff:3.500A) Processing sheet with id= ED, first strand: chain 'E' and resid 196 through 199 removed outlier: 3.707A pdb=" N ASN E 211 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY E 212 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG E 227 " --> pdb=" O GLY E 212 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE E 214 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER E 216 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE F 213 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE F 210 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE F 204 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 212 " --> pdb=" O SER F 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 192 " --> pdb=" O PHE F 203 " (cutoff:3.500A) Processing sheet with id= FA, first strand: chain 'F' and resid 45 through 50 removed outlier: 3.798A pdb=" N GLY F 58 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS F 69 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP F 146 " --> pdb=" O HIS F 69 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR F 71 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP F 144 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU F 73 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR F 142 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER F 75 " --> pdb=" O TYR F 140 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR F 140 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL F 77 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE F 138 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY F 79 " --> pdb=" O ASP F 136 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP F 136 " --> pdb=" O GLY F 79 " (cutoff:3.500A) Processing sheet with id= GA, first strand: chain 'G' and resid 2 through 5 Processing sheet with id= GB, first strand: chain 'G' and resid 25 through 27 Processing sheet with id= GC, first strand: chain 'G' and resid 71 through 79 removed outlier: 6.773A pdb=" N GLU G 133 " --> pdb=" O CYS G 124 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER G 98 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing sheet with id= GD, first strand: chain 'G' and resid 154 through 157 removed outlier: 3.540A pdb=" N VAL G 196 " --> pdb=" O MET G 154 " (cutoff:3.500A) Processing sheet with id= HC, first strand: chain 'H' and resid 75 through 76 Processing sheet with id= HD, first strand: chain 'H' and resid 86 through 91 Processing sheet with id= HE, first strand: chain 'H' and resid 111 through 119 removed outlier: 7.586A pdb=" N SER H 183 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS H 185 " --> pdb=" O SER H 175 " (cutoff:3.500A) removed outlier: 12.618A pdb=" N ALA H 182 " --> pdb=" O MET H 137 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET H 137 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL H 135 " --> pdb=" O LEU H 184 " (cutoff:3.500A) Processing sheet with id= HF, first strand: chain 'H' and resid 197 through 201 removed outlier: 3.700A pdb=" N ILE H 221 " --> pdb=" O LEU H 217 " (cutoff:3.500A) Processing sheet with id= IA, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.555A pdb=" N THR I 63 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU I 111 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER I 109 " --> pdb=" O ARG I 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU I 67 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS I 104 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN I 34 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE I 106 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL I 36 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU I 24 " --> pdb=" O ILE I 31 " (cutoff:3.500A) Processing sheet with id= IB, first strand: chain 'I' and resid 16 through 19 removed outlier: 7.035A pdb=" N ILE I 56 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU I 54 " --> pdb=" O PRO I 19 " (cutoff:3.500A) Processing sheet with id= IC, first strand: chain 'I' and resid 138 through 146 removed outlier: 6.879A pdb=" N TYR I 244 " --> pdb=" O GLN I 233 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR I 246 " --> pdb=" O LEU I 235 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE I 204 " --> pdb=" O LEU I 245 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 150 through 158 current: chain 'I' and resid 138 through 146 Processing sheet with id= ID, first strand: chain 'I' and resid 269 through 271 removed outlier: 6.422A pdb=" N MET I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing sheet with id= JA, first strand: chain 'J' and resid 11 through 14 removed outlier: 7.071A pdb=" N LEU J 17 " --> pdb=" O LEU J 13 " (cutoff:3.500A) Processing sheet with id= JB, first strand: chain 'J' and resid 78 through 79 removed outlier: 6.696A pdb=" N HIS J 86 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing sheet with id= JC, first strand: chain 'J' and resid 144 through 148 removed outlier: 5.767A pdb=" N ASP J 110 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE J 214 " --> pdb=" O VAL J 192 " (cutoff:3.500A) Processing sheet with id= JD, first strand: chain 'J' and resid 144 through 148 removed outlier: 5.767A pdb=" N ASP J 110 " --> pdb=" O HIS J 86 " (cutoff:3.500A) Processing sheet with id= JE, first strand: chain 'J' and resid 274 through 280 removed outlier: 7.211A pdb=" N GLN J 315 " --> pdb=" O ILE J 395 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE J 395 " --> pdb=" O GLN J 315 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE J 317 " --> pdb=" O VAL J 393 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL J 302 " --> pdb=" O ALA J 390 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL J 392 " --> pdb=" O VAL J 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER J 291 " --> pdb=" O ASN J 277 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN J 277 " --> pdb=" O SER J 291 " (cutoff:3.500A) Processing sheet with id= JF, first strand: chain 'J' and resid 403 through 407 removed outlier: 4.849A pdb=" N LEU J 407 " --> pdb=" O LYS J 447 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS J 447 " --> pdb=" O LEU J 407 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ARG J 448 " --> pdb=" O ASP J 470 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP J 470 " --> pdb=" O ARG J 448 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 450 " --> pdb=" O VAL J 468 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU J 464 " --> pdb=" O ASP J 454 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG J 437 " --> pdb=" O GLY J 465 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE J 467 " --> pdb=" O ARG J 437 " (cutoff:3.500A) Processing sheet with id= JG, first strand: chain 'J' and resid 532 through 533 removed outlier: 3.968A pdb=" N ASN J 638 " --> pdb=" O GLU J 629 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER J 648 " --> pdb=" O VAL J 619 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL J 619 " --> pdb=" O SER J 648 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP J 552 " --> pdb=" O ILE J 542 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE J 542 " --> pdb=" O ASP J 552 " (cutoff:3.500A) Processing sheet with id= JH, first strand: chain 'J' and resid 751 through 754 Processing sheet with id= JI, first strand: chain 'J' and resid 936 through 939 removed outlier: 6.766A pdb=" N VAL J 927 " --> pdb=" O ILE J 919 " (cutoff:3.500A) Processing sheet with id= JJ, first strand: chain 'J' and resid 952 through 954 1154 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.37 Time building geometry restraints manager: 10.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 4834 1.31 - 1.46: 9304 1.46 - 1.61: 12755 1.61 - 1.77: 164 1.77 - 1.92: 176 Bond restraints: 27233 Sorted by residual: bond pdb=" CA GLY I 265 " pdb=" C GLY I 265 " ideal model delta sigma weight residual 1.516 1.418 0.099 8.90e-03 1.26e+04 1.23e+02 bond pdb=" N VAL J 113 " pdb=" CA VAL J 113 " ideal model delta sigma weight residual 1.460 1.378 0.082 7.60e-03 1.73e+04 1.18e+02 bond pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 1.520 1.391 0.129 1.22e-02 6.72e+03 1.12e+02 bond pdb=" CA GLY B 188 " pdb=" C GLY B 188 " ideal model delta sigma weight residual 1.513 1.404 0.108 1.03e-02 9.43e+03 1.11e+02 bond pdb=" CA GLY C 298 " pdb=" C GLY C 298 " ideal model delta sigma weight residual 1.510 1.394 0.116 1.11e-02 8.12e+03 1.10e+02 ... (remaining 27228 not shown) Histogram of bond angle deviations from ideal: 83.49 - 94.35: 18 94.35 - 105.21: 2007 105.21 - 116.07: 16219 116.07 - 126.93: 17474 126.93 - 137.79: 1128 Bond angle restraints: 36846 Sorted by residual: angle pdb=" CA PHE J 641 " pdb=" CB PHE J 641 " pdb=" CG PHE J 641 " ideal model delta sigma weight residual 113.80 99.54 14.26 1.00e+00 1.00e+00 2.03e+02 angle pdb=" CA LEU J 225 " pdb=" C LEU J 225 " pdb=" O LEU J 225 " ideal model delta sigma weight residual 119.75 108.32 11.43 9.40e-01 1.13e+00 1.48e+02 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 112.03 96.52 15.51 1.31e+00 5.83e-01 1.40e+02 angle pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N PRO A 255 " ideal model delta sigma weight residual 118.85 129.76 -10.91 9.50e-01 1.11e+00 1.32e+02 angle pdb=" CA LEU J 225 " pdb=" C LEU J 225 " pdb=" N PRO J 226 " ideal model delta sigma weight residual 118.87 129.20 -10.33 9.00e-01 1.23e+00 1.32e+02 ... (remaining 36841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.29: 15231 19.29 - 38.58: 1102 38.58 - 57.87: 241 57.87 - 77.16: 114 77.16 - 96.45: 69 Dihedral angle restraints: 16757 sinusoidal: 6794 harmonic: 9963 Sorted by residual: dihedral pdb=" C ILE C 12 " pdb=" N ILE C 12 " pdb=" CA ILE C 12 " pdb=" CB ILE C 12 " ideal model delta harmonic sigma weight residual -122.00 -151.11 29.11 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CA ILE C 12 " pdb=" CB ILE C 12 " ideal model delta harmonic sigma weight residual 123.40 147.06 -23.66 0 2.50e+00 1.60e-01 8.96e+01 dihedral pdb=" N ALA J 634 " pdb=" C ALA J 634 " pdb=" CA ALA J 634 " pdb=" CB ALA J 634 " ideal model delta harmonic sigma weight residual 122.90 145.13 -22.23 0 2.50e+00 1.60e-01 7.91e+01 ... (remaining 16754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 3004 0.213 - 0.426: 1107 0.426 - 0.638: 143 0.638 - 0.851: 16 0.851 - 1.064: 1 Chirality restraints: 4271 Sorted by residual: chirality pdb=" CA ILE C 12 " pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CB