Starting phenix.real_space_refine (version: dev) on Tue Feb 28 00:09:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2023/6jqn_9875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2023/6jqn_9875.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2023/6jqn_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_9875/02_2023/6jqn_9875_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2023/6jqn_9875_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2023/6jqn_9875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2023/6jqn_9875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2023/6jqn_9875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2023/6jqn_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 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 19.02, per 1000 atoms: 0.61 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: 12.94 Conformation dependent library (CDL) restraints added in 4.9 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: 4.18 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: 10.95 Time building geometry restraints manager: 13.75 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 1.655 1.425 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1B CO8 C 802 " pdb=" O4B CO8 C 802 " ideal model delta sigma weight residual 1.655 1.426 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1B CO8 D 802 " pdb=" O4B CO8 D 802 " ideal model delta sigma weight residual 1.655 1.426 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1B CO8 B 802 " pdb=" O4B CO8 B 802 " ideal model delta sigma weight residual 1.655 1.427 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1B CO8 F 802 " pdb=" O4B CO8 F 802 " ideal model delta sigma weight residual 1.655 1.429 0.226 2.00e-02 2.50e+03 1.28e+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 109.11 121.61 -12.50 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 109.11 121.59 -12.48 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C TRP E 513 " pdb=" N VAL E 514 " pdb=" CA VAL E 514 " ideal model delta sigma weight residual 121.97 114.59 7.38 1.80e+00 3.09e-01 1.68e+01 ... (remaining 43423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 18727 33.29 - 66.58: 259 66.58 - 99.86: 25 99.86 - 133.15: 0 133.15 - 166.44: 3 Dihedral angle restraints: 19014 sinusoidal: 7494 harmonic: 11520 Sorted by residual: dihedral pdb=" CA ASP E 522 " pdb=" C ASP E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ASP B 522 " pdb=" C ASP B 522 " pdb=" N ARG B 523 " pdb=" CA ARG B 523 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP D 522 " pdb=" C ASP D 522 " pdb=" N ARG D 523 " pdb=" CA ARG D 523 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 19011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3604 0.057 - 0.114: 1087 0.114 - 0.171: 185 0.171 - 0.227: 30 0.227 - 0.284: 8 Chirality restraints: 4914 Sorted by residual: chirality pdb=" C1B NAP F 801 " pdb=" C2B NAP F 801 " pdb=" N9A NAP F 801 " pdb=" O4B NAP F 801 " both_signs ideal model delta sigma weight residual False 2.31 2.59 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C1B NAP E 801 " pdb=" C2B NAP E 801 " pdb=" N9A NAP E 801 " pdb=" O4B NAP E 801 " both_signs ideal model delta sigma weight residual False 2.31 2.57 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C1B NAP B 801 " pdb=" C2B NAP B 801 " pdb=" N9A NAP B 801 " pdb=" O4B NAP B 801 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.47e+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: 3.740 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: 0.010 Extract box with map and model: 17.890 Check model and map are aligned: 0.460 Process input model: 81.500 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.280 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.570 ------------------------------------------------------------------------------- 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 0.230 31932 Z= 0.671 Angle : 1.011 12.498 43428 Z= 0.491 Chirality : 0.055 0.284 4914 Planarity : 0.010 0.300 5610 Dihedral : 11.565 166.440 11610 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.69 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 : 3.534 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 784 average time/residue: 0.5295 time to fit residues: 621.0448 Evaluate side-chains 394 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 3.637 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9031 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.0940 ------------------------------------------------------------------------------- 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 158 ASN 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 261 ASN 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 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN F 409 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 31932 Z= 0.246 Angle : 0.608 8.033 43428 Z= 0.312 Chirality : 0.044 0.201 4914 Planarity : 0.006 0.049 5610 Dihedral : 9.318 177.039 4560 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 1.26 % 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: -2.92 (0.12), residues: 4056 helix: -1.35 (0.13), residues: 1386 sheet: -2.83 (0.16), residues: 732 loop : -1.92 (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 452 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 412 time to evaluate : 3.530 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 441 average time/residue: 0.5048 time to fit residues: 343.6894 Evaluate side-chains 346 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 328 time to evaluate : 3.811 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3550 time to fit residues: 16.2982 ------------------------------------------------------------------------------- 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: 