Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 06:23:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4a_22662/07_2023/7k4a_22662_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4a_22662/07_2023/7k4a_22662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4a_22662/07_2023/7k4a_22662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4a_22662/07_2023/7k4a_22662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4a_22662/07_2023/7k4a_22662_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4a_22662/07_2023/7k4a_22662_neut.pdb" } resolution = 3.26 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= 0.019 sd= 0.056 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 8 5.49 5 S 160 5.16 5 C 13784 2.51 5 N 3324 2.21 5 O 3548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "C ARG 636": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Residue "D ARG 636": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 20825 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4868 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 1 Chain: "B" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4868 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 1 Chain: "C" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4868 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 1 Chain: "D" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4868 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 1 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Unusual residues: {' CA': 1, 'PCW': 13, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 568 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PCW:plan-1': 11, 'PCW:plan-2': 3, 'PCW:plan-3': 11, 'PCW:plan-4': 11} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 373 Unusual residues: {'PCW': 13, 'Y01': 4} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 568 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PCW:plan-1': 11, 'PCW:plan-2': 3, 'PCW:plan-3': 11, 'PCW:plan-4': 11} Unresolved non-hydrogen planarities: 123 Chain: "C" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 338 Unusual residues: {'PCW': 13, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 568 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PCW:plan-1': 11, 'PCW:plan-2': 3, 'PCW:plan-3': 11, 'PCW:plan-4': 11} Unresolved non-hydrogen planarities: 123 Chain: "D" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Unusual residues: {'PCW': 13, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 568 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PCW:plan-1': 11, 'PCW:plan-2': 3, 'PCW:plan-3': 11, 'PCW:plan-4': 11} Unresolved non-hydrogen planarities: 123 Time building chain proxies: 10.57, per 1000 atoms: 0.51 Number of scatterers: 20825 At special positions: 0 Unit cell: (142.636, 142.636, 122.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 160 16.00 P 8 15.00 O 3548 8.00 N 3324 7.00 C 13784 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: 8.07 Conformation dependent library (CDL) restraints added in 2.7 seconds 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4592 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 52.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 removed outlier: 3.639A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.510A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.229A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.590A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.912A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.518A pdb=" N ARG A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.578A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.935A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.629A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 203' Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.944A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 253 through 261 removed outlier: 4.219A pdb=" N LEU A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.592A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.501A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 310 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 380 through 395 removed outlier: 3.641A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.514A pdb=" N ILE A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 445 removed outlier: 4.016A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.890A pdb=" N ASN A 464 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.558A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.605A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.033A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 578 removed outlier: 3.629A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 588 through 607 removed outlier: 3.519A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.574A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.509A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.229A pdb=" N ILE B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.590A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.912A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.519A pdb=" N ARG B 134 " --> pdb=" O MET B 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.578A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.934A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.631A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 203' Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.944A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 