Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:35:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/12_2022/7jpw_22425_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/12_2022/7jpw_22425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/12_2022/7jpw_22425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/12_2022/7jpw_22425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/12_2022/7jpw_22425_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/12_2022/7jpw_22425_updated_updated.pdb" } resolution = 3.2 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= -0.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 598": "OD1" <-> "OD2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1121": "OE1" <-> "OE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1196": "OD1" <-> "OD2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A PHE 1260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1343": "OD1" <-> "OD2" Residue "A GLU 1348": "OE1" <-> "OE2" Residue "A TYR 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A GLU 1408": "OE1" <-> "OE2" Residue "A GLU 1412": "OE1" <-> "OE2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1428": "NH1" <-> "NH2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 219": "OE1" <-> "OE2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 373": "OE1" <-> "OE2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 441": "OD1" <-> "OD2" Residue "F GLU 476": "OE1" <-> "OE2" Residue "F ASP 493": "OD1" <-> "OD2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 603": "OD1" <-> "OD2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F ASP 654": "OD1" <-> "OD2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "F PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 668": "OD1" <-> "OD2" Residue "F ASP 677": "OD1" <-> "OD2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "F ASP 711": "OD1" <-> "OD2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F GLU 753": "OE1" <-> "OE2" Residue "F TYR 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 774": "OD1" <-> "OD2" Residue "F TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 846": "NH1" <-> "NH2" Residue "F ASP 849": "OD1" <-> "OD2" Residue "F ASP 869": "OD1" <-> "OD2" Residue "F GLU 880": "OE1" <-> "OE2" Residue "F ASP 882": "OD1" <-> "OD2" Residue "F PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 987": "OD1" <-> "OD2" Residue "F ARG 1004": "NH1" <-> "NH2" Residue "F GLU 1069": "OE1" <-> "OE2" Residue "F ASP 1070": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18583 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 9009 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1078} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "A" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 444 Unusual residues: {' CA': 1, '3PE': 9, 'PC1': 1, 'VFY': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 10.76, per 1000 atoms: 0.58 Number of scatterers: 18583 At special positions: 0 Unit cell: (144.82, 137.022, 158.188, 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) Ca 1 19.99 S 109 16.00 P 10 15.00 F 3 9.00 O 3349 8.00 N 2985 7.00 C 12126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.02 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.02 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.04 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 2.7 seconds 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 12 sheets defined 47.2% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain 'A' and resid 53 through 69 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.617A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 141 removed outlier: 3.535A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.678A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 3.708A pdb=" N SER A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 195 through 217 removed outlier: 4.201A pdb=" N HIS A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 199 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 207 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 211 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.092A pdb=" N VAL A 315 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR A 316 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 318 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 319 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 344 removed outlier: 3.879A pdb=" N LYS A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 451 removed outlier: 4.266A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 485 removed outlier: 4.057A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.712A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 527 through 540 removed outlier: 4.063A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 549 through 558 removed outlier: 4.495A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 removed outlier: 3.626A pdb=" N LEU A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 632 through 646 removed outlier: 3.996A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N CYS A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.666A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 671 Processing helix chain 'A' and resid 802 through 817 removed outlier: 4.250A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 812 " --> pdb=" O PHE A 808 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 844 removed outlier: 4.036A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 851 No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 869 through 881 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.511A pdb=" N VAL A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 915 through 