0.0980 chunk 303 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 365 optimal weight: 0.9980 chunk 395 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 362 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 659 HIS F 158 ASN F 245 ASN F 339 ASN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 31932 Z= 0.252 Angle : 0.574 7.903 43428 Z= 0.291 Chirality : 0.043 0.173 4914 Planarity : 0.005 0.044 5610 Dihedral : 8.891 179.416 4560 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.17 % 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: -2.42 (0.12), residues: 4056 helix: -0.76 (0.13), residues: 1398 sheet: -2.64 (0.17), residues: 750 loop : -1.72 (0.13), residues: 1908 *********************** 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 400 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 363 time to evaluate : 3.650 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 386 average time/residue: 0.4949 time to fit residues: 296.0738 Evaluate side-chains 330 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 315 time to evaluate : 3.569 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2882 time to fit residues: 13.3434 ------------------------------------------------------------------------------- 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: 8.9990 chunk 274 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 388 optimal weight: 0.4980 chunk 191 optimal weight: 3.9990 chunk 347 optimal weight: 0.4980 chunk 104 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN ** A 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 409 GLN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 492 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 31932 Z= 0.278 Angle : 0.580 8.755 43428 Z= 0.292 Chirality : 0.044 0.153 4914 Planarity : 0.005 0.044 5610 Dihedral : 8.708 176.807 4560 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -2.09 (0.12), residues: 4056 helix: -0.37 (0.14), residues: 1398 sheet: -2.57 (0.17), residues: 786 loop : -1.52 (0.13), residues: 1872 *********************** 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 392 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 349 time to evaluate : 3.355 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 378 average time/residue: 0.5098 time to fit residues: 297.0321 Evaluate side-chains 328 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 309 time to evaluate : 3.711 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2937 time to fit residues: 15.2062 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 0.3980 chunk 289 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 331 optimal weight: 0.0970 chunk 268 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 348 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 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 46 GLN E 158 ASN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 31932 Z= 0.251 Angle : 0.561 8.862 43428 Z= 0.282 Chirality : 0.043 0.145 4914 Planarity : 0.004 0.047 5610 Dihedral : 8.583 177.209 4560 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.98 % 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: -1.85 (0.13), residues: 4056 helix: -0.11 (0.14), residues: 1404 sheet: -2.46 (0.17), residues: 786 loop : -1.44 (0.13), residues: 1866 *********************** 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 369 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 338 time to evaluate : 3.761 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 358 average time/residue: 0.5136 time to fit residues: 285.5087 Evaluate side-chains 321 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 309 time to evaluate : 3.770 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2987 time to fit residues: 12.0345 ------------------------------------------------------------------------------- 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: 3.9990 chunk 349 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 228 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 388 optimal weight: 0.0980 chunk 322 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 128 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31932 Z= 0.191 Angle : 0.537 9.290 43428 Z= 0.268 Chirality : 0.042 0.139 4914 Planarity : 0.004 0.065 5610 Dihedral : 8.406 178.666 4560 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.85 % 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: -1.65 (0.13), residues: 4056 helix: 0.11 (0.14), residues: 1404 sheet: -2.33 (0.17), residues: 780 loop : -1.38 (0.13), 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 380 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 353 time to evaluate : 3.840 Fit side-chains outliers start: 27 outliers final: 7 residues processed: 373 average time/residue: 0.5021 time to fit residues: 289.3646 Evaluate side-chains 328 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 321 time to evaluate : 3.506 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2792 time to fit residues: 8.4463 ------------------------------------------------------------------------------- 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: 0.8980 chunk 43 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 284 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 327 optimal weight: 0.4980 chunk 217 optimal weight: 0.9980 chunk 387 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 31932 Z= 0.187 Angle : 0.533 9.323 43428 Z= 0.265 Chirality : 0.042 0.139 4914 Planarity : 0.004 0.050 5610 Dihedral : 8.286 179.282 4560 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.63 % 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: -1.48 (0.13), residues: 4056 helix: 0.28 (0.14), residues: 1404 sheet: -2.23 (0.17), residues: 780 loop : -1.31 (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 