Starting phenix.real_space_refine (version: dev) on Mon May 16 10:01:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/05_2022/6jqn_9875_updated.pdb" } resolution = 3.1 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= 0.016 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 PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 544": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 544": "NH1" <-> "NH2" Residue "E ARG 545": "NH1" <-> "NH2" Residue "E TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "E PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 545": "NH1" <-> "NH2" Residue "F ARG 580": "NH1" <-> "NH2" Residue "F PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 31278 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "C" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "D" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "E" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "F" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.33, per 1000 atoms: 0.55 Number of scatterers: 31278 At special positions: 0 Unit cell: (178.08, 174.9, 108.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 36 15.00 O 5934 8.00 N 5508 7.00 C 19644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.16 Conformation dependent library (CDL) restraints added in 4.7 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 46 sheets defined 32.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 41 through 57 removed outlier: 4.085A pdb=" N ALA A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.094A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 116 removed outlier: 3.604A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 187 through 200 removed outlier: 4.336A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 274 through 292 removed outlier: 6.268A pdb=" N LYS A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 321 removed outlier: 3.725A pdb=" N VAL A 308 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 313 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 319 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN A 320 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 Processing helix chain 'A' and resid 412 through 419 removed outlier: 4.430A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.650A pdb=" N ASP A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.788A pdb=" N ALA A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 490 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 4.028A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 564 through 567 No H-bonds generated for 'chain 'A' and resid 564 through 567' Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.540A pdb=" N ALA A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 573' Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.636A pdb=" N ALA A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 removed outlier: 4.012A pdb=" N ALA B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 61 through 77 Processing helix chain 'B' and resid 80 through 89 removed outlier: 3.612A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 116 removed outlier: 3.997A pdb=" N LEU B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 removed outlier: 4.326A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 187 through 200 removed outlier: 4.211A pdb=" N SER B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.672A pdb=" N MET B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 274 through 292 removed outlier: 6.076A pdb=" N LYS B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 319 removed outlier: 3.655A pdb=" N VAL B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 316 " --> pdb=" O ASP B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 355 removed outlier: 3.516A pdb=" N ALA B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 removed outlier: 4.403A pdb=" N GLY B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 removed outlier: 3.667A pdb=" N ARG B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 503 through 510 removed outlier: 3.888A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 564 through 567 No H-bonds generated for 'chain 'B' and resid 564 through 567' Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.732A pdb=" N ALA B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 569 through 573' Processing helix chain 'B' and resid 584 through 595 removed outlier: 3.718A pdb=" N ALA B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 removed outlier: 3.890A pdb=" N ALA C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Proline residue: C 54 - end of helix Processing helix chain 'C' and resid 61 through 77 removed outlier: 3.676A pdb=" N SER C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 4.050A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 117 removed outlier: 3.520A pdb=" N LEU C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 173 removed outlier: 4.505A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 187 through 200 removed outlier: 4.219A pdb=" N SER C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.744A pdb=" N MET C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 292 removed outlier: 6.100A pdb=" N LYS C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.637A pdb=" N VAL C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN C 309 