Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 13:39:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq8_25379/04_2023/7sq8_25379_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq8_25379/04_2023/7sq8_25379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.598 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq8_25379/04_2023/7sq8_25379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq8_25379/04_2023/7sq8_25379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq8_25379/04_2023/7sq8_25379_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq8_25379/04_2023/7sq8_25379_neut.pdb" } resolution = 2.598 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 S 96 5.16 5 Na 1 4.78 5 C 9904 2.51 5 N 2500 2.21 5 O 2616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 462": "OE1" <-> "OE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "D GLU 462": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15117 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3749 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Chain: "B" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3749 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Chain: "C" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3749 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Chain: "D" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3749 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.79, per 1000 atoms: 0.52 Number of scatterers: 15117 At special positions: 0 Unit cell: (108.73, 108.73, 114.54, 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 96 16.00 Na 1 11.00 O 2616 8.00 N 2500 7.00 C 9904 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 2.3 seconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 66.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.997A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.819A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 508 through 526 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.998A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.813A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 508 through 526 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG C 57 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 349 Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.998A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.837A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 508 Processing helix chain 'C' and resid 508 through 526 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG D 57 " --> pdb=" O CYS D 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 106 removed outlier: 4.072A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 349 Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.998A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.063A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.814A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 508 Processing helix chain 'D' and resid 508 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP A 176 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP B 176 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP C 252 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP C 252 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP C 176 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP D 252 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP D 252 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.597A pdb=" N ASP D 176 " --> pdb=" O THR D 181 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 6.74 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: 3190 1.33 - 1.45: 3635 1.45 - 1.57: 8511 1.57 - 1.69: 4 1.69 - 1.81: 132 Bond restraints: 15472 Sorted by residual: bond pdb=" CA ASP A 196 " pdb=" C ASP A 196 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.06e-02 8.90e+03 2.32e+01 bond pdb=" CA ASP D 196 " pdb=" C ASP D 196 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.06e-02 8.90e+03 2.31e+01 bond pdb=" CA ASP B 196 " pdb=" C ASP B 196 " ideal model delta sigma weight residual 1.523 1.573 -0.051 1.06e-02 8.90e+03 2.28e+01 bond pdb=" CA ASP C 196 " pdb=" C ASP C 196 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.06e-02 8.90e+03 2.26e+01 bond pdb=" C ASP C 196 " pdb=" N PRO C 197 " ideal model delta sigma weight residual 1.335 1.377 -0.043 1.15e-02 7.56e+03 1.37e+01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.39: 312 106.39 - 113.31: 8467 113.31 - 120.23: 5638 120.23 - 127.15: 6411 127.15 - 134.07: 152 Bond angle restraints: 20980 Sorted by residual: angle pdb=" C ALA B 58 " pdb=" N LYS B 59 " pdb=" CA LYS B 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA C 58 " pdb=" N LYS C 59 " pdb=" CA LYS C 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA A 58 " pdb=" N LYS A 59 " pdb=" CA LYS A 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA D 58 " pdb=" N LYS D 59 " pdb=" CA LYS D 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N ALA C 482 " pdb=" CA ALA C 482 " pdb=" C ALA C 482 " ideal model delta sigma weight residual 110.97 114.61 -3.64 1.09e+00 8.42e-01 1.12e+01 ... (remaining 20975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 8168 17.30 - 34.59: 681 34.59 - 51.89: 112 51.89 - 69.18: 11 69.18 - 86.48: 20 Dihedral angle restraints: 8992 sinusoidal: 3556 harmonic: 5436 Sorted by residual: dihedral pdb=" CG ARG D 419 " pdb=" CD ARG D 419 " pdb=" NE ARG D 419 " pdb=" CZ ARG D 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.89 41.89 2 1.50e+01 4.44e-03 9.51e+00 dihedral pdb=" CG ARG C 419 " pdb=" CD ARG C 419 " pdb=" NE ARG C 419 " pdb=" CZ ARG C 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.84 41.84 2 1.50e+01 4.44e-03 9.49e+00 dihedral pdb=" CG ARG B 419 " pdb=" CD