359 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 339 time to evaluate : 3.838 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 351 average time/residue: 0.5134 time to fit residues: 280.1508 Evaluate side-chains 332 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 323 time to evaluate : 3.894 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3164 time to fit residues: 10.1182 ------------------------------------------------------------------------------- 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: 0.0980 chunk 154 optimal weight: 5.9990 chunk 231 optimal weight: 0.1980 chunk 116 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 191 optimal weight: 0.0570 chunk 36 optimal weight: 8.9990 chunk 304 optimal weight: 10.0000 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** 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 158 ASN ** 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: 0.8433 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 31932 Z= 0.151 Angle : 0.521 9.710 43428 Z= 0.258 Chirality : 0.041 0.138 4914 Planarity : 0.004 0.053 5610 Dihedral : 8.135 176.899 4560 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.54 % 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: -1.33 (0.13), residues: 4056 helix: 0.41 (0.14), residues: 1404 sheet: -2.18 (0.18), residues: 726 loop : -1.26 (0.13), residues: 1926 *********************** 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 366 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 349 time to evaluate : 3.435 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 361 average time/residue: 0.4962 time to fit residues: 278.3063 Evaluate side-chains 321 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 316 time to evaluate : 3.524 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2965 time to fit residues: 7.4649 ------------------------------------------------------------------------------- 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: 1.9990 chunk 371 optimal weight: 10.0000 chunk 338 optimal weight: 3.9990 chunk 361 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 110 optimal weight: 0.0870 chunk 326 optimal weight: 2.9990 chunk 341 optimal weight: 0.8980 chunk 359 optimal weight: 0.9980 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN B 23 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 409 GLN ** D 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** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 31932 Z= 0.280 Angle : 0.578 9.886 43428 Z= 0.287 Chirality : 0.044 0.178 4914 Planarity : 0.004 0.063 5610 Dihedral : 8.237 176.445 4560 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.63 % 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: 0.36 (0.14), residues: 1404 sheet: -2.12 (0.17), residues: 780 loop : -1.25 (0.14), residues: 1872 *********************** 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 348 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 3.405 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 344 average time/residue: 0.5302 time to fit residues: 281.9216 Evaluate side-chains 320 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 311 time to evaluate : 3.791 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3078 time to fit residues: 9.9115 ------------------------------------------------------------------------------- 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: 5.9990 chunk 181 optimal weight: 0.5980 chunk 265 optimal weight: 0.0270 chunk 400 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 chunk 318 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 246 optimal weight: 0.0470 chunk 195 optimal weight: 0.6980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 23 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 31932 Z= 0.154 Angle : 0.529 10.279 43428 Z= 0.264 Chirality : 0.042 0.169 4914 Planarity : 0.004 0.056 5610 Dihedral : 8.002 173.067 4560 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -1.20 (0.13), residues: 4056 helix: 0.52 (0.14), residues: 1404 sheet: -2.09 (0.18), residues: 726 loop : -1.19 (0.13), residues: 1926 ********************** 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 349 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 339 time to evaluate : 3.441 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 345 average time/residue: 0.4991 time to fit residues: 266.4724 Evaluate side-chains 327 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 323 time to evaluate : 3.417 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4699 time to fit residues: 7.4519 ------------------------------------------------------------------------------- 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: 3.9990 chunk 339 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 294 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 319 optimal weight: 0.0030 chunk 133 optimal weight: 0.7980 chunk 327 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 C 191 GLN ** D 191 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098377 restraints weight = 44567.764| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.79 r_work: 0.2990 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 31932 Z= 0.175 Angle : 0.536 9.471 43428 Z= 0.265 Chirality : 0.042 0.182 4914 Planarity : 0.004 0.063 5610 Dihedral : 7.903 170.058 4560 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.06 % 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: -1.13 (0.13), residues: 4056 helix: 0.56 (0.14), residues: 1404 sheet: -2.03 (0.18), residues: 726 loop : -1.15 (0.14), residues: 1926 =============================================================================== Job complete usr+sys time: 7282.11 seconds wall clock time: 133 minutes 8.64 seconds (7988.64 seconds total)