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 313 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 354 Processing helix chain 'C' and resid 411 through 419 removed outlier: 4.426A pdb=" N GLY C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 442 removed outlier: 3.667A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 503 through 510 removed outlier: 3.947A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 559 Processing helix chain 'C' and resid 564 through 567 No H-bonds generated for 'chain 'C' and resid 564 through 567' Processing helix chain 'C' and resid 570 through 573 No H-bonds generated for 'chain 'C' and resid 570 through 573' Processing helix chain 'C' and resid 584 through 595 removed outlier: 3.548A pdb=" N ALA C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 57 removed outlier: 3.967A pdb=" N ALA D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Proline residue: D 54 - end of helix Processing helix chain 'D' and resid 61 through 77 removed outlier: 3.607A pdb=" N SER D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 89 removed outlier: 4.072A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 116 Processing helix chain 'D' and resid 160 through 173 removed outlier: 3.730A pdb=" N MET D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 187 through 200 removed outlier: 4.389A pdb=" N SER D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.745A pdb=" N GLN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 274 through 292 removed outlier: 6.226A pdb=" N LYS D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA D 291 " --> pdb=" O MET D 287 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLY D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 321 removed outlier: 3.726A pdb=" N VAL D 308 " --> pdb=" O GLN D 305 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN D 309 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D 313 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 318 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 319 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN D 320 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 354 removed outlier: 3.545A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 412 through 419 removed outlier: 4.307A pdb=" N GLY D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 442 removed outlier: 3.668A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 503 through 509 removed outlier: 3.973A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 559 Processing helix chain 'D' and resid 564 through 567 No H-bonds generated for 'chain 'D' and resid 564 through 567' Processing helix chain 'D' and resid 569 through 573 removed outlier: 3.505A pdb=" N ALA D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 569 through 573' Processing helix chain 'D' and resid 584 through 595 removed outlier: 3.545A pdb=" N ALA D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 57 removed outlier: 3.834A pdb=" N ALA E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 80 through 89 removed outlier: 3.656A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 117 removed outlier: 3.781A pdb=" N LEU E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 173 removed outlier: 4.288A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 187 through 200 removed outlier: 4.261A pdb=" N SER E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 234 through 240 removed outlier: 3.744A pdb=" N MET E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 274 through 292 removed outlier: 6.018A pdb=" N LYS E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA E 291 " --> pdb=" O MET E 287 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 319 removed outlier: 3.692A pdb=" N VAL E 308 " --> pdb=" O GLN E 305 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASN E 309 " --> pdb=" O ALA E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 411 through 419 removed outlier: 4.295A pdb=" N GLY E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 removed outlier: 3.650A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 486 through 488 No H-bonds generated for 'chain 'E' and resid 486 through 488' Processing helix chain 'E' and resid 503 through 510 removed outlier: 3.902A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 559 Processing helix chain 'E' and resid 564 through 567 No H-bonds generated for 'chain 'E' and resid 564 through 567' Processing helix chain 'E' and resid 570 through 573 No H-bonds generated for 'chain 'E' and resid 570 through 573' Processing helix chain 'E' and resid 584 through 595 removed outlier: 3.611A pdb=" N ALA E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 57 removed outlier: 4.051A pdb=" N ALA F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Proline residue: F 54 - end of helix Processing helix chain 'F' and resid 61 through 77 Processing helix chain 'F' and resid 80 through 89 removed outlier: 4.274A pdb=" N GLN F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 116 removed outlier: 3.812A pdb=" N LEU F 107 " --> pdb=" O GLY F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 173 removed outlier: 4.327A pdb=" N LYS F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Proline residue: F 170 - end of helix Processing helix chain 'F' and resid 187 through 200 removed outlier: 4.336A