ARG B 419 " pdb=" NE ARG B 419 " pdb=" CZ ARG B 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.80 41.80 2 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1991 0.052 - 0.104: 367 0.104 - 0.156: 66 0.156 - 0.208: 0 0.208 - 0.260: 12 Chirality restraints: 2436 Sorted by residual: chirality pdb=" CA HIS D 486 " pdb=" N HIS D 486 " pdb=" C HIS D 486 " pdb=" CB HIS D 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA HIS C 486 " pdb=" N HIS C 486 " pdb=" C HIS C 486 " pdb=" CB HIS C 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA HIS A 486 " pdb=" N HIS A 486 " pdb=" C HIS A 486 " pdb=" CB HIS A 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2433 not shown) Planarity restraints: 2572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 471 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C ASP D 471 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP D 471 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP D 472 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 471 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ASP B 471 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP B 471 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP B 472 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 471 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C ASP C 471 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP C 471 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP C 472 " -0.007 2.00e-02 2.50e+03 ... (remaining 2569 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 994 2.74 - 3.28: 15338 3.28 - 3.82: 25994 3.82 - 4.36: 30876 4.36 - 4.90: 52933 Nonbonded interactions: 126135 Sorted by model distance: nonbonded pdb=" OD1 ASP C 134 " pdb=" OH TYR C 218 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP D 134 " pdb=" OH TYR D 218 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP B 134 " pdb=" OH TYR B 218 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP A 384 " pdb=" OH TYR B 450 " model vdw 2.243 2.440 ... (remaining 126130 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' selection = chain 'B' selection = (chain 'C' and resid 40 through 527) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.220 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: 6.580 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 40.200 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.004 0.051 15472 Z= 0.229 Angle : 0.554 6.426 20980 Z= 0.325 Chirality : 0.044 0.260 2436 Planarity : 0.003 0.028 2568 Dihedral : 13.373 86.476 5488 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.20), residues: 1828 helix: 2.07 (0.16), residues: 1140 sheet: 1.05 (0.34), residues: 252 loop : -0.70 (0.26), residues: 436 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.954 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 1.0905 time to fit residues: 231.4825 Evaluate side-chains 126 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 0.0270 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 chunk 167 optimal weight: 2.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 226 HIS A 352 ASN B 194 GLN B 226 HIS B 352 ASN C 194 GLN C 226 HIS C 352 ASN D 194 GLN D 226 HIS D 352 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15472 Z= 0.180 Angle : 0.495 4.710 20980 Z= 0.271 Chirality : 0.040 0.128 2436 Planarity : 0.004 0.030 2568 Dihedral : 3.850 14.079 2040 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 1.45 % 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: 2.05 (0.19), residues: 1828 helix: 2.19 (0.15), residues: 1140 sheet: 1.08 (0.34), residues: 252 loop : -0.74 (0.25), residues: 436 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.910 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 136 average time/residue: 1.0678 time to fit residues: 164.8978 Evaluate side-chains 122 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.1903 time to fit residues: 3.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 chunk 57 optimal weight: 0.0980 chunk 134 optimal weight: 2.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 483 GLN B 352 ASN B 483 GLN C 194 GLN C 352 ASN C 483 GLN D 352 ASN D 483 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 15472 Z= 0.336 Angle : 0.595 4.836 20980 Z= 0.323 Chirality : 0.045 0.149 2436 Planarity : 0.005 0.038 2568 Dihedral : 4.188 16.576 2040 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.19), residues: 1828 helix: 2.08 (0.15), residues: 1120 sheet: 1.06 (0.34), residues: 252 loop : -0.51 (0.26), residues: 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 1.756 Fit side-chains outliers start: 42 outliers final: 17 residues processed: 159 average time/residue: 1.0156 time to fit residues: 183.6686 Evaluate side-chains 135 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1824 time to fit residues: 3.6971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 15472 Z= 0.250 Angle : 0.543 6.467 20980 Z= 0.295 Chirality : 0.042 0.136 2436 Planarity : 0.004 0.030 2568 Dihedral : 4.088 15.853 2040 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 1.75 % 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: 1.92 (0.19), residues: 1828 helix: 2.11 (0.15), residues: 1140 sheet: 1.16 (0.34), residues: 252 loop : -0.95 (0.25), residues: 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.862 Fit side-chains outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 1.1117 time to fit residues: 175.6378 Evaluate side-chains 137 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1858 time to fit residues: 3.8198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 132 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 15472 Z= 0.232 Angle : 0.528 6.150 20980 Z= 0.287 Chirality : 0.041 