Starting phenix.real_space_refine on Wed Feb 21 17:13:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2024/6jqn_9875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2024/6jqn_9875.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2024/6jqn_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_2024/6jqn_9875_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2024/6jqn_9875_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2024/6jqn_9875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2024/6jqn_9875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2024/6jqn_9875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqn_9875/02_2024/6jqn_9875_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.34, per 1000 atoms: 0.49 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: 11.24 Conformation dependent library (CDL) restraints added in 5.7 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: 7.15 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: 9.91 Time building geometry restraints manager: 12.20 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: 18952 33.29 - 66.58: 337 66.58 - 99.86: 46 99.86 - 133.15: 0 133.15 - 166.44: 3 Dihedral angle restraints: 19338 sinusoidal: 7818 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 19335 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 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.830 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 77.780 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 12.753 166.440 11934 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 % Allowed : 3.21 % Favored : 96.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP F 124 HIS 0.009 0.002 HIS A 472 PHE 0.021 0.003 PHE B 563 TYR 0.022 0.003 TYR E 666 ARG 0.018 0.001 ARG C 361 *********************** 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 : 3.508 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7446 (tp30) cc_final: 0.7204 (tp30) REVERT: A 414 GLN cc_start: 0.7911 (mt0) cc_final: 0.7706 (mt0) REVERT: A 547 MET cc_start: 0.8456 (mmt) cc_final: 0.8187 (mmt) REVERT: B 196 SER cc_start: 0.8921 (m) cc_final: 0.8706 (t) REVERT: B 202 LEU cc_start: 0.8179 (mt) cc_final: 0.7969 (mt) REVERT: B 309 ASN cc_start: 0.8335 (m110) cc_final: 0.7983 (m110) REVERT: B 321 LYS cc_start: 0.8468 (mttp) cc_final: 0.8098 (mtpp) REVERT: B 333 LYS cc_start: 0.8270 (mttt) cc_final: 0.7856 (mmmt) REVERT: C 255 MET cc_start: 0.8267 (ttp) cc_final: 0.8019 (ttp) REVERT: C 309 ASN cc_start: 0.7879 (m110) cc_final: 0.7629 (m110) REVERT: C 321 LYS cc_start: 0.8467 (mttp) cc_final: 0.7489 (ttpp) REVERT: C 333 LYS cc_start: 0.8279 (mttt) cc_final: 0.7970 (mttp) REVERT: C 345 ASP cc_start: 0.8303 (m-30) cc_final: 0.8015 (m-30) REVERT: D 127 ASP cc_start: 0.7735 (m-30) cc_final: 0.7399 (m-30) REVERT: D 321 LYS cc_start: 0.8690 (mttp) cc_final: 0.8465 (mtmt) REVERT: D 414 GLN cc_start: 0.7952 (mt0) cc_final: 0.7721 (mt0) REVERT: D 511 LYS cc_start: 0.8695 (mttt) cc_final: 0.8446 (mtpt) REVERT: E 83 TYR cc_start: 0.8439 (m-80) cc_final: 0.8051 (m-80) REVERT: E 159 PHE cc_start: 0.8932 (m-80) cc_final: 0.8582 (m-80) REVERT: E 166 GLU cc_start: 0.8056 (pp20) cc_final: 0.7688 (pp20) REVERT: E 196 SER cc_start: 0.8964 (m) cc_final: 0.8750 (t) REVERT: E 309 ASN cc_start: 0.8140 (m110) cc_final: 0.7865 (m110) REVERT: E 313 ASP cc_start: 0.7413 (m-30) cc_final: 0.7213 (m-30) REVERT: E 321 LYS cc_start: 0.8766 (mttp) cc_final: 0.7757 (ttpp) REVERT: E 333 LYS cc_start: 0.8290 (mttt) cc_final: 0.7931 (mttp) REVERT: E 465 SER cc_start: 0.8567 (m) cc_final: 0.8097 (p) REVERT: E 654 GLU cc_start: 0.6907 (tt0) cc_final: 0.6582 (tm-30) REVERT: F 414 GLN cc_start: 0.7972 (mt0) cc_final: 0.7626 (mt0) REVERT: F 511 LYS cc_start: 0.8656 (mttt) cc_final: 0.8440 (mtmt) REVERT: F 547 MET cc_start: 0.8635 (mmt) cc_final: 0.8433 (mmt) outliers start: 0 outliers final: 0 residues processed: 784 average time/residue: 0.5209 time to fit residues: 609.3680 Evaluate side-chains 408 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 3.830 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.0740 ------------------------------------------------------------------------------- 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 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 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: 0.8156 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31932 Z= 0.239 Angle : 0.599 7.248 43428 Z= 0.307 Chirality : 0.044 0.200 4914 Planarity : 0.006 0.049 5610 Dihedral : 11.840 177.700 4884 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.35 % Allowed : 8.51 % Favored : 90.14 % 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: -1.30 (0.13), residues: 1386 sheet: -2.81 (0.17), residues: 732 loop : -1.90 (0.12), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 124 HIS 0.006 0.001 HIS A 463 PHE 0.027 0.002 PHE E 595 TYR 0.014 0.002 TYR B 110 ARG 0.008 0.001 ARG D 116 *********************** 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 470 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 427 time to evaluate : 3.250 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8911 (tmm) cc_final: 0.8624 (tmm) REVERT: A 522 ASP cc_start: 0.7021 (p0) cc_final: 0.6573 (m-30) REVERT: A 567 MET cc_start: 0.7770 (mmp) cc_final: 0.7453 (mmm) REVERT: B 166 GLU cc_start: 0.8202 (pp20) cc_final: 0.7566 (pp20) REVERT: B 321 LYS cc_start: 0.8591 (mttp) cc_final: 0.7498 (ttpt) REVERT: B 333 LYS cc_start: 0.8223 (mttt) cc_final: 0.7866 (mttp) REVERT: B 505 MET cc_start: 0.8715 (tpp) cc_final: 0.8418 (mmp) REVERT: C 51 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8366 (tttp) REVERT: C 321 LYS cc_start: 0.8484 (mttp) cc_final: 0.7580 (ttpp) REVERT: C 333 LYS cc_start: 0.8279 (mttt) cc_final: 0.7977 (mttp) REVERT: C 345 ASP cc_start: 0.8237 (m-30) cc_final: 0.7626 (m-30) REVERT: C 465 SER cc_start: 0.8569 (t) cc_final: 0.8346 (t) REVERT: C 538 ASP cc_start: 0.7847 (m-30) cc_final: 0.7556 (m-30) REVERT: E 83 TYR cc_start: 0.8374 (m-80) cc_final: 0.8168 (m-80) REVERT: E 166 GLU cc_start: 0.8124 (pp20) cc_final: 0.7714 (pp20) REVERT: E 321 LYS cc_start: 0.8803 (mttp) cc_final: 0.8127 (ttpp) REVERT: E 333 LYS cc_start: 0.8318 (mttt) cc_final: 0.7859 (mmmt) REVERT: E 465 SER cc_start: 0.8556 (m) cc_final: 0.8112 (p) REVERT: F 32 TRP cc_start: 0.7989 (m100) cc_final: 0.7785 (m100) REVERT: F 96 SER cc_start: 0.8759 (t) cc_final: 0.8546 (p) REVERT: F 285 ARG cc_start: 0.7405 (ttp-110) cc_final: 0.7137 (ptp-170) REVERT: F 345 ASP cc_start: 0.8156 (m-30) cc_final: 0.7818 (m-30) REVERT: F 511 LYS cc_start: 0.8584 (mttt) cc_final: 0.8384 (mtpt) REVERT: F 528 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.7598 (mmp80) outliers start: 43 outliers final: 19 residues processed: 457 average time/residue: 0.4832 time to fit residues: 341.0061 Evaluate side-chains 363 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 343 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 510 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 8.9990 chunk 113 optimal weight: 0.0980 chunk 303 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 365 optimal weight: 1.9990 chunk 395 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 chunk 362 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 293 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** 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 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 659 HIS F 158 ASN F 245 ASN F 339 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2533 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= 0.238 Angle : 0.564 8.720 43428 Z= 0.286 Chirality : 0.043 0.165 4914 Planarity : 0.005 0.043 5610 Dihedral : 11.275 178.708 4884 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.58 % Allowed : 10.43 % Favored : 88.00 % 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: -2.31 (0.12), residues: 4056 helix: -0.63 (0.14), residues: 1392 sheet: -2.60 (0.17), residues: 750 loop : -1.66 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 124 HIS 0.007 0.001 HIS A 463 PHE 0.024 0.002 PHE D 595 TYR 0.015 0.001 TYR C 110 ARG 0.009 0.001 ARG F 116 *********************** 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 414 