pdb=" N SER F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'F' and resid 274 through 292 removed outlier: 6.174A pdb=" N LYS F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA F 291 " --> pdb=" O MET F 287 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLY F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 321 removed outlier: 3.729A pdb=" N VAL F 308 " --> pdb=" O GLN F 305 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASN F 309 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP F 313 " --> pdb=" O ALA F 310 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 319 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN F 320 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 353 Processing helix chain 'F' and resid 412 through 419 removed outlier: 4.302A pdb=" N GLY F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 442 removed outlier: 3.690A pdb=" N ASP F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 486 through 488 No H-bonds generated for 'chain 'F' and resid 486 through 488' Processing helix chain 'F' and resid 503 through 510 removed outlier: 4.048A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 559 Processing helix chain 'F' and resid 564 through 567 No H-bonds generated for 'chain 'F' and resid 564 through 567' Processing helix chain 'F' and resid 569 through 573 removed outlier: 3.693A pdb=" N ALA F 573 " --> pdb=" O LYS F 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 569 through 573' Processing helix chain 'F' and resid 584 through 595 removed outlier: 3.704A pdb=" N ALA F 592 " --> pdb=" O LEU F 588 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 139 through 146 Processing sheet with id= C, first strand: chain 'A' and resid 252 through 254 removed outlier: 7.613A pdb=" N HIS A 153 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 179 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 180 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 262 through 264 removed outlier: 7.020A pdb=" N ARG A 300 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR A 402 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL A 303 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET A 404 " --> pdb=" O VAL A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 425 through 427 Processing sheet with id= F, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.465A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 545 through 547 removed outlier: 3.616A pdb=" N ASP A 622 " --> pdb=" O MET A 547 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.771A pdb=" N TRP A 32 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 6 through 8 Processing sheet with id= J, first strand: chain 'B' and resid 139 through 146 Processing sheet with id= K, first strand: chain 'B' and resid 252 through 256 removed outlier: 7.534A pdb=" N HIS B 153 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 179 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 180 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 402 through 404 removed outlier: 5.934A pdb=" N ASN B 261 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 301 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS B 263 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 425 through 428 Processing sheet with id= N, first strand: chain 'B' and resid 545 through 547 Processing sheet with id= O, first strand: chain 'B' and resid 665 through 673 removed outlier: 5.645A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.796A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 6 through 8 Processing sheet with id= R, first strand: chain 'C' and resid 139 through 146 Processing sheet with id= S, first strand: chain 'C' and resid 252 through 254 removed outlier: 7.641A pdb=" N HIS C 153 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 179 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 402 through 406 removed outlier: 6.039A pdb=" N ASN C 261 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE C 301 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N CYS C 263 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL C 303 " --> pdb=" O CYS C 263 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 425 through 428 Processing sheet with id= V, first strand: chain 'C' and resid 539 through 541 removed outlier: 6.549A pdb=" N GLU C 650 " --> pdb=" O LYS C 631 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 545 through 547 Processing sheet with id= X, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.875A pdb=" N TRP C 32 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= Z, first strand: chain 'D' and resid 139 through 146 Processing sheet with id= AA, first strand: chain 'D' and resid 252 through 254 removed outlier: 7.712A pdb=" N HIS D 153 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 179 " --> pdb=" O HIS D 153 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 402 through 406 removed outlier: 6.101A pdb=" N ASN D 261 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE D 301 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS D 263 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL D 303 " --> pdb=" O CYS D 263 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 425 through 427 Processing sheet with id= AD, first strand: chain 'D' and resid 539 through 541 removed outlier: 