253 through 261 removed outlier: 4.219A pdb=" N LEU B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.592A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.501A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 310 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 380 through 395 removed outlier: 3.641A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.514A pdb=" N ILE B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 445 removed outlier: 4.016A pdb=" N TYR B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.889A pdb=" N ASN B 464 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.557A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.606A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.033A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 578 removed outlier: 3.629A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 588 through 607 removed outlier: 3.519A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.640A pdb=" N GLN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.510A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.229A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.590A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.912A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.519A pdb=" N ARG C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.578A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.935A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.630A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 203' Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.943A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.220A pdb=" N LEU C 259 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.593A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.500A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN C 310 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 318 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 339 through 346 Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.642A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.514A pdb=" N ILE C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 445 removed outlier: 4.016A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 removed outlier: 3.890A pdb=" N ASN C 464 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 499 through 512 removed outlier: 3.557A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 539 removed outlier: 3.606A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.032A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 578 removed outlier: 3.628A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.519A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 47 removed outlier: 3.639A pdb=" N GLN D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.510A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.230A pdb=" N ILE D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.590A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.913A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.518A pdb=" N ARG D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.578A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.935A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.629A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 203' Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 210 through 222 removed outlier: 3.944A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 253 through 261 removed outlier: 4.220A pdb=" N LEU D 259 " --> pdb=" O MET D 255 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.592A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.786A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN D 310 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 339 through 346 Processing helix chain 'D' and resid 380 through 395 removed outlier: 3.641A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 403 through 411 removed outlier: 3.514A pdb=" N ILE D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 445 removed outlier: 4.016A pdb=" N TYR D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.890A pdb=" N ASN D 464 " --> pdb=" O GLY D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 499 through 512 removed outlier: 3.557A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.605A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.032A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.628A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 588 through 607 removed outlier: 3.519A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 617 hydrogen bonds defined for protein. 1776 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: 5.75 Time building geometry restraints manager: 8.