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 364 time to evaluate : 3.613 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: A 522 ASP cc_start: 0.7153 (p0) cc_final: 0.6681 (m-30) REVERT: B 41 MET cc_start: 0.8365 (mmt) cc_final: 0.8071 (mmt) REVERT: B 321 LYS cc_start: 0.8553 (mttp) cc_final: 0.7561 (ttpp) REVERT: B 333 LYS cc_start: 0.8296 (mttt) cc_final: 0.7883 (mttp) REVERT: C 321 LYS cc_start: 0.8510 (mttp) cc_final: 0.7804 (ttpp) REVERT: C 333 LYS cc_start: 0.8207 (mttt) cc_final: 0.7904 (mttp) REVERT: C 341 GLU cc_start: 0.7313 (tp30) cc_final: 0.6458 (tp30) REVERT: C 345 ASP cc_start: 0.8178 (m-30) cc_final: 0.7667 (m-30) REVERT: C 441 ASP cc_start: 0.7568 (m-30) cc_final: 0.7368 (m-30) REVERT: C 465 SER cc_start: 0.8565 (t) cc_final: 0.8333 (t) REVERT: D 50 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: D 334 MET cc_start: 0.8155 (ttm) cc_final: 0.7890 (ttm) REVERT: E 166 GLU cc_start: 0.8100 (pp20) cc_final: 0.7748 (pp20) REVERT: E 321 LYS cc_start: 0.8800 (mttp) cc_final: 0.7915 (ttpp) REVERT: E 465 SER cc_start: 0.8589 (m) cc_final: 0.8137 (p) REVERT: F 511 LYS cc_start: 0.8598 (mttt) cc_final: 0.8356 (mtpt) outliers start: 50 outliers final: 31 residues processed: 400 average time/residue: 0.4738 time to fit residues: 294.4949 Evaluate side-chains 346 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 313 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain F residue 629 THR 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: 0.0040 chunk 174 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 367 optimal weight: 5.9990 chunk 388 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 347 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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 339 ASN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN D 191 GLN 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2756 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= 0.194 Angle : 0.531 8.263 43428 Z= 0.268 Chirality : 0.042 0.142 4914 Planarity : 0.004 0.043 5610 Dihedral : 10.982 179.951 4884 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.89 % Allowed : 11.31 % Favored : 86.80 % 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: -1.98 (0.13), residues: 4056 helix: -0.21 (0.14), residues: 1398 sheet: -2.53 (0.17), residues: 780 loop : -1.52 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 124 HIS 0.005 0.001 HIS A 463 PHE 0.023 0.001 PHE F 595 TYR 0.012 0.001 TYR C 110 ARG 0.008 0.000 ARG F 116 *********************** 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 406 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 346 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: A 189 LEU cc_start: 0.8333 (tp) cc_final: 0.8097 (tp) REVERT: A 282 GLU cc_start: 0.7557 (tp30) cc_final: 0.7147 (tp30) REVERT: A 522 ASP cc_start: 0.7166 (p0) cc_final: 0.6685 (m-30) REVERT: B 41 MET cc_start: 0.8358 (mmt) cc_final: 0.8110 (mmt) REVERT: B 321 LYS cc_start: 0.8507 (mttp) cc_final: 0.7879 (ttpp) REVERT: C 321 LYS cc_start: 0.8429 (mttp) cc_final: 0.7664 (ttpp) REVERT: C 333 LYS cc_start: 0.8148 (mttt) cc_final: 0.7904 (mttp) REVERT: C 341 GLU cc_start: 0.7312 (tp30) cc_final: 0.6407 (tp30) REVERT: C 345 ASP cc_start: 0.8163 (m-30) cc_final: 0.7620 (m-30) REVERT: C 465 SER cc_start: 0.8664 (t) cc_final: 0.8419 (t) REVERT: D 50 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: D 59 MET cc_start: 0.9128 (mtp) cc_final: 0.8882 (mtm) REVERT: D 334 MET cc_start: 0.8130 (ttm) cc_final: 0.7887 (ttm) REVERT: E 166 GLU cc_start: 0.8005 (pp20) cc_final: 0.7733 (pp20) REVERT: E 321 LYS cc_start: 0.8785 (mttp) cc_final: 0.7807 (ttpp) REVERT: E 465 SER cc_start: 0.8573 (m) cc_final: 0.8127 (p) REVERT: F 511 LYS cc_start: 0.8573 (mttt) cc_final: 0.8305 (mtpt) outliers start: 60 outliers final: 35 residues processed: 391 average time/residue: 0.4576 time to fit residues: 279.5191 Evaluate side-chains 355 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 318 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 331 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN B 23 HIS B 155 