6.545A pdb=" N GLU D 650 " --> pdb=" O LYS D 631 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 545 through 547 removed outlier: 3.697A pdb=" N ASP D 622 " --> pdb=" O MET D 547 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.864A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 6 through 8 Processing sheet with id= AH, first strand: chain 'E' and resid 139 through 146 Processing sheet with id= AI, first strand: chain 'E' and resid 252 through 254 removed outlier: 7.683A pdb=" N HIS E 153 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE E 179 " --> pdb=" O HIS E 153 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 180 " --> pdb=" O SER E 209 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 402 through 406 removed outlier: 5.947A pdb=" N ASN E 261 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE E 301 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS E 263 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL E 303 " --> pdb=" O CYS E 263 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 425 through 428 Processing sheet with id= AL, first strand: chain 'E' and resid 545 through 547 removed outlier: 6.507A pdb=" N GLU E 650 " --> pdb=" O LYS E 631 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 665 " --> pdb=" O ARG E 613 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG E 613 " --> pdb=" O LEU E 665 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 611 " --> pdb=" O SER E 667 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU E 669 " --> pdb=" O LEU E 609 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU E 609 " --> pdb=" O LEU E 669 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.919A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 6 through 8 Processing sheet with id= AO, first strand: chain 'F' and resid 139 through 146 Processing sheet with id= AP, first strand: chain 'F' and resid 252 through 254 removed outlier: 7.603A pdb=" N HIS F 153 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE F 179 " --> pdb=" O HIS F 153 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'F' and resid 449 through 451 removed outlier: 6.672A pdb=" N GLY F 425 " --> pdb=" O GLN F 450 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS F 262 " --> pdb=" O THR F 426 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL F 428 " --> pdb=" O CYS F 262 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL F 264 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N CYS F 263 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE F 301 " --> pdb=" O CYS F 263 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU F 265 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL F 303 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR F 402 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL F 303 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET F 404 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 539 through 541 removed outlier: 6.458A pdb=" N GLU F 650 " --> pdb=" O LYS F 631 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'F' and resid 545 through 547 removed outlier: 3.632A pdb=" N ASP F 622 " --> pdb=" O MET F 547 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.909A pdb=" N TRP F 32 " --> pdb=" O ILE F 22 " (cutoff:3.500A) 1003 hydrogen bonds defined for protein. 2709 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: 10.73 Time building geometry restraints manager: 13.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9153 1.33 - 1.45: 4937 1.45 - 1.57: 17530 1.57 - 1.69: 66 1.69 - 1.81: 246 Bond restraints: 31932 Sorted by residual: bond pdb=" C1B CO8 E 802 " pdb=" O4B CO8 E 802 " ideal model delta sigma weight residual 1.652 1.425 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1B CO8 C 802 " pdb=" O4B CO8 C 802 " ideal model delta sigma weight residual 1.652 1.426 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1B CO8 D 802 " pdb=" O4B CO8 D 802 " ideal model delta sigma weight residual 1.652 1.426 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1B CO8 B 802 " pdb=" O4B CO8 B 802 " ideal model delta sigma weight residual 1.652 1.427 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1B CO8 F 802 " pdb=" O4B CO8 F 802 " ideal model delta sigma weight residual 1.652 1.429 0.223 2.00e-02 2.50e+03 1.25e+02 ... (remaining 31927 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.55: 869 105.55 - 113.30: 17753 113.30 - 121.05: 15416 121.05 - 128.81: 9147 128.81 - 136.56: 243 Bond angle restraints: 43428 Sorted by residual: angle pdb=" C TRP D 513 " pdb=" N VAL D 514 " pdb=" CA VAL D 514 " ideal model delta sigma weight residual 121.97 113.86 8.11 1.80e+00 3.09e-01 2.03e+01 angle pdb=" C TRP F 513 " pdb=" N VAL F 514 " pdb=" CA VAL F 514 " ideal model delta sigma weight residual 121.97 114.27 7.70 1.80e+00 3.09e-01 1.83e+01 angle pdb=" N1A CO8 A 802 " pdb=" C6A CO8 A 802 " pdb=" N6A CO8 A 802 " ideal model delta sigma weight residual 109.09 121.61 -12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" N1A CO8 F 802 " pdb=" C6A CO8 F 802 " pdb=" N6A CO8 F 802 " ideal model delta sigma weight residual 109.09 121.59 -12.50 3.00e+00 1.11e-01 1.74e+01 angle pdb=" N1A CO8 E 802 " pdb=" C6A CO8 E 802 " pdb=" N6A CO8 E 802 " ideal model delta sigma weight residual 109.09 121.41 -12.32 3.00e+00 1.11e-01 1.69e+01 ... (remaining 