923 removed outlier: 3.523A pdb=" N CYS A 920 " --> pdb=" O HIS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 950 removed outlier: 3.614A pdb=" N LEU A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1039 through 1051 removed outlier: 3.775A pdb=" N ALA A1042 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A1044 " --> pdb=" O MET A1041 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A1047 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A1048 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A1049 " --> pdb=" O ILE A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1068 removed outlier: 4.051A pdb=" N VAL A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 4.268A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 removed outlier: 4.283A pdb=" N ALA A1126 " --> pdb=" O TYR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1172 removed outlier: 3.944A pdb=" N ALA A1171 " --> pdb=" O LEU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1205 removed outlier: 3.635A pdb=" N ILE A1191 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1192 " --> pdb=" O LEU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1248 removed outlier: 3.818A pdb=" N ARG A1239 " --> pdb=" O ARG A1236 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A1242 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A1248 " --> pdb=" O LYS A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1264 removed outlier: 3.798A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1288 removed outlier: 3.519A pdb=" N LEU A1273 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 Processing helix chain 'A' and resid 1325 through 1331 Processing helix chain 'A' and resid 1355 through 1387 removed outlier: 4.299A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A1365 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A1371 " --> pdb=" O CYS A1368 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A1372 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A1378 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A1382 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP A1385 " --> pdb=" O ASP A1382 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A1387 " --> pdb=" O PHE A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1409 removed outlier: 3.582A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1427 No H-bonds generated for 'chain 'A' and resid 1425 through 1427' Processing helix chain 'E' and resid 7 through 25 Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 135 through 163 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 181 through 203 Processing helix chain 'F' and resid 30 through 52 Processing helix chain 'F' and resid 54 through 64 removed outlier: 4.058A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 110 removed outlier: 3.734A pdb=" N ARG F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 201 removed outlier: 3.545A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 284 removed outlier: 4.155A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.804A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 347 removed outlier: 3.786A pdb=" N LEU F 347 " --> pdb=" O PHE F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 419 through 425 removed outlier: 4.824A pdb=" N ILE F 423 " --> pdb=" O GLY F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 429 No H-bonds generated for 'chain 'F' and resid 427 through 429' Processing helix chain 'F' and resid 434 through 439 Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'F' and resid 496 through 499 No H-bonds generated for 'chain 'F' and resid 496 through 499' Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 641 through 650 removed outlier: 3.714A pdb=" N THR F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 5.489A pdb=" N GLU F 657 " --> pdb=" O ASP F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 702 through 721 Processing helix chain 'F' and resid 723 through 725 No H-bonds generated for 'chain 'F' and resid 723 through 725' Processing helix chain 'F' and resid 749 through 753 removed outlier: 3.659A pdb=" N GLU F 753 " --> pdb=" O GLU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 763 No H-bonds generated for 'chain 'F' and resid 761 through 763' Processing helix chain 'F' and resid 765 through 772 removed outlier: 3.512A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 821 through 829 Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 892 Processing helix chain 'F' and resid 1046 through 1049 No H-bonds generated for 'chain 'F' and resid 1046 through 1049' Processing sheet with id= A, first strand: chain 'A' and resid 225 through 228 Processing sheet with id= B, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= C, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= D, first strand: chain 'E' and resid 48 through 50 Processing sheet with id= E, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= F, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.903A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 300 through 302 removed outlier: 8.007A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR F 411 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER F 390 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR F 413 " --> pdb=" O SER F 390 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= I, first strand: chain 'F' and resid 662 through 664 removed outlier: 4.089A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 992 through 997 removed outlier: 6.001A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP F 857 " --> pdb=" O LEU F 862 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU F 862 " --> pdb=" O ASP F 857 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 895 through 902 removed outlier: 4.341A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 905 through 907 732 hydrogen bonds defined for protein. 