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN ** C 583 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 31932 Z= 0.602 Angle : 0.735 8.420 43428 Z= 0.368 Chirality : 0.050 0.204 4914 Planarity : 0.006 0.058 5610 Dihedral : 11.578 177.897 4884 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.96 % Allowed : 11.50 % Favored : 85.54 % 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: -2.12 (0.12), residues: 4056 helix: -0.42 (0.13), residues: 1398 sheet: -2.47 (0.17), residues: 780 loop : -1.60 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 124 HIS 0.012 0.002 HIS A 463 PHE 0.027 0.003 PHE E 527 TYR 0.021 0.003 TYR C 110 ARG 0.010 0.001 ARG F 361 *********************** 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 429 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 335 time to evaluate : 3.641 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7568 (tp30) cc_final: 0.7262 (tp30) REVERT: A 567 MET cc_start: 0.7911 (mmp) cc_final: 0.7524 (mmm) REVERT: B 41 MET cc_start: 0.8372 (mmt) cc_final: 0.8134 (mmt) REVERT: B 321 LYS cc_start: 0.8570 (mttp) cc_final: 0.7767 (ttpp) REVERT: B 333 LYS cc_start: 0.8307 (mttt) cc_final: 0.7886 (mttp) REVERT: B 361 ARG cc_start: 0.7109 (mtp180) cc_final: 0.6905 (ttt-90) REVERT: C 321 LYS cc_start: 0.8532 (mttp) cc_final: 0.7824 (ttpp) REVERT: C 333 LYS cc_start: 0.8220 (mttt) cc_final: 0.7847 (mttp) REVERT: C 341 GLU cc_start: 0.7397 (tp30) cc_final: 0.6494 (tp30) REVERT: C 345 ASP cc_start: 0.8319 (m-30) cc_final: 0.7679 (m-30) REVERT: C 465 SER cc_start: 0.8744 (t) cc_final: 0.8465 (t) REVERT: C 467 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9110 (mm) REVERT: D 50 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: D 285 ARG cc_start: 0.7547 (ptp-170) cc_final: 0.7253 (ptp-170) REVERT: E 166 GLU cc_start: 0.8118 (pp20) cc_final: 0.7908 (pp20) REVERT: E 321 LYS cc_start: 0.8900 (mttp) cc_final: 0.8157 (ttpp) REVERT: E 465 SER cc_start: 0.8832 (m) cc_final: 0.8281 (p) REVERT: F 50 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: F 116 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8235 (ttm110) REVERT: F 511 LYS cc_start: 0.8733 (mttt) cc_final: 0.8411 (mtmt) outliers start: 94 outliers final: 64 residues processed: 409 average time/residue: 0.4898 time to fit residues: 310.0220 Evaluate side-chains 380 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 313 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 0.8980 chunk 349 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 228 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 388 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN D 339 ASN ** 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 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3162 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= 0.196 Angle : 0.553 9.992 43428 Z= 0.278 Chirality : 0.042 0.143 4914 Planarity : 0.004 0.048 5610 Dihedral : 10.975 177.516 4884 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.48 % Allowed : 13.26 % Favored : 85.26 % 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: -1.70 (0.13), residues: 4056 helix: 0.03 (0.14), residues: 1398 sheet: -2.35 (0.17), residues: 774 loop : -1.37 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 651 HIS 0.006 0.001 HIS A 463 PHE 0.023 0.001 PHE F 595 TYR 0.015 0.001 TYR F 381 ARG 0.009 0.000 ARG A 116 *********************** 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 394 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 347 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8423 (mtp) cc_final: 0.8144 (tpp) REVERT: A 282 GLU cc_start: 0.7525 (tp30) cc_final: 0.7250 (tp30) REVERT: A 494 MET cc_start: 0.9404 (mtp) cc_final: 0.9180 (mtt) REVERT: A 540 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9091 (tp) REVERT: B 166 GLU cc_start: 0.8081 (pp20) cc_final: 0.7619 (pp20) REVERT: B 321 LYS cc_start: 0.8550 (mttp) cc_final: 0.7729 (ttpp) REVERT: B 333 LYS cc_start: 0.8289 (mttt) cc_final: 0.7896 (mttp) REVERT: C 220 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8221 (t0) REVERT: C 321 LYS cc_start: 0.8523 (mttp) cc_final: 0.7747 (ttpp) REVERT: C 333 LYS cc_start: 0.8202 (mttt) cc_final: 0.7849 (mttp) REVERT: C 341 GLU cc_start: 0.7300 (tp30) cc_final: 0.6459 (tp30) REVERT: C 345 ASP cc_start: 0.8280 (m-30) cc_final: 0.7667 (m-30) REVERT: C 465 SER cc_start: 0.8744 (t) cc_final: 0.8455 (t) REVERT: C 538 ASP cc_start: 0.7916 (m-30) cc_final: 0.7610 (m-30) REVERT: D 50 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: D 189 LEU cc_start: 0.8336 (tp) cc_final: 0.8120 (tp) REVERT: D 275 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8044 (mm-30) REVERT: D 285 ARG cc_start: 0.7459 (ptp-170) cc_final: 0.7087 (ptp-170) REVERT: D 334 MET cc_start: 0.7992 (ttm) cc_final: 0.7579 (ttm) REVERT: E 321 LYS cc_start: 0.8867 (mttp) cc_final: 0.8057 (ttpp) REVERT: E 465 SER cc_start: 0.8660 (m) cc_final: 0.8140 (p) REVERT: E 467 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9096 (mm) REVERT: F 32 TRP cc_start: 0.7661 (m100) cc_final: 0.6987 (m100) REVERT: F 50 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: F 511 LYS cc_start: 0.8640 (mttt) cc_final: 0.8330 (mtmt) outliers start: 47 outliers final: 32 residues processed: 385 average time/residue: 0.5383 time to fit residues: 324.3286 Evaluate side-chains 365 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 510 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 221 optimal weight: 0.3980 chunk 284 optimal weight: 0.9980 chunk 220 optimal weight: 0.5980 chunk 327 optimal weight: 0.6980 chunk 217 optimal weight: 0.3980 chunk 387 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN ** 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 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31932 Z= 0.165 Angle : 0.529 9.631 43428 Z= 0.264 Chirality : 0.041 0.145 4914 Planarity : 0.004 0.050 5610 Dihedral : 10.550 172.156 4884 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.98 % Allowed : 13.33 % Favored : 84.69 % 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: -1.43 (0.13), residues: 4056 helix: 0.30 (0.14), residues: 1398 sheet: -2.20 (0.17), residues: 780 loop : -1.26 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 162 HIS 0.005 0.001 HIS A 463 PHE 0.021 0.001 PHE F 595 TYR 0.014 0.001 TYR C 607 ARG 0.014 0.000 ARG F 116 *********************** 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 426 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 363 time to evaluate : 3.584 Fit side-chains REVERT: A 193 MET cc_start: 0.8407 (mtp) cc_final: 0.8069 (tpp) REVERT: A 282 GLU cc_start: 0.7534 (tp30) cc_final: 0.7303 (tp30) REVERT: A 330 GLU cc_start: 0.6338 (tp30) cc_final: 0.6105 (tp30) REVERT: A 540 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9099 (tp) REVERT: A 551 ASP cc_start: 0.8266 (m-30) cc_final: 0.8004 (m-30) REVERT: B 166 GLU cc_start: 0.7992 (pp20) cc_final: 0.7634 (pp20) REVERT: B 321 LYS cc_start: 0.8572 (mttp) cc_final: 0.8027 (ttpp) REVERT: B 333 LYS cc_start: 0.8249 (mttt) cc_final: 0.7728 (mmmt) REVERT: B 634 THR cc_start: 0.8508 (t) cc_final: 0.8234 (m) REVERT: C 166 GLU cc_start: 0.8036 (pp20) cc_final: 0.7752 (pp20) REVERT: C 293 GLN cc_start: 0.8037 (mt0) cc_final: 0.7687 (mt0) REVERT: C 321 LYS cc_start: 0.8382 (mttp) cc_final: 0.7681 (ttpp) REVERT: C 341 GLU cc_start: 0.7347 (tp30) cc_final: 0.6537 (tp30) REVERT: C 345 ASP cc_start: 0.8257 (m-30) cc_final: 0.7667 (m-30) REVERT: C 465 SER cc_start: 0.8761 (t) cc_final: 0.8480 (t) REVERT: C 467 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8894 (mm) REVERT: C 538 ASP cc_start: 0.7942 (m-30) cc_final: 0.7628 (m-30) REVERT: D 50 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: D 59 MET cc_start: 0.9089 (mtp) cc_final: 0.8763 (mtm) REVERT: D 110 TYR cc_start: 0.8894 (m-80) cc_final: 0.8527 (m-80) REVERT: D 275 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8155 (mm-30) REVERT: D 285 ARG cc_start: 0.7391 (ptp-170) cc_final: 0.7061 (ptp-170) REVERT: D 334 MET cc_start: 0.7716 (ttm) cc_final: 0.7409 (ttm) REVERT: E 321 LYS cc_start: 0.8736 (mttp) cc_final: 0.7784 (ttpp) REVERT: E 465 SER cc_start: 0.8518 (m) cc_final: 0.8056 (p) REVERT: E 467 