43423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 18788 35.97 - 71.93: 206 71.93 - 107.90: 31 107.90 - 143.87: 8 143.87 - 179.84: 17 Dihedral angle restraints: 19050 sinusoidal: 7530 harmonic: 11520 Sorted by residual: dihedral pdb=" O3 NAP C 801 " pdb="NO5* NAP C 801 " pdb="NP NAP C 801 " pdb="NC5* NAP C 801 " ideal model delta sinusoidal sigma weight residual 278.31 98.47 179.84 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3 NAP B 801 " pdb="NO5* NAP B 801 " pdb="NP NAP B 801 " pdb="NC5* NAP B 801 " ideal model delta sinusoidal sigma weight residual -81.69 92.95 -174.64 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb="NC2 NAP A 801 " pdb="NC3 NAP A 801 " pdb="NC7 NAP A 801 " pdb="NO7 NAP A 801 " ideal model delta sinusoidal sigma weight residual 168.83 -16.82 -174.35 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 19047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3151 0.046 - 0.092: 1257 0.092 - 0.138: 426 0.138 - 0.185: 63 0.185 - 0.231: 17 Chirality restraints: 4914 Sorted by residual: chirality pdb=" C2B CO8 D 802 " pdb=" C1B CO8 D 802 " pdb=" C3B CO8 D 802 " pdb=" O2B CO8 D 802 " both_signs ideal model delta sigma weight residual False -2.41 -2.65 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C2B CO8 F 802 " pdb=" C1B CO8 F 802 " pdb=" C3B CO8 F 802 " pdb=" O2B CO8 F 802 " both_signs ideal model delta sigma weight residual False -2.41 -2.64 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb="AC3* NAP E 801 " pdb="AC2* NAP E 801 " pdb="AC4* NAP E 801 " pdb="AO3* NAP E 801 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 4911 not shown) Planarity restraints: 5610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CO8 C 802 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C9P CO8 C 802 " -0.070 2.00e-02 2.50e+03 pdb=" CAP CO8 C 802 " 0.103 2.00e-02 2.50e+03 pdb=" N8P CO8 C 802 " -0.539 2.00e-02 2.50e+03 pdb=" O9P CO8 C 802 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P CO8 E 802 " -0.329 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C9P CO8 E 802 " 0.066 2.00e-02 2.50e+03 pdb=" CAP CO8 E 802 " -0.155 2.00e-02 2.50e+03 pdb=" N8P CO8 E 802 " 0.506 2.00e-02 2.50e+03 pdb=" O9P CO8 E 802 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P CO8 A 802 " 0.271 2.00e-02 2.50e+03 2.33e-01 6.77e+02 pdb=" C9P CO8 A 802 " -0.051 2.00e-02 2.50e+03 pdb=" CAP CO8 A 802 " -0.020 2.00e-02 2.50e+03 pdb=" N8P CO8 A 802 " -0.395 2.00e-02 2.50e+03 pdb=" O9P CO8 A 802 " 0.196 2.00e-02 2.50e+03 ... (remaining 5607 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8182 2.80 - 3.32: 27884 3.32 - 3.85: 55022 3.85 - 4.37: 64576 4.37 - 4.90: 112538 Nonbonded interactions: 268202 Sorted by model distance: nonbonded pdb=" OG SER D 19 " pdb=" OE1 GLU D 33 " model vdw 2.274 2.440 nonbonded pdb=" O6A CO8 C 802 " pdb=" OAP CO8 C 802 " model vdw 2.287 2.440 nonbonded pdb=" OH TYR A 607 " pdb=" O9A CO8 B 802 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR B 607 " pdb=" O9A CO8 A 802 " model vdw 2.302 2.440 nonbonded pdb=" OH TYR F 607 " pdb=" O8A CO8 E 802 " model vdw 2.310 2.440 ... (remaining 268197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 679) selection = (chain 'B' and resid 2 through 679) selection = (chain 'C' and resid 2 through 679) selection = (chain 'D' and resid 2 through 679) selection = (chain 'E' and resid 2 through 679) selection = (chain 'F' and resid 2 through 679) } 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 156 5.16 5 C 19644 2.51 5 N 5508 2.21 5 O 5934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 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: 0.030 Extract box with map and model: 17.800 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.230 Process input model: 78.810 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.170 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.010 0.227 31932 Z= 0.682 Angle : 0.976 12.518 43428 Z= 0.483 Chirality : 0.055 0.231 4914 Planarity : 0.010 0.300 5610 Dihedral : 13.820 179.836 11646 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.15 (0.10), residues: 4056 helix: -2.76 (0.10), residues: 1374 sheet: -3.27 (0.15), residues: 810 loop : -2.35 (0.12), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 784 time to evaluate : 3.664 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 784 average time/residue: 0.5026 time to fit residues: 595.0612 Evaluate side-chains 393 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 3.509 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 3.9990 chunk 304 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 365 optimal weight: 0.0770 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 450 GLN ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 261 ASN B 329 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 450 GLN B 463 HIS B 500 GLN B 659 HIS C 158 ASN C 339 ASN C 347 GLN C 409 GLN C 450 GLN C 500 GLN D 309 ASN D 329 GLN D 450 GLN D 500 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 329 GLN E 339 ASN E 384 GLN E 409 GLN E 450 GLN ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN E 525 HIS F 23 HIS F 158 ASN ** F 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN F 450 GLN F 463 HIS F 492 HIS F 500 GLN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 31932 Z= 0.258 Angle : 0.647 8.920 43428 Z= 0.319 Chirality : 0.044 