ILE C 12 " both_signs ideal model delta sigma weight residual False 2.43 1.37 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA ALA J 634 " pdb=" N ALA J 634 " pdb=" C ALA J 634 " pdb=" CB ALA J 634 " both_signs ideal model delta sigma weight residual False 2.48 1.64 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA LEU J 48 " pdb=" N LEU J 48 " pdb=" C LEU J 48 " pdb=" CB LEU J 48 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.62e+01 ... (remaining 4268 not shown) Planarity restraints: 4773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 21 " 0.168 2.00e-02 2.50e+03 1.30e-01 3.35e+02 pdb=" CG TYR I 21 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR I 21 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR I 21 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 TYR I 21 " -0.140 2.00e-02 2.50e+03 pdb=" CE2 TYR I 21 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR I 21 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR I 21 " 0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 180 " -0.232 2.00e-02 2.50e+03 1.15e-01 3.33e+02 pdb=" CG TRP J 180 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP J 180 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP J 180 " 0.080 2.00e-02 2.50e+03 pdb=" NE1 TRP J 180 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP J 180 " 0.051 2.00e-02 2.50e+03 pdb=" CE3 TRP J 180 " 0.134 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 180 " -0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 180 " 0.068 2.00e-02 2.50e+03 pdb=" CH2 TRP J 180 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 221 " 0.141 2.00e-02 2.50e+03 1.08e-01 2.34e+02 pdb=" CG TYR J 221 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR J 221 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR J 221 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR J 221 " -0.090 2.00e-02 2.50e+03 pdb=" CE2 TYR J 221 " -0.129 2.00e-02 2.50e+03 pdb=" CZ TYR J 221 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR J 221 " 0.207 2.00e-02 2.50e+03 ... (remaining 4770 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 11 1.93 - 2.67: 1398 2.67 - 3.42: 32699 3.42 - 4.16: 64893 4.16 - 4.90: 113998 Nonbonded interactions: 212999 Sorted by model distance: nonbonded pdb=" OE2 GLU C 48 " pdb=" CB ASN P 49 " model vdw 1.189 3.440 nonbonded pdb=" CD2 TRP I 272 " pdb=" NZ LYS P 82 " model vdw 1.318 3.340 nonbonded pdb=" CD GLU C 48 " pdb=" CB ASN P 49 " model vdw 1.410 3.670 nonbonded pdb=" CD LYS C 81 " pdb=" CD LYS P 35 " model vdw 1.485 3.840 nonbonded pdb=" N LEU I 16 " pdb=" NZ LYS P 15 " model vdw 1.542 3.200 ... (remaining 212994 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: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 16865 2.51 5 N 4641 2.21 5 O 5158 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 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: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 0.010 Extract box with map and model: 3.760 Check model and map are aligned: 0.420 Convert atoms to be neutral: 0.230 Process input model: 67.020 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4614 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 : 0.036 0.151 27233 Z= 2.347 Angle : 3.534 17.412 36846 Z= 2.392 Chirality : 0.208 1.064 4271 Planarity : 0.029 0.366 4773 Dihedral : 17.027 96.449 10279 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 1.87 % Allowed : 5.86 % Favored : 92.27 % Rotamer Outliers : 3.01 % Cbeta Deviations : 7.60 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.69 % Twisted General : 0.12 % 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: -2.39 (0.12), residues: 3378 helix: -0.80 (0.15), residues: 927 sheet: -0.35 (0.19), residues: 656 loop : -2.59 (0.12), residues: 1795 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 983 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 13 residues processed: 1056 average time/residue: 0.4175 time to fit residues: 668.9834 Evaluate side-chains 459 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 446 time to evaluate : 3.172 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3757 time to fit residues: 12.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 291 ASN B 20 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 208 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 150 ASN E 173 HIS E 195 ASN E 196 ASN E 204 ASN E 210 ASN F 99 ASN F 235 ASN G 53 GLN H 53 GLN H 92 ASN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN H 302 ASN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN J 279 GLN J 284 ASN J 406 GLN J 420 GLN J 460 HIS J 478 GLN J 555 HIS J 569 HIS J 667 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 771 ASN J 923 ASN ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN P 49 ASN P 85 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5195 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 27233 Z= 0.372 Angle : 0.831 13.465 36846 Z= 0.450 Chirality : 0.048 0.236 4271 Planarity : 0.007 0.100 4773 Dihedral : 6.359 54.813 3690 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.58 % Favored : 96.24 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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 (0.13), residues: 3378 helix: 0.80 (0.16), residues: 973 sheet: 0.14 (0.19), residues: 688 loop : -1.91 (0.13), residues: 1717 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 511 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 519 average time/residue: 0.4215 time to fit residues: 336.6781 Evaluate side-chains 324 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 3.473 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2365 time to fit residues: 5.4963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 20.0000 chunk 95 optimal weight: 0.2980 chunk 255 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 307 optimal weight: 20.0000 chunk 332 optimal weight: 8.9990 chunk 273 optimal weight: 20.0000 chunk 304 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 overall best weight: 7.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 359 GLN D 4 GLN D 45 GLN D 81 HIS D 86 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 GLN H 213 HIS H 295 GLN I 45 GLN J 39 HIS J 97 GLN J 323 GLN ** J 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 466 HIS ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 841 HIS ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5467 moved from start: 0.6366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.121 27233 Z= 0.404 Angle : 0.814 15.516 36846 Z= 0.435 Chirality : 0.047 0.233 4271 Planarity : 0.006 0.077 4773 Dihedral : 6.144 52.038 3690 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.14 % Favored : 95.71 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.93 (0.14), residues: 3378 helix: 0.52 (0.16), residues: 983 sheet: -0.02 (0.19), residues: 705 loop : -1.60 (0.14), residues: 1690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 432 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 440 average time/residue: 0.4221 time to fit residues: 288.5055 Evaluate side-chains 295 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 3.217 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2942 time to fit residues: 5.0023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 308 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN C 57 ASN C 67 ASN D 208 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS I 130 ASN ** I 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 HIS J 338 HIS J 713 ASN J 888 HIS ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5343 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 27233 Z= 0.210 Angle : 0.633 12.584 36846 Z= 0.334 Chirality : 0.045 0.193 4271 Planarity : 0.004 0.073 4773 Dihedral : 5.413 49.669 3690 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.08 % Favored : 96.77 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.53 (0.14), residues: 3378 helix: 1.01 (0.16), residues: 993 sheet: 0.14 (0.19), residues: 688 loop : -1.42 (0.14), residues: 1697 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 433 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 434 average time/residue: 0.4064 time to fit residues: 277.8115 Evaluate side-chains 304 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 68.2943 > 50: distance: 94 - 101: 28.422 distance: 101 - 102: 44.752 distance: 102 - 103: 40.378 distance: 102 - 105: 17.111 distance: 103 - 104: 40.938 distance: 103 - 108: 48.113 distance: 105 - 106: 18.063 distance: 105 - 107: 42.752 distance: 108 - 109: 42.354 distance: 108 - 176: 31.711 distance: 109 - 110: 51.572 distance: 110 - 111: 11.447 distance: 110 - 116: 17.246 distance: 112 - 113: 38.559 distance: 113 - 114: 25.708 distance: 113 - 115: 22.560 distance: 116 - 117: 13.624 distance: 117 - 118: 33.186 distance: 117 - 120: 33.650 distance: 118 - 119: 52.100 distance: 118 - 122: 15.919 distance: 120 - 121: 29.886 distance: 122 - 123: 40.429 distance: 123 - 124: 36.531 distance: 123 - 126: 33.387 distance: 124 - 125: 27.500 distance: 124 - 130: 19.808 distance: 126 - 127: 31.175 distance: 127 - 128: 24.894 distance: 127 - 129: 25.296 distance: 130 - 131: 23.772 distance: 131 - 132: 31.420 distance: 132 - 133: 34.570 distance: 132 - 134: 24.684 distance: 134 - 135: 44.466 distance: 135 - 136: 21.719 distance: 135 - 138: 24.988 distance: 136 - 137: 33.701 distance: 136 - 142: 22.467 distance: 138 - 139: 42.101 distance: 139 - 140: 23.640 distance: 139 - 141: 44.962 distance: 142 - 143: 42.209 distance: 143 - 144: 56.197 distance: 144 - 145: 42.705 distance: 144 - 146: 25.118 distance: 146 - 147: 31.090 distance: 147 - 148: 25.122 distance: 147 - 150: 20.820 distance: 148 - 149: 27.377 distance: 148 - 153: 19.545 distance: 150 - 151: 68.294 distance: 150 - 152: 15.833 distance: 153 - 154: 29.980 distance: 154 - 155: 15.725 distance: 154 - 157: 8.604 distance: 155 - 156: 48.213 distance: 155 - 161: 39.310 distance: 157 - 158: 38.280 distance: 158 - 159: 35.688 distance: 158 - 160: 20.354 distance: 161 - 162: 16.041 distance: 162 - 163: 26.767 distance: 162 - 165: 36.958 distance: 163 - 164: 21.391 distance: 163 - 173: 13.208 distance: 165 - 166: 48.233 distance: 166 - 167: 21.134 distance: 166 - 168: 19.352 distance: 167 - 169: 33.009 distance: 168 - 170: 18.643 distance: 169 - 171: 16.219 distance: 170 - 171: 11.347 distance: 171 - 172: 17.651