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9095 (mm) REVERT: F 32 TRP cc_start: 0.7570 (m100) cc_final: 0.6923 (m100) REVERT: F 193 MET cc_start: 0.8075 (mtp) cc_final: 0.7746 (tpp) REVERT: F 469 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: F 511 LYS cc_start: 0.8629 (mttt) cc_final: 0.8293 (mtmt) outliers start: 63 outliers final: 36 residues processed: 414 average time/residue: 0.4605 time to fit residues: 297.6008 Evaluate side-chains 368 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 327 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain F residue 524 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 0.0570 chunk 154 optimal weight: 4.9990 chunk 231 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 304 optimal weight: 10.0000 overall best weight: 1.7102 ------------------------------------------------------------------------------- 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 46 GLN B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 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 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31932 Z= 0.321 Angle : 0.593 9.268 43428 Z= 0.296 Chirality : 0.044 0.149 4914 Planarity : 0.005 0.059 5610 Dihedral : 10.684 171.935 4884 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.98 % Allowed : 13.61 % Favored : 84.40 % 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: -1.44 (0.13), residues: 4056 helix: 0.24 (0.14), residues: 1398 sheet: -2.20 (0.17), residues: 786 loop : -1.22 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 97 HIS 0.008 0.001 HIS A 463 PHE 0.021 0.002 PHE F 595 TYR 0.016 0.002 TYR C 110 ARG 0.013 0.001 ARG F 116 *********************** 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 395 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 332 time to evaluate : 3.654 Fit side-chains REVERT: A 193 MET cc_start: 0.8577 (mtp) cc_final: 0.8318 (tpp) REVERT: A 282 GLU cc_start: 0.7545 (tp30) cc_final: 0.7298 (tp30) REVERT: A 330 GLU cc_start: 0.6491 (tp30) cc_final: 0.6226 (tp30) REVERT: A 540 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9107 (tp) REVERT: A 551 ASP cc_start: 0.8273 (m-30) cc_final: 0.7969 (m-30) REVERT: B 166 GLU cc_start: 0.8058 (pp20) cc_final: 0.7688 (pp20) REVERT: B 321 LYS cc_start: 0.8573 (mttp) cc_final: 0.7755 (ttpp) REVERT: B 333 LYS cc_start: 0.8291 (mttt) cc_final: 0.7898 (mttp) REVERT: C 166 GLU cc_start: 0.8053 (pp20) cc_final: 0.7748 (pp20) REVERT: C 220 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8354 (t0) REVERT: C 321 LYS cc_start: 0.8440 (mttp) cc_final: 0.7560 (ttpp) REVERT: C 333 LYS cc_start: 0.8216 (mttt) cc_final: 0.7835 (mttp) REVERT: C 341 GLU cc_start: 0.7405 (tp30) cc_final: 0.6614 (tp30) REVERT: C 345 ASP cc_start: 0.8315 (m-30) cc_final: 0.7677 (m-30) REVERT: C 348 GLU cc_start: 0.7908 (tp30) cc_final: 0.7611 (tp30) REVERT: C 465 SER cc_start: 0.8749 (t) cc_final: 0.8442 (t) REVERT: C 467 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8973 (mm) REVERT: C 538 ASP cc_start: 0.8001 (m-30) cc_final: 0.7683 (m-30) REVERT: D 50 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: D 59 MET cc_start: 0.9143 (mtp) cc_final: 0.8907 (mtm) REVERT: D 275 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7909 (mm-30) REVERT: D 285 ARG cc_start: 0.7427 (ptp-170) cc_final: 0.7131 (ptp-170) REVERT: D 334 MET cc_start: 0.7961 (ttm) cc_final: 0.7638 (ttm) REVERT: E 321 LYS cc_start: 0.8819 (mttp) cc_final: 0.7884 (ttpp) REVERT: E 465 SER cc_start: 0.8694 (m) cc_final: 0.8169 (p) REVERT: E 467 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9181 (mm) REVERT: F 32 TRP cc_start: 0.7755 (m100) cc_final: 0.6933 (m100) REVERT: F 193 MET cc_start: 0.8193 (mtp) cc_final: 0.7657 (tpp) REVERT: F 511 LYS cc_start: 0.8697 (mttt) cc_final: 0.8379 (mtmt) outliers start: 63 outliers final: 50 residues processed: 386 average time/residue: 0.4846 time to fit residues: 290.6351 Evaluate side-chains 381 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 326 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 523 ARG Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 0.9980 chunk 371 optimal