0.202 4914 Planarity : 0.006 0.089 5610 Dihedral : 13.563 178.589 4596 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4056 helix: -1.31 (0.13), residues: 1386 sheet: -2.80 (0.17), residues: 732 loop : -1.90 (0.12), residues: 1938 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 413 time to evaluate : 3.263 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 444 average time/residue: 0.4651 time to fit residues: 320.0384 Evaluate side-chains 351 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 332 time to evaluate : 3.696 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2990 time to fit residues: 15.4959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 303 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 365 optimal weight: 1.9990 chunk 395 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 362 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 339 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN C 46 GLN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 HIS D 158 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 463 HIS ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 HIS E 659 HIS F 158 ASN F 339 ASN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.075 31932 Z= 0.500 Angle : 0.733 9.040 43428 Z= 0.362 Chirality : 0.049 0.222 4914 Planarity : 0.006 0.079 5610 Dihedral : 13.405 176.066 4596 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.64 (0.12), residues: 4056 helix: -0.99 (0.13), residues: 1398 sheet: -2.68 (0.16), residues: 780 loop : -1.80 (0.13), residues: 1878 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 350 time to evaluate : 3.859 Fit side-chains outliers start: 45 outliers final: 23 residues processed: 383 average time/residue: 0.5306 time to fit residues: 317.1077 Evaluate side-chains 328 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 305 time to evaluate : 3.717 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3033 time to fit residues: 18.2717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 367 optimal weight: 0.5980 chunk 388 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 347 optimal weight: 0.7980 chunk 104 optimal weight: 0.0670 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 409 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN D 492 HIS ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 31932 Z= 0.177 Angle : 0.576 8.576 43428 Z= 0.282 Chirality : 0.042 0.149 4914 Planarity : 0.005 0.073 5610 Dihedral : 12.881 179.075 4596 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.12), residues: 4056 helix: -0.41 (0.14), residues: 1398 sheet: -2.51 (0.17), residues: 774 loop : -1.54 (0.13), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 356 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 376 average time/residue: 0.5049 time to fit residues: 295.2468 Evaluate side-chains 322 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 313 time to evaluate : 3.658 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2889 time to fit residues: 10.2507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 3.9990 chunk 220 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 331 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 155 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 384 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 31932 Z= 0.307 Angle : 0.623 8.324 43428 Z= 0.305 Chirality : 0.044 0.176 4914 Planarity : 0.005 0.078 5610 Dihedral : 12.704 177.753 4596 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.13), residues: 4056 helix: -0.21 (0.14), residues: 1398 sheet: -2.48 (0.16), residues: 822 loop : -1.43 (0.14), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 328 time to evaluate : 4.034 Fit side-chains outliers start: 45 outliers final: 15 residues processed: 362 average time/residue: 0.4798 time to fit residues: 269.2833 Evaluate side-chains 330 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 315 time to evaluate : 3.984 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3578 time to fit residues: 14.1838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 0.6980 chunk 349 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 388 optimal weight: 0.7980 chunk 322 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 128 optimal weight: 0.1980 chunk 204 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 31932 Z= 0.242 Angle : 0.590 9.060 43428 Z= 0.288 Chirality : 0.043 0.143 4914 Planarity : 0.005 0.080 5610 Dihedral : 12.442 178.902 4596 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.13), residues: 4056 helix: -0.01 (0.14), residues: 1398 sheet: -2.36 (0.17), residues: 786 loop : -1.35 (0.14), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 340 time to evaluate : 3.778 Fit side-chains outliers start: 36 outliers final: 19 residues processed: 365 average time/residue: 0.4871 time to fit residues: 273.5953 Evaluate side-chains 335 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 316 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2792 time to fit residues: 14.6060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 221 optimal weight: 0.1980 chunk 284 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 387 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 339 ASN F 472 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 31932 Z= 0.184 Angle : 0.573 10.307 43428 Z= 0.277 Chirality : 0.042 0.149 4914 Planarity : 0.005 0.086 5610 Dihedral : 12.073 179.560 4596 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.13), residues: 4056 helix: 0.19 (0.14), residues: 1398 sheet: -2.22 (0.17), residues: 786 loop : -1.28 (0.14), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 355 time to evaluate : 3.371 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 365 average time/residue: 0.4778 time to fit residues: 272.6916 Evaluate side-chains 321 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 315 time to evaluate : 3.564 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2728 time to fit residues: 7.