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3164 1.31 - 1.44: 5457 1.44 - 1.56: 12227 1.56 - 1.69: 128 1.69 - 1.82: 272 Bond restraints: 21248 Sorted by residual: bond pdb=" C19 PCW C 701 " pdb=" C20 PCW C 701 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C19 PCW D 704 " pdb=" C20 PCW D 704 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C19 PCW A 815 " pdb=" C20 PCW A 815 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C19 PCW B 702 " pdb=" C20 PCW B 702 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C19 PCW A 813 " pdb=" C20 PCW A 813 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.19e+02 ... (remaining 21243 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.81: 543 105.81 - 112.90: 11230 112.90 - 119.99: 7952 119.99 - 127.07: 8588 127.07 - 134.16: 275 Bond angle restraints: 28588 Sorted by residual: angle pdb=" C19 PCW D 703 " pdb=" C20 PCW D 703 " pdb=" C21 PCW D 703 " ideal model delta sigma weight residual 127.82 111.01 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" C19 PCW A 813 " pdb=" C20 PCW A 813 " pdb=" C21 PCW A 813 " ideal model delta sigma weight residual 127.82 111.03 16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C19 PCW B 717 " pdb=" C20 PCW B 717 " pdb=" C21 PCW B 717 " ideal model delta sigma weight residual 127.82 111.07 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" C19 PCW C 716 " pdb=" C20 PCW C 716 " pdb=" C21 PCW C 716 " ideal model delta sigma weight residual 127.82 111.11 16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C19 PCW C 707 " pdb=" C20 PCW C 707 " pdb=" C21 PCW C 707 " ideal model delta sigma weight residual 127.82 111.25 16.57 3.00e+00 1.11e-01 3.05e+01 ... (remaining 28583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 11995 24.33 - 48.67: 608 48.67 - 73.00: 113 73.00 - 97.33: 8 97.33 - 121.67: 8 Dihedral angle restraints: 12732 sinusoidal: 5636 harmonic: 7096 Sorted by residual: dihedral pdb=" CA TYR C 67 " pdb=" C TYR C 67 " pdb=" N GLU C 68 " pdb=" CA GLU C 68 " ideal model delta harmonic sigma weight residual 180.00 149.45 30.55 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA TYR A 67 " pdb=" C TYR A 67 " pdb=" N GLU A 68 " pdb=" CA GLU A 68 " ideal model delta harmonic sigma weight residual 180.00 149.46 30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA TYR D 67 " pdb=" C TYR D 67 " pdb=" N GLU D 68 " pdb=" CA GLU D 68 " ideal model delta harmonic sigma weight residual 180.00 149.48 30.52 0 5.00e+00 4.00e-02 3.73e+01 ... (remaining 12729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2345 0.059 - 0.118: 667 0.118 - 0.178: 99 0.178 - 0.237: 41 0.237 - 0.296: 20 Chirality restraints: 3172 Sorted by residual: chirality pdb=" C2 PCW D 708 " pdb=" C1 PCW D 708 " pdb=" C3 PCW D 708 " pdb=" O2 PCW D 708 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2 PCW B 707 " pdb=" C1 PCW B 707 " pdb=" C3 PCW B 707 " pdb=" O2 PCW B 707 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2 PCW C 706 " pdb=" C1 PCW C 706 " pdb=" C3 PCW C 706 " pdb=" O2 PCW C 706 " both_signs ideal model delta sigma weight residual False -2.32 -2.61 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3169 not shown) Planarity restraints: 3500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW C 701 " -0.167 2.00e-02 2.50e+03 2.43e-01 5.91e+02 pdb=" C19 PCW C 701 " 0.344 2.00e-02 2.50e+03 pdb=" C20 PCW C 701 " -0.281 2.00e-02 2.50e+03 pdb=" C21 PCW C 701 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW D 704 " -0.166 2.00e-02 2.50e+03 2.42e-01 5.87e+02 pdb=" C19 PCW D 704 " 0.342 2.00e-02 2.50e+03 pdb=" C20 PCW D 704 " -0.281 2.00e-02 2.50e+03 pdb=" C21 PCW D 704 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW B 702 " 0.164 2.00e-02 2.50e+03 2.39e-01 5.70e+02 pdb=" C19 PCW B 702 " -0.336 2.00e-02 2.50e+03 pdb=" C20 PCW B 702 " 0.278 2.00e-02 2.50e+03 pdb=" C21 PCW B 702 " -0.106 2.00e-02 2.50e+03 ... (remaining 3497 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4927 2.79 - 3.32: 17146 3.32 - 3.85: 30713 3.85 - 4.37: 38375 4.37 - 4.90: 65716 Nonbonded interactions: 156877 Sorted by model distance: nonbonded pdb=" OD2 ASP A 489 " pdb=" OG1 THR A 581 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASP C 489 " pdb=" OG1 THR C 581 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASP B 489 " pdb=" OG1 THR B 581 " model vdw 2.264 2.440 nonbonded pdb=" OD2 ASP D 489 " pdb=" OG1 THR D 581 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.323 2.440 ... (remaining 156872 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 25 through 638 or (resid 808 and (name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 809 and (name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 8 \ 10 and (name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 812 \ through 813 and (name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19)) or (resid 815 and (name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'B' and (resid 25 through 638 or (resid 708 and (name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 709 and (name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 7 \ 10 and (name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 712 \ through 713 and (name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19)) or (resid 715 and (name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'C' and (resid 25 through 638 or (resid 708 and (name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 709 and (name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 7 \ 10 and (name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 712 \ through 713 and (name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19)) or (resid 715 and (name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'D' and (resid 25 through 638 or (resid 708 and (name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 709 and (name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 7 \ 10 and (name C15 or name C16 or name C17 or name C18 or name C19)) or resid 712 \ through 713 or resid 715)) } 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.690 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 50.470 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.130 