weight: 0.9990 chunk 338 optimal weight: 4.9990 chunk 361 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 326 optimal weight: 2.9990 chunk 341 optimal weight: 0.5980 chunk 359 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN ** 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31932 Z= 0.169 Angle : 0.530 9.721 43428 Z= 0.264 Chirality : 0.042 0.177 4914 Planarity : 0.004 0.055 5610 Dihedral : 10.314 167.890 4884 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.70 % Allowed : 13.99 % Favored : 84.31 % 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: -1.23 (0.13), residues: 4056 helix: 0.45 (0.14), residues: 1398 sheet: -2.07 (0.18), residues: 732 loop : -1.18 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 97 HIS 0.005 0.001 HIS A 463 PHE 0.022 0.001 PHE F 595 TYR 0.015 0.001 TYR C 607 ARG 0.013 0.000 ARG A 116 *********************** 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 402 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 348 time to evaluate : 4.478 Fit side-chains REVERT: A 193 MET cc_start: 0.8515 (mtp) cc_final: 0.8221 (tpp) REVERT: A 282 GLU cc_start: 0.7535 (tp30) cc_final: 0.7284 (tp30) REVERT: A 540 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9111 (tp) REVERT: A 551 ASP cc_start: 0.8263 (m-30) cc_final: 0.7976 (m-30) REVERT: B 166 GLU cc_start: 0.7916 (pp20) cc_final: 0.7705 (pp20) REVERT: B 193 MET cc_start: 0.8352 (mtp) cc_final: 0.8050 (tpp) REVERT: B 321 LYS cc_start: 0.8546 (mttp) cc_final: 0.7666 (ttpp) REVERT: B 333 LYS cc_start: 0.8215 (mttt) cc_final: 0.7851 (mttp) REVERT: B 567 MET cc_start: 0.7775 (mmm) cc_final: 0.7537 (mmm) REVERT: C 321 LYS cc_start: 0.8383 (mttp) cc_final: 0.7470 (ttpp) REVERT: C 333 LYS cc_start: 0.8181 (mttt) cc_final: 0.7843 (mttp) REVERT: C 341 GLU cc_start: 0.7365 (tp30) cc_final: 0.6606 (tp30) REVERT: C 345 ASP cc_start: 0.8266 (m-30) cc_final: 0.7686 (m-30) REVERT: C 348 GLU cc_start: 0.7894 (tp30) cc_final: 0.7622 (tp30) REVERT: C 465 SER cc_start: 0.8754 (t) cc_final: 0.8467 (t) REVERT: C 467 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8903 (mm) REVERT: C 538 ASP cc_start: 0.7954 (m-30) cc_final: 0.7630 (m-30) REVERT: D 50 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: D 275 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8131 (mm-30) REVERT: D 285 ARG cc_start: 0.7424 (ptp-170) cc_final: 0.7116 (ptp-170) REVERT: E 321 LYS cc_start: 0.8729 (mttp) cc_final: 0.7765 (ttpp) REVERT: E 465 SER cc_start: 0.8601 (m) cc_final: 0.8105 (p) REVERT: E 467 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9125 (mm) REVERT: F 32 TRP cc_start: 0.7645 (m100) cc_final: 0.6937 (m100) REVERT: F 189 LEU cc_start: 0.8396 (tp) cc_final: 0.8185 (tp) REVERT: F 193 MET cc_start: 0.8194 (mtp) cc_final: 0.7714 (tpp) REVERT: F 469 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: F 511 LYS cc_start: 0.8654 (mttt) cc_final: 0.8343 (mtmt) outliers start: 54 outliers final: 37 residues processed: 391 average time/residue: 0.4972 time to fit residues: 302.5774 Evaluate side-chains 370 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 328 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 523 ARG Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 7.9990 chunk 381 optimal weight: 0.6980 chunk 233 optimal weight: 0.0060 chunk 181 optimal weight: 0.0970 chunk 265 optimal weight: 3.9990 chunk 400 optimal weight: 0.5980 chunk 368 optimal weight: 8.9990 chunk 318 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 246 optimal weight: 0.0030 chunk 195 optimal weight: 0.5980 overall best weight: 0.2604 ------------------------------------------------------------------------------- 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN C 409 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 24 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: 0.8140 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31932 Z= 0.138 Angle : 0.516 9.578 43428 Z= 0.256 Chirality : 0.041 0.158 4914 Planarity : 0.004 0.060 5610 Dihedral : 9.886 161.187 4884 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.10 % Allowed : 14.59 % Favored : 84.31 % 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: -1.04 (0.13), residues: 4056 helix: 0.65 (0.14), residues: 1398 sheet: -2.00 (0.18), residues: 726 loop : -1.09 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 97 HIS 0.004 0.000 HIS A 463 PHE 0.021 0.001 PHE F 595 TYR 0.017 0.001 TYR C 607 ARG 0.014 0.000 ARG A 116 ********************** 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 413 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 378 time to evaluate : 3.738 Fit side-chains REVERT: A 193 MET cc_start: 0.8542 (mtp) cc_final: 0.8221 (tpp) REVERT: A 282 GLU cc_start: 0.7476 (tp30) cc_final: 0.7232 (tp30) REVERT: A 540 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9114 (tp) REVERT: A 551 ASP cc_start: 0.8284 (m-30) cc_final: 0.7983 (m-30) REVERT: B 321 LYS cc_start: 0.8524 (mttp) cc_final: 0.7645 (ttpp) REVERT: B 333 LYS cc_start: 0.8165 (mttt) cc_final: 0.7837 (mttp) REVERT: B 634 THR cc_start: 0.8496 (t) cc_final: 0.8201 (m) REVERT: B 654 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6693 (tm-30) REVERT: C 121 ASP cc_start: 0.7867 (t0) cc_final: 0.7587 (t0) REVERT: C 293 GLN cc_start: 0.8026 (mt0) cc_final: 0.7708 (mt0) REVERT: C 321 LYS cc_start: 0.8368 (mttp) cc_final: 0.7371 (ttpp) REVERT: C 333 LYS cc_start: 0.8201 (mttt) cc_final: 0.7824 (mttp) REVERT: C 341 GLU cc_start: 0.7459 (tp30) cc_final: 0.6797 (tp30) REVERT: C 345 ASP cc_start: 0.8128 (m-30) cc_final: 0.7602 (m-30) REVERT: C 348 GLU cc_start: 0.7928 (tp30) cc_final: 0.7632 (tp30) REVERT: C 465 SER cc_start: 0.8669 (t) cc_final: 0.8361 (t) REVERT: C 467 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8843 (mm) REVERT: C 505 MET cc_start: 0.8738 (tpp) cc_final: 0.8467 (mmp) REVERT: C 538 ASP cc_start: 0.8011 (m-30) cc_final: 0.7685 (m-30) REVERT: D 50 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: D 285 ARG cc_start: 0.7406 (ptp-170) cc_final: 0.7075 (ptp-170) REVERT: D 351 ASN cc_start: 0.8808 (m110) cc_final: 0.8261 (m-40) REVERT: E 59 MET cc_start: 0.9043 (ptp) cc_final: 0.8829 (ptp) REVERT: E 321 LYS cc_start: 0.8738 (mttp) cc_final: 0.7790 (ttpp) REVERT: E 433 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7313 (tp-100) REVERT: E 465 SER cc_start: 0.8447 (m) cc_final: 0.8021 (p) REVERT: E 523 ARG cc_start: 0.6341 (ttp-110) cc_final: 0.6003 (ptt90) REVERT: F 32 TRP cc_start: 0.7564 (m100) cc_final: 0.6916 (m100) REVERT: F 193 MET cc_start: 0.8206 (mtp) cc_final: 0.7745 (tpp) REVERT: F 511 LYS cc_start: 0.8638 (mttt) cc_final: 0.8270 (mtmt) outliers start: 35 outliers final: 24 residues processed: 406 average time/residue: 0.4842 time to fit residues: 308.0037 Evaluate side-chains 365 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 338 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 2.9990 chunk 339 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 294 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 319 optimal weight: 0.2980 chunk 133 optimal weight: 0.7980 chunk 327 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 309 ASN D 158 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN D 339 ASN ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 HIS ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN F 158 ASN ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.099860 restraints weight = 44479.676| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.81 r_work: 0.3014 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31932 Z= 0.149 Angle : 0.520 9.502 43428 Z= 0.257 Chirality : 0.041 0.190 4914 Planarity : 0.004 0.062 5610 Dihedral : 9.757 158.662 4884 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.01 % Allowed : 15.06 % Favored : 83.93 % 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: -0.95 (0.13), residues: 4056 helix: 0.74 (0.14), residues: 1392 sheet: -1.93 (0.18), residues: 726 loop : -1.05 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 97 HIS 0.004 0.001 HIS A 463 PHE 0.021 0.001 PHE F 595 TYR 0.021 0.001 TYR C 607 ARG 0.015 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7572.55 seconds wall clock time: 138 minutes 1.42 seconds (8281.42 seconds total)