Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 12:50:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/10_2023/6e1n_8958_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/10_2023/6e1n_8958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/10_2023/6e1n_8958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/10_2023/6e1n_8958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/10_2023/6e1n_8958_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/10_2023/6e1n_8958_neut_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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 6 9.91 5 P 8 5.49 5 S 46 5.16 5 C 7164 2.51 5 N 1576 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 10682 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5145 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 18, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5145 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 18, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' CA': 3, '3PH': 1, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' CA': 3, '3PH': 1, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.72, per 1000 atoms: 0.54 Number of scatterers: 10682 At special positions: 0 Unit cell: (137.363, 91.17, 106.973, 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 6 19.99 S 46 16.00 P 8 15.00 O 1882 8.00 N 1576 7.00 C 7164 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 1.3 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 37 through 44 removed outlier: 3.884A pdb=" N GLY A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.626A pdb=" N PHE A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.791A pdb=" N ALA A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 117 through 140 removed outlier: 3.830A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 144 through 147 No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 151 through 172 removed outlier: 3.512A pdb=" N VAL A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 163 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 4.067A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.923A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 237 removed outlier: 4.161A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.967A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.412A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.858A pdb=" N VAL A 283 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 288 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 332 removed outlier: 3.630A pdb=" N LEU A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.896A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 removed outlier: 5.370A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 4.122A pdb=" N LEU A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 3.690A pdb=" N LEU A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.622A pdb=" N LEU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 486 removed outlier: 3.727A pdb=" N PHE A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 474 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 476 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 478 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 481 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS A 482 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 483 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 512 removed outlier: 3.616A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 4.700A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.922A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 567 through 586 removed outlier: 4.028A pdb=" N ILE A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 617 through 628 removed outlier: 3.668A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 removed outlier: 3.938A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 3.607A pdb=" N ILE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.545A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.731A pdb=" N GLY B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 63 through 73 removed outlier: 3.719A pdb=" N PHE B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 4.705A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 117 through 140 removed outlier: 3.823A pdb=" N ILE B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 144 through 147 No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 151 through 172 removed outlier: 3.959A pdb=" N LYS B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 163 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 removed outlier: 4.044A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 193 " --> pdb=" O TYR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.927A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 237 removed outlier: 4.205A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.981A pdb=" N GLN B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.389A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 279 through 294 removed outlier: 3.790A pdb=" N VAL B 283 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B 286 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL B 289 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 293 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR B 294 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 332 removed outlier: 3.654A pdb=" N LEU B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 4.060A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 370 removed outlier: 5.159A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 removed outlier: 4.151A pdb=" N LEU B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.714A pdb=" N LEU B 419 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.596A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.780A pdb=" N VAL B 448 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 449 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 450 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 454 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 486 removed outlier: 3.740A pdb=" N PHE B 471 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 474 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 476 " --> pdb=" O TRP B 473 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 477 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 478 " --> pdb=" O TYR B 475 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 481 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 482 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE B 483 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 512 removed outlier: 3.692A pdb=" N LEU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 removed outlier: 4.727A pdb=" N LEU B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ALA B 536 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 540 " --> pdb=" O ALA B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 552 through 564 removed outlier: 3.934A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 567 through 586 removed outlier: 4.095A pdb=" N ILE B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 No H-bonds generated for 'chain 'B' and