0.133 2436 Planarity : 0.004 0.030 2568 Dihedral : 4.047 15.456 2040 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.29 % 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: 2.01 (0.19), residues: 1828 helix: 2.15 (0.15), residues: 1144 sheet: 1.24 (0.34), residues: 252 loop : -0.87 (0.25), residues: 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.736 Fit side-chains outliers start: 38 outliers final: 18 residues processed: 150 average time/residue: 1.0890 time to fit residues: 184.4361 Evaluate side-chains 133 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1909 time to fit residues: 3.6799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN B 486 HIS C 327 GLN C 486 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 15472 Z= 0.232 Angle : 0.530 6.393 20980 Z= 0.287 Chirality : 0.041 0.132 2436 Planarity : 0.004 0.030 2568 Dihedral : 4.044 15.533 2040 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 2.23 % 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: 2.05 (0.19), residues: 1828 helix: 2.19 (0.15), residues: 1144 sheet: 1.27 (0.34), residues: 252 loop : -0.90 (0.25), residues: 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 1.786 Fit side-chains outliers start: 37 outliers final: 18 residues processed: 136 average time/residue: 1.1119 time to fit residues: 170.0222 Evaluate side-chains 128 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1759 time to fit residues: 3.4392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 149 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 483 GLN C 483 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 15472 Z= 0.285 Angle : 0.563 6.309 20980 Z= 0.304 Chirality : 0.043 0.135 2436 Planarity : 0.004 0.030 2568 Dihedral : 4.149 15.978 2040 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.99 % 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: 2.15 (0.19), residues: 1828 helix: 2.29 (0.15), residues: 1116 sheet: 1.26 (0.33), residues: 252 loop : -0.67 (0.26), residues: 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 1.771 Fit side-chains outliers start: 33 outliers final: 19 residues processed: 144 average time/residue: 1.1372 time to fit residues: 184.1267 Evaluate side-chains 129 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.3763 time to fit residues: 4.9042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 483 GLN A 486 HIS B 486 HIS C 469 ASN C 483 GLN C 486 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 ASN D 483 GLN D 486 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15472 Z= 0.141 Angle : 0.469 6.369 20980 Z= 0.256 Chirality : 0.038 0.126 2436 Planarity : 0.003 0.032 2568 Dihedral : 3.859 14.493 2040 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.21 % 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: 2.35 (0.19), residues: 1828 helix: 2.50 (0.15), residues: 1132 sheet: 1.38 (0.34), residues: 252 loop : -0.92 (0.25), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.808 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 139 average time/residue: 1.1965 time to fit residues: 185.8745 Evaluate side-chains 123 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 2.5618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS B 226 HIS C 226 HIS D 226 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15472 Z= 0.199 Angle : 0.509 6.190 20980 Z= 0.275 Chirality : 0.040 0.127 2436 Planarity : 0.003 0.031 2568 Dihedral : 3.929 14.546 2040 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 1.21 % 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: 2.29 (0.19), residues: 1828 helix: 2.39 (0.15), residues: 1144 sheet: 1.34 (0.34), residues: 252 loop : -0.85 (0.25), residues: 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.887 Fit side-chains outliers start: 20 outliers final: 17 residues processed: 133 average time/residue: 1.2081 time to fit residues: 180.5077 Evaluate side-chains 129 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1834 time to fit residues: 3.7716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS C 486 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS D 526 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 15472 Z= 0.262 Angle : 0.552 6.721 20980 Z= 0.297 Chirality : 0.042 0.133 2436 Planarity : 0.004 0.030 2568 Dihedral : 4.074 15.781 2040 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.91 % 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: 2.11 (0.19), residues: 1828 helix: 2.26 (0.15), residues: 1144 sheet: 1.27 (0.33), residues: 252 loop : -0.96 (0.25), residues: 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.745 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 133 average time/residue: 1.1661 time to fit residues: 174.8299 Evaluate side-chains 133 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 2.5708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN C 483 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN D 526 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104944 restraints weight = 16216.256| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.88 r_work: 0.2843 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15472 Z= 0.184 Angle : 0.501 6.659 20980 Z= 0.273 Chirality : 0.040 0.127 2436 Planarity : 0.003 0.031 2568 Dihedral : 3.926 15.007 2040 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.45 % 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: 2.27 (0.19), residues: 1828 helix: 2.46 (0.15), residues: 1132 sheet: 1.32 (0.34), residues: 252 loop : -1.01 (0.25), residues: 444 =============================================================================== Job complete usr+sys time: 3949.25 seconds wall clock time: 71 minutes 53.68 seconds (4313.68 seconds total)