1898 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: 5.13 Time building geometry restraints manager: 6.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2981 1.31 - 1.45: 5361 1.45 - 1.58: 10467 1.58 - 1.72: 20 1.72 - 1.86: 168 Bond restraints: 18997 Sorted by residual: bond pdb=" C05 VFY A1912 " pdb=" C06 VFY A1912 " ideal model delta sigma weight residual 1.375 1.532 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C09 VFY A1912 " pdb=" C11 VFY A1912 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C21 3PE A1906 " pdb=" O21 3PE A1906 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C21 3PE A1907 " pdb=" O21 3PE A1907 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 18992 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.82: 315 104.82 - 112.16: 9401 112.16 - 119.51: 6567 119.51 - 126.86: 9182 126.86 - 134.20: 214 Bond angle restraints: 25679 Sorted by residual: angle pdb=" C SER E 81 " pdb=" N TYR E 82 " pdb=" CA TYR E 82 " ideal model delta sigma weight residual 121.29 132.21 -10.92 1.74e+00 3.30e-01 3.94e+01 angle pdb=" N VAL A 661 " pdb=" CA VAL A 661 " pdb=" C VAL A 661 " ideal model delta sigma weight residual 113.71 107.85 5.86 9.50e-01 1.11e+00 3.80e+01 angle pdb=" C TYR A 541 " pdb=" N TRP A 542 " pdb=" CA TRP A 542 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" N LEU A 522 " pdb=" CA LEU A 522 " pdb=" C LEU A 522 " ideal model delta sigma weight residual 111.36 105.62 5.74 1.09e+00 8.42e-01 2.77e+01 angle pdb=" N PHE A 536 " pdb=" CA PHE A 536 " pdb=" C PHE A 536 " ideal model delta sigma weight residual 111.28 116.17 -4.89 1.09e+00 8.42e-01 2.01e+01 ... (remaining 25674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 9478 17.76 - 35.53: 1274 35.53 - 53.29: 440 53.29 - 71.06: 106 71.06 - 88.82: 21 Dihedral angle restraints: 11319 sinusoidal: 4703 harmonic: 6616 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -146.18 60.18 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA ASP F 227 " pdb=" C ASP F 227 " pdb=" N ASN F 228 " pdb=" CA ASN F 228 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP F 518 " pdb=" C ASP F 518 " pdb=" N PRO F 519 " pdb=" CA PRO F 519 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1936 0.056 - 0.112: 765 0.112 - 0.168: 127 0.168 - 0.224: 18 0.224 - 0.281: 2 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA TRP A 542 " pdb=" N TRP A 542 " pdb=" C TRP A 542 " pdb=" CB TRP A 542 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA PRO A 268 " pdb=" N PRO A 268 " pdb=" C PRO A 268 " pdb=" CB PRO A 268 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASN F 379 " pdb=" N ASN F 379 " pdb=" C ASN F 379 " pdb=" CB ASN F 379 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2845 not shown) Planarity restraints: 3203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 81 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C SER E 81 " -0.051 2.00e-02 2.50e+03 pdb=" O SER E 81 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR E 82 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 75 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 52 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.034 5.00e-02 4.00e+02 ... (remaining 3200 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 373 2.63 - 3.20: 17255 3.20 - 3.77: 27385 3.77 - 4.33: 39899 4.33 - 4.90: 65794 Nonbonded interactions: 150706 Sorted by model distance: nonbonded pdb=" OD2 ASP F 711 " pdb=" OG1 THR F 739 " model vdw 2.068 2.440 nonbonded pdb=" N 3PE A1906 " pdb=" O11 3PE A1906 " model vdw 2.079 2.520 nonbonded pdb=" N 3PE A1911 " pdb=" O14 3PE A1911 " model vdw 2.079 2.520 nonbonded pdb=" O SER A1232 " pdb=" OG SER A1232 " model vdw 2.105 2.440 nonbonded pdb=" OH TYR F 452 " pdb=" OG1 THR F 463 " model vdw 2.121 2.440 ... (remaining 150701 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 Ca 1 9.91 5 P 10 5.49 5 S 109 5.16 5 C 12126 2.51 5 N 2985 2.21 5 O 3349 1.98 5 F 3 1.80 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=0.50 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: 1.460 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: 0.020 Extract box with map and model: 5.900 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 42.040 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.015 0.157 18997 Z= 0.962 Angle : 1.060 11.014 25679 Z= 0.555 Chirality : 0.058 0.281 2848 Planarity : 0.006 0.062 3203 Dihedral : 18.756 88.820 7008 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.64 % Favored : 90.27 % Rotamer Outliers : 11.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.14), residues: 2222 helix: -2.69 (0.12), residues: 1094 sheet: -2.28 (0.30), residues: 219 loop : -3.51 (0.16), residues: 909 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 208 time to evaluate : 2.112 Fit side-chains revert: symmetry clash outliers start: 220 outliers final: 156 residues processed: 408 average time/residue: 0.2761 time to fit residues: 175.2246 Evaluate side-chains 340 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 184 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 0 residues processed: 156 average time/residue: 0.1843 time to fit residues: 54.4149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 239 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 453 HIS A 803 ASN A 909 ASN A 958 ASN ** A1058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN A1138 GLN A1154 ASN A1183 ASN A1383 ASN A1398 HIS E 209 GLN F 56 GLN F 164 GLN F 169 HIS F 308 HIS F 395 ASN F 470 ASN F 511 ASN F 551 GLN F 556 GLN F 644 GLN