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.013 0.220 21248 Z= 0.791 Angle : 1.438 16.811 28588 Z= 0.681 Chirality : 0.060 0.296 3172 Planarity : 0.014 0.243 3500 Dihedral : 14.778 121.667 8140 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.48 % Favored : 89.35 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -6.74 (0.11), residues: 2404 helix: -4.58 (0.06), residues: 1332 sheet: -5.14 (0.26), residues: 84 loop : -4.06 (0.16), residues: 988 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 460 time to evaluate : 2.397 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 471 average time/residue: 0.3934 time to fit residues: 270.6037 Evaluate side-chains 277 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 269 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1923 time to fit residues: 6.1703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 217 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 118 GLN A 165 HIS A 174 ASN A 206 GLN A 217 ASN A 237 ASN A 238 HIS A 265 HIS A 426 HIS A 522 HIS ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 118 GLN B 165 HIS B 174 ASN B 206 GLN B 217 ASN B 237 ASN B 238 HIS B 265 HIS B 290 GLN B 426 HIS B 522 HIS ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 217 ASN C 237 ASN C 238 HIS C 265 HIS C 426 HIS C 522 HIS D 118 GLN D 165 HIS D 174 ASN D 206 GLN D 217 ASN D 237 ASN D 238 HIS D 265 HIS D 290 GLN D 426 HIS D 522 HIS ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 21248 Z= 0.161 Angle : 0.657 9.126 28588 Z= 0.329 Chirality : 0.040 0.177 3172 Planarity : 0.005 0.051 3500 Dihedral : 14.238 91.220 3432 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.16 (0.14), residues: 2404 helix: -3.03 (0.11), residues: 1280 sheet: -4.89 (0.31), residues: 84 loop : -3.74 (0.17), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 305 time to evaluate : 2.565 Fit side-chains outliers start: 54 outliers final: 5 residues processed: 338 average time/residue: 0.2872 time to fit residues: 157.4405 Evaluate side-chains 250 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1737 time to fit residues: 4.6375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 127 ASN A 265 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS B 174 ASN B 265 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 HIS C 174 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 HIS D 265 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 21248 Z= 0.306 Angle : 0.701 9.008 28588 Z= 0.348 Chirality : 0.044 0.179 3172 Planarity : 0.005 0.045 3500 Dihedral : 13.353 89.272 3432 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.33 (0.15), residues: 2404 helix: -2.22 (0.13), residues: 1320 sheet: -4.36 (0.35), residues: 84 loop : -3.60 (0.18), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 2.300 Fit side-chains outliers start: 46 outliers final: 18 residues processed: 285 average time/residue: 0.2994 time to fit residues: 136.7051 Evaluate side-chains 260 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 242 time to evaluate : 2.266 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1859 time to fit residues: 9.4615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 231 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 546 ASN A 637 GLN B 265 HIS B 546 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 546 ASN D 265 HIS D 546 ASN D 637 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 21248 Z= 0.169 Angle : 0.604 8.892 28588 Z= 0.301 Chirality : 0.040 0.164 3172 Planarity : 0.004 0.042 3500 Dihedral : 12.194 82.856 3432 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer Outliers : 1.33 % 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: -3.79 (0.16), residues: 2404 helix: -1.60 (0.14), residues: 1284 sheet: -4.03 (0.38), residues: 84 loop : -3.59 (0.17), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 270 time to evaluate : 2.520 Fit side-chains outliers start: 28 outliers final: 6 residues processed: 288 average time/residue: 0.2981 time to fit residues: 138.4672 Evaluate side-chains 250 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 2.419 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1734 time to fit residues: 5.1193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS B 37 ASN B 265 HIS D 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 21248 Z= 0.250 Angle : 0.653 10.819 28588 Z= 0.320 Chirality : 0.042 0.165 3172 Planarity : 0.004 0.040 3500 Dihedral : 12.073 82.264 3432 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer Outliers : 1.94 % 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: -3.43 (0.16), residues: 2404 helix: -1.31 (0.14), residues: 1320 sheet: -3.87 (0.41), residues: 84 loop : -3.47 (0.18), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 262 time to evaluate : 2.270 Fit side-chains outliers start: 41 outliers final: 16 residues processed: 287 average time/residue: 0.2960 time to fit residues: 137.1608 Evaluate side-chains 250 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 234 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1846 time to fit residues: 8.7219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 0.0470 chunk 232 optimal weight: 0.7980 chunk 192 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 0.0570 chunk 121 optimal weight: 5.