resid 602 through 605' Processing helix chain 'B' and resid 617 through 628 removed outlier: 3.644A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 642 removed outlier: 3.952A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 removed outlier: 3.510A pdb=" N ILE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.557A pdb=" N LEU B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1155 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: 2.49 Time building geometry restraints manager: 4.81 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: 1657 1.31 - 1.43: 3084 1.43 - 1.56: 6077 1.56 - 1.68: 32 1.68 - 1.81: 74 Bond restraints: 10924 Sorted by residual: bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C31 3PH A 812 " pdb=" O31 3PH A 812 " ideal model delta sigma weight residual 1.325 1.409 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 93.10 - 101.42: 27 101.42 - 109.75: 1771 109.75 - 118.07: 6461 118.07 - 126.40: 6346 126.40 - 134.72: 159 Bond angle restraints: 14764 Sorted by residual: angle pdb=" C ILE A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta sigma weight residual 121.19 130.14 -8.95 1.59e+00 3.96e-01 3.17e+01 angle pdb=" C ILE B 371 " pdb=" N PHE B 372 " pdb=" CA PHE B 372 " ideal model delta sigma weight residual 121.19 130.12 -8.93 1.59e+00 3.96e-01 3.15e+01 angle pdb=" C THR B 264 " pdb=" CA THR B 264 " pdb=" CB THR B 264 " ideal model delta sigma weight residual 111.80 104.25 7.55 1.46e+00 4.69e-01 2.67e+01 angle pdb=" C THR A 264 " pdb=" CA THR A 264 " pdb=" CB THR A 264 " ideal model delta sigma weight residual 111.80 104.38 7.42 1.46e+00 4.69e-01 2.58e+01 angle pdb=" C VAL A 628 " pdb=" N MET A 629 " pdb=" CA MET A 629 " ideal model delta sigma weight residual 122.35 129.25 -6.90 1.46e+00 4.69e-01 2.23e+01 ... (remaining 14759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5731 17.40 - 34.80: 478 34.80 - 52.20: 113 52.20 - 69.61: 38 69.61 - 87.01: 6 Dihedral angle restraints: 6366 sinusoidal: 2590 harmonic: 3776 Sorted by residual: dihedral pdb=" CA THR B 378 " pdb=" C THR B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual -180.00 -133.46 -46.54 0 5.00e+00 4.00e-02 8.66e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LEU B 661 " pdb=" CA LEU B 661 " ideal model delta harmonic sigma weight residual 180.00 135.77 44.23 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CA ILE A 660 " pdb=" C ILE A 660 " pdb=" N LEU A 661 " pdb=" CA LEU A 661 " ideal model delta harmonic sigma weight residual 180.00 138.04 41.96 0 5.00e+00 4.00e-02 7.04e+01 ... (remaining 6363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1276 0.081 - 0.163: 322 0.163 - 0.244: 46 0.244 - 0.325: 2 0.325 - 0.407: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C2 3PH A 812 " pdb=" C1 3PH A 812 " pdb=" C3 3PH A 812 " pdb=" O21 3PH A 812 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1647 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 587 " -0.035 2.00e-02 2.50e+03 2.34e-02 9.55e+00 pdb=" CG PHE B 587 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 587 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 587 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 587 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 587 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 587 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 153 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" CG ASN A 153 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 153 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 153 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 89 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO A 90 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.040 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 188 2.62 - 3.19: 9945 3.19 - 3.76: 16427 3.76 - 4.33: 23086 4.33 - 4.90: 35712 Nonbonded interactions: 85358 Sorted by model distance: nonbonded pdb=" O LEU B 197 " pdb=" NH1 ARG B 203 " model vdw 2.054 2.520 nonbonded pdb=" O LEU A 197 " pdb=" NH1 ARG A 203 " model vdw 2.058 2.520 nonbonded pdb=" OD2 ASP A 606 " pdb=" O HOH A 901 " model vdw 2.204 2.440 nonbonded pdb=" NZ LYS B 344 " pdb=" OG SER B 364 " model vdw 2.209 2.520 nonbonded pdb=" OD2 ASP B 606 " pdb=" O HOH B 901 " model vdw 2.236 2.440 ... (remaining 85353 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' } 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 group one per residue 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 4.180 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.900 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.015 0.124 10924 Z= 0.938 Angle : 1.548 12.441 14764 Z= 0.818 Chirality : 0.072 0.407 1650 Planarity : 0.008 0.071 1794 Dihedral : 14.721 87.007 3926 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.25 % Favored : 91.59 % Rotamer: Outliers : 0.37 % Allowed : 2.89 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -5.21 (0.17), residues: 1248 helix: -3.82 (0.11), residues: 732 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 409 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 413 average time/residue: 0.2120 time to fit residues: 124.1427 Evaluate side-chains 295 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1180 time to fit residues: 1.7563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 257 GLN A 454 ASN A 618 ASN B 89 GLN B 257 GLN B 454 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN B 665 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10924 Z= 0.239 Angle : 0.778 9.893 14764 Z= 0.397 Chirality : 0.044 0.195 1650 Planarity : 0.005 0.042 1794 Dihedral : 14.611 81.209 1684 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.17 % Allowed : 12.38 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.84 (0.20), residues: 1248 helix: -2.57 (0.14), residues: 798 sheet: None (None), residues: 0 loop : -2.16 (0.27), residues: 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 368 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 378 average time/residue: 0.2068 time to fit residues: 111.7313 Evaluate side-chains 302 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 287 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1055 time to fit residues: 4.4185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 123 optimal weight: 0.1980 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 39 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 134 HIS A 497 ASN A 585 GLN B 89 GLN B 134 HIS B 497 ASN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10924 Z= 0.205 Angle : 0.705 9.864 14764 Z= 0.352 Chirality : 0.042 0.183 1650 Planarity : 0.004 0.036 1794 Dihedral : 13.370 79.739 1684 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.61 % Allowed : 17.32 % Favored : 80.07 % 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: -3.21 (0.21), residues: 1248 helix: -1.92 (0.15), residues: 826 sheet: None (None), residues: 0 loop : -2.24 (0.29), residues: 422 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 311 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 322 average time/residue: 0.2071 time to fit residues: 96.4017 Evaluate side-chains 283 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 