F 679 ASN F 685 ASN F 720 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 888 HIS F 988 ASN F1039 GLN F1065 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 18997 Z= 0.185 Angle : 0.588 9.117 25679 Z= 0.299 Chirality : 0.041 0.171 2848 Planarity : 0.005 0.054 3203 Dihedral : 10.838 59.596 2737 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.16), residues: 2222 helix: -1.22 (0.15), residues: 1106 sheet: -1.83 (0.32), residues: 216 loop : -2.74 (0.18), residues: 900 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 2.256 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 11 residues processed: 263 average time/residue: 0.3014 time to fit residues: 123.4596 Evaluate side-chains 209 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1777 time to fit residues: 6.4290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 169 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 644 GLN F 847 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 18997 Z= 0.165 Angle : 0.539 9.067 25679 Z= 0.273 Chirality : 0.040 0.138 2848 Planarity : 0.004 0.052 3203 Dihedral : 9.670 59.994 2737 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2222 helix: -0.58 (0.15), residues: 1115 sheet: -1.57 (0.32), residues: 218 loop : -2.35 (0.19), residues: 889 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 214 time to evaluate : 2.180 Fit side-chains outliers start: 43 outliers final: 18 residues processed: 243 average time/residue: 0.2857 time to fit residues: 110.8200 Evaluate side-chains 216 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2148 time to fit residues: 10.2930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 105 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.0970 chunk 136 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 HIS A1287 GLN F 165 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 18997 Z= 0.173 Angle : 0.533 10.223 25679 Z= 0.270 Chirality : 0.040 0.139 2848 Planarity : 0.004 0.051 3203 Dihedral : 9.235 58.963 2737 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2222 helix: -0.23 (0.16), residues: 1118 sheet: -1.34 (0.32), residues: 217 loop : -2.13 (0.19), residues: 887 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 2.035 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 232 average time/residue: 0.2985 time to fit residues: 108.1383 Evaluate side-chains 204 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 2.149 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1716 time to fit residues: 5.4889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 663 ASN A1058 ASN F 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 18997 Z= 0.257 Angle : 0.567 12.041 25679 Z= 0.285 Chirality : 0.042 0.156 2848 Planarity : 0.004 0.051 3203 Dihedral : 9.254 59.541 2737 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2222 helix: -0.23 (0.15), residues: 1131 sheet: -1.34 (0.33), residues: 220 loop : -2.08 (0.20), residues: 871 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 208 time to evaluate : 2.125 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 225 average time/residue: 0.2917 time to fit residues: 104.1680 Evaluate side-chains 212 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1847 time to fit residues: 7.2698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 113 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN E 209 GLN F 484 GLN F 655 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 18997 Z= 0.179 Angle : 0.530 13.428 25679 Z= 0.267 Chirality : 0.040 0.143 2848 Planarity : 0.004 0.050 3203 Dihedral : 8.970 59.454 2737 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2222 helix: 0.08 (0.16), residues: 1113 sheet: -1.23 (0.33), residues: 220 loop : -1.93 (0.20), residues: 889 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 2.147 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 224 average time/residue: 0.2939 time to fit residues: 105.9535 Evaluate side-chains 209 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 2.037 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2197 time to fit residues: 5.8756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 72.031 > 50: distance: 15 - 19: 35.907 distance: 19 - 20: 39.303 distance: 20 - 21: 38.827 distance: 20 - 23: 37.542 distance: 21 - 27: 56.506 distance: 23 - 24: 23.362 distance: 27 - 28: 32.781 distance: 28 - 29: 57.407 distance: 28 - 31: 57.526 distance: 29 - 30: 46.566 distance: 29 - 35: 24.886 distance: 31 - 32: 40.197 distance: 35 - 36: 55.439 distance: 36 - 37: 39.601 distance: 37 - 38: 56.562 distance: 37 - 47: 40.435 distance: 41 - 43: 39.646 distance: 44 - 45: 40.311 distance: 45 - 46: 40.312 distance: 47 - 48: 40.853 distance: 47 - 181: 35.939 distance: 48 - 51: 40.677 distance: 50 - 178: 37.527 distance: 51 - 52: 40.686 distance: 54 - 55: 55.324 distance: 55 - 56: 54.802 distance: 56 - 57: 53.325 distance: 56 - 61: 5.642 distance: 58 - 59: 41.212 distance: 58 - 60: 55.844 distance: 61 - 62: 28.799 distance: 61 - 161: 27.910 distance: 62 - 63: 56.836 distance: 62 - 65: 39.357 distance: 63 - 64: 56.991 distance: 63 - 70: 62.136 distance: 64 - 158: 33.970 distance: 66 - 67: 55.981 distance: 67 - 69: 56.770 distance: 70 - 71: 42.249 distance: 70 - 76: 28.508 distance: 71 - 74: 39.550 distance: 72 - 73: 38.851 distance: 72 - 77: 38.861 distance: 74 - 75: 39.307 distance: 77 - 78: 58.531 distance: 78 - 79: 39.769 distance: 78 - 81: 24.231 distance: 79 - 80: 48.507 distance: 79 - 85: 37.606 distance: 82 - 84: 40.533 distance: 85 - 86: 41.071 distance: 86 - 89: 44.197 distance: 87 - 88: 24.894 distance: 87 - 93: 66.893 distance: 89 - 90: 43.779 distance: 93 - 94: 66.489 distance: 94 - 97: 40.485 distance: 95 - 98: 34.202