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 265 HIS A 464 ASN B 265 HIS B 464 ASN C 464 ASN D 265 HIS D 464 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 21248 Z= 0.145 Angle : 0.592 8.964 28588 Z= 0.293 Chirality : 0.040 0.172 3172 Planarity : 0.003 0.038 3500 Dihedral : 11.101 75.971 3432 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer Outliers : 1.28 % 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: -3.02 (0.17), residues: 2404 helix: -0.95 (0.14), residues: 1320 sheet: -3.53 (0.44), residues: 84 loop : -3.35 (0.18), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 275 time to evaluate : 2.499 Fit side-chains outliers start: 27 outliers final: 8 residues processed: 296 average time/residue: 0.3070 time to fit residues: 146.2960 Evaluate side-chains 244 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1922 time to fit residues: 6.0134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 464 ASN B 265 HIS B 464 ASN C 265 HIS C 464 ASN D 265 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21248 Z= 0.166 Angle : 0.604 8.871 28588 Z= 0.295 Chirality : 0.040 0.158 3172 Planarity : 0.003 0.039 3500 Dihedral : 10.516 73.303 3432 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer Outliers : 1.71 % 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: -2.74 (0.17), residues: 2404 helix: -0.63 (0.15), residues: 1300 sheet: -3.19 (0.45), residues: 84 loop : -3.34 (0.18), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 2.350 Fit side-chains outliers start: 36 outliers final: 7 residues processed: 290 average time/residue: 0.3004 time to fit residues: 139.5478 Evaluate side-chains 234 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1924 time to fit residues: 5.6535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 0.0470 chunk 21 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS B 265 HIS C 265 HIS D 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 21248 Z= 0.142 Angle : 0.602 10.146 28588 Z= 0.291 Chirality : 0.039 0.156 3172 Planarity : 0.003 0.038 3500 Dihedral : 9.877 68.212 3432 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer Outliers : 1.23 % 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: -2.42 (0.17), residues: 2404 helix: -0.35 (0.15), residues: 1304 sheet: -2.86 (0.46), residues: 84 loop : -3.26 (0.18), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 257 time to evaluate : 2.521 Fit side-chains outliers start: 26 outliers final: 6 residues processed: 269 average time/residue: 0.3070 time to fit residues: 132.0352 Evaluate side-chains 227 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 221 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2149 time to fit residues: 5.7535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS B 265 HIS C 265 HIS D 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 21248 Z= 0.309 Angle : 0.703 11.187 28588 Z= 0.336 Chirality : 0.044 0.173 3172 Planarity : 0.004 0.037 3500 Dihedral : 10.629 71.353 3432 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer Outliers : 0.62 % 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: -2.60 (0.17), residues: 2404 helix: -0.54 (0.15), residues: 1316 sheet: -2.87 (0.47), residues: 84 loop : -3.32 (0.18), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 246 time to evaluate : 2.585 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 256 average time/residue: 0.3000 time to fit residues: 123.4700 Evaluate side-chains 236 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 2.185 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1803 time to fit residues: 4.1229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS B 265 HIS C 265 HIS D 265 HIS ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 21248 Z= 0.259 Angle : 0.678 10.684 28588 Z= 0.327 Chirality : 0.043 0.174 3172 Planarity : 0.004 0.038 3500 Dihedral : 10.686 71.231 3432 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer Outliers : 0.62 % 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: -2.55 (0.17), residues: 2404 helix: -0.43 (0.15), residues: 1304 sheet: -2.81 (0.49), residues: 84 loop : -3.37 (0.17), residues: 1016 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 2.130 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 249 average time/residue: 0.3194 time to fit residues: 127.0581 Evaluate side-chains 239 residues out of total 2108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 232 time to evaluate : 2.404 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2141 time to fit residues: 5.9682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.2980 chunk 202 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 0.1980 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 265 HIS B 265 HIS C 265 HIS ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.178856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133217 restraints weight = 23769.181| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.44 r_work: 0.3359 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21248 Z= 0.165 Angle : 0.626 9.797 28588 Z= 0.302 Chirality : 0.040 0.161 3172 Planarity : 0.003 0.039 3500 Dihedral : 10.119 67.143 3432 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer Outliers : 0.33 % 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: -2.20 (0.17), residues: 2404 helix: -0.10 (0.15), residues: 1300 sheet: -2.62 (0.49), residues: 84 loop : -3.27 (0.18), residues: 1020 =============================================================================== Job complete usr+sys time: 4278.14 seconds wall clock time: 78 minutes 20.08 seconds (4700.08 seconds total)