268 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1016 time to fit residues: 4.4273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 497 ASN A 585 GLN B 89 GLN B 497 ASN B 528 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10924 Z= 0.200 Angle : 0.676 9.491 14764 Z= 0.337 Chirality : 0.042 0.150 1650 Planarity : 0.004 0.034 1794 Dihedral : 12.542 78.260 1684 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.42 % Allowed : 18.99 % Favored : 78.58 % 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: -2.59 (0.22), residues: 1248 helix: -1.48 (0.16), residues: 842 sheet: None (None), residues: 0 loop : -1.90 (0.32), residues: 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 291 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 303 average time/residue: 0.2102 time to fit residues: 91.4624 Evaluate side-chains 286 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 272 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1004 time to fit residues: 4.1263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN B 89 GLN B 311 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10924 Z= 0.210 Angle : 0.677 9.064 14764 Z= 0.334 Chirality : 0.042 0.176 1650 Planarity : 0.004 0.031 1794 Dihedral : 12.073 77.353 1684 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.05 % Allowed : 20.86 % Favored : 77.09 % 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: -2.17 (0.22), residues: 1248 helix: -1.18 (0.16), residues: 838 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 301 average time/residue: 0.1976 time to fit residues: 86.7051 Evaluate side-chains 288 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 280 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1373 time to fit residues: 3.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10924 Z= 0.180 Angle : 0.667 9.510 14764 Z= 0.325 Chirality : 0.041 0.213 1650 Planarity : 0.003 0.032 1794 Dihedral : 11.558 77.086 1684 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.40 % Allowed : 22.25 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1248 helix: -0.86 (0.16), residues: 844 sheet: None (None), residues: 0 loop : -1.80 (0.32), residues: 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 299 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 303 average time/residue: 0.1922 time to fit residues: 85.2958 Evaluate side-chains 269 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 264 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0979 time to fit residues: 2.4025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.0040 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 89 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10924 Z= 0.191 Angle : 0.681 11.102 14764 Z= 0.326 Chirality : 0.041 0.171 1650 Planarity : 0.003 0.031 1794 Dihedral : 11.344 76.798 1684 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.77 % Allowed : 23.56 % Favored : 74.67 % 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: -1.62 (0.23), residues: 1248 helix: -0.62 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -1.81 (0.32), residues: 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 288 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 297 average time/residue: 0.2018 time to fit residues: 87.3378 Evaluate side-chains 275 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 263 time to evaluate : 1.158 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1565 time to fit residues: 4.5620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 110 optimal weight: 0.0670 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 89 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10924 Z= 0.188 Angle : 0.692 11.291 14764 Z= 0.330 Chirality : 0.041 0.165 1650 Planarity : 0.003 0.031 1794 Dihedral : 11.118 76.894 1684 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.12 % Allowed : 23.93 % Favored : 74.95 % 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: -1.41 (0.23), residues: 1248 helix: -0.45 (0.17), residues: 838 sheet: None (None), residues: 0 loop : -1.74 (0.32), residues: 410 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 303 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 310 average time/residue: 0.2021 time to fit residues: 91.7511 Evaluate side-chains 285 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 278 time to evaluate : 1.131 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.0990 time to fit residues: 2.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN B 89 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10924 Z= 0.188 Angle : 0.707 11.526 14764 Z= 0.332 Chirality : 0.041 0.192 1650 Planarity : 0.003 0.031 1794 Dihedral : 10.991 77.070 1684 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.47 % Allowed : 25.70 % Favored : 73.84 % 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: -1.24 (0.23), residues: 1248 helix: -0.29 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -1.76 (0.32), residues: 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 282 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 284 average time/residue: 0.1980 time to fit residues: 82.6013 Evaluate side-chains 276 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 272 time to evaluate : 1.117 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1022 time to fit residues: 2.3487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 89 GLN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10924 Z= 0.190 Angle : 0.714 11.543 14764 Z= 0.336 Chirality : 0.041 0.172 1650 Planarity : 0.003 0.031 1794 Dihedral : 10.869 77.235 1684 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.47 % Allowed : 26.72 % Favored : 72.81 % 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: -1.06 (0.24), residues: 1248 helix: -0.14 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -1.73 (0.32), residues: 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 279 average time/residue: 0.2094 time to fit residues: 85.3079 Evaluate side-chains 276 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 273 time to evaluate : 1.211 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1198 time to fit residues: 2.3266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.0670 chunk 5 optimal weight: 0.0970 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 89 GLN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.207700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.167419 restraints weight = 16175.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.171451 restraints weight = 7544.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173929 restraints weight = 4610.215| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10924 Z= 0.179 Angle : 0.720 13.651 14764 Z= 0.336 Chirality : 0.041 0.176 1650 Planarity : 0.003 0.031 1794 Dihedral : 10.701 77.407 1684 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.74 % Allowed : 26.07 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1248 helix: -0.06 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -1.70 (0.32), residues: 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.32 seconds wall clock time: 44 minutes 46.21 seconds (2686.21 seconds total)