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 0.0470 chunk 154 optimal weight: 4.9990 chunk 231 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 304 optimal weight: 9.9990 overall best weight: 1.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 23 HIS B 46 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 31932 Z= 0.314 Angle : 0.624 10.723 43428 Z= 0.303 Chirality : 0.045 0.149 4914 Planarity : 0.005 0.091 5610 Dihedral : 12.071 176.307 4596 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 4056 helix: 0.19 (0.14), residues: 1398 sheet: -2.21 (0.17), residues: 786 loop : -1.26 (0.14), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 3.756 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 335 average time/residue: 0.4986 time to fit residues: 257.5478 Evaluate side-chains 326 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 313 time to evaluate : 3.702 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3783 time to fit residues: 13.9417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 0.8980 chunk 371 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 217 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 283 optimal weight: 0.0770 chunk 110 optimal weight: 0.5980 chunk 326 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN B 23 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 HIS ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 31932 Z= 0.204 Angle : 0.580 10.201 43428 Z= 0.281 Chirality : 0.043 0.143 4914 Planarity : 0.005 0.084 5610 Dihedral : 11.801 179.047 4596 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.13), residues: 4056 helix: 0.32 (0.14), residues: 1398 sheet: -2.11 (0.17), residues: 780 loop : -1.23 (0.14), residues: 1878 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 329 time to evaluate : 3.618 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 335 average time/residue: 0.4889 time to fit residues: 251.5597 Evaluate side-chains 319 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 313 time to evaluate : 3.559 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2875 time to fit residues: 8.0583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 8.9990 chunk 381 optimal weight: 1.9990 chunk 233 optimal weight: 0.0970 chunk 181 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 400 optimal weight: 0.9980 chunk 368 optimal weight: 4.9990 chunk 318 optimal weight: 0.0020 chunk 33 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 HIS ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.168 31932 Z= 0.215 Angle : 0.582 10.981 43428 Z= 0.284 Chirality : 0.043 0.139 4914 Planarity : 0.005 0.108 5610 Dihedral : 11.580 178.699 4596 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.13), residues: 4056 helix: 0.41 (0.14), residues: 1398 sheet: -2.04 (0.17), residues: 780 loop : -1.18 (0.14), residues: 1878 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 329 time to evaluate : 3.507 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 334 average time/residue: 0.4953 time to fit residues: 255.0031 Evaluate side-chains 315 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2885 time to fit residues: 5.4652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 294 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 319 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 327 optimal weight: 0.0000 chunk 40 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN E 339 ASN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.097933 restraints weight = 44521.106| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.80 r_work: 0.3083 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 1.61 restraints_weight: 0.2500 r_work: 0.3049 rms_B_bonded: 1.72 restraints_weight: 0.1250 r_work: 0.3029 rms_B_bonded: 1.91 restraints_weight: 0.0625 r_work: 0.3005 rms_B_bonded: 2.19 restraints_weight: 0.0312 r_work: 0.2977 rms_B_bonded: 2.56 restraints_weight: 0.0156 r_work: 0.2942 rms_B_bonded: 3.07 restraints_weight: 0.0078 r_work: 0.2899 rms_B_bonded: 3.76 restraints_weight: 0.0039 r_work: 0.2843 rms_B_bonded: 4.73 restraints_weight: 0.0020 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.500 31932 Z= 0.322 Angle : 0.594 24.980 43428 Z= 0.298 Chirality : 0.042 0.153 4914 Planarity : 0.005 0.124 5610 Dihedral : 11.332 179.372 4596 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.13), residues: 4056 helix: 0.52 (0.14), residues: 1392 sheet: -2.00 (0.18), residues: 726 loop : -1.18 (0.14), residues: 1938 =============================================================================== Job complete usr+sys time: 6284.27 seconds wall clock time: 115 minutes 4.62 seconds (6904.62 seconds total)