Starting phenix.real_space_refine (version: dev) on Fri Mar 17 13:35:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/03_2023/6o1p_0594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/03_2023/6o1p_0594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/03_2023/6o1p_0594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/03_2023/6o1p_0594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/03_2023/6o1p_0594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/03_2023/6o1p_0594.pdb" } resolution = 3.0 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= 0.008 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "B" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "C" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "D" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Time building chain proxies: 11.34, per 1000 atoms: 0.58 Number of scatterers: 19608 At special positions: 0 Unit cell: (132.375, 132.375, 124.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3488 8.00 N 3320 7.00 C 12660 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: 7.34 Conformation dependent library (CDL) restraints added in 3.1 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 59.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.586A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.578A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.621A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.711A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.678A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.584A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 removed outlier: 3.518A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.587A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.619A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.578A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.621A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.954A pdb=" N VAL B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.711A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 443 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.678A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.584A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.513A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 3.928A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 585 removed outlier: 3.518A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.740A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.586A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.577A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.620A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.711A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 443 Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.677A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.583A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 486 removed outlier: 3.633A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 585 removed outlier: 3.517A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.587A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.577A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.620A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.512A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.711A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 443 Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.677A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.583A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 585 removed outlier: 3.517A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 585 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.551A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP D 593 " --> pdb=" O ARG D 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 266 Processing sheet with id=AA3, first strand: chain 'C' and resid 264 through 266 Processing sheet with id=AA4, first strand: chain 'D' and resid 264 through 266 820 hydrogen bonds defined for protein. 2352 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: 5.87 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3484 1.32 - 1.45: 5405 1.45 - 1.57: 10947 1.57 - 1.70: 0 1.70 - 1.83: 228 Bond restraints: 20064 Sorted by residual: bond pdb=" CA TRP B 286 " pdb=" C TRP B 286 " ideal model delta sigma weight residual 1.526 1.422 0.103 1.31e-02 5.83e+03 6.21e+01 bond pdb=" CA TRP D 286 " pdb=" C TRP D 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" CA TRP A 286 " pdb=" C TRP A 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" CA TRP C 286 " pdb=" C TRP C 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" N TRP A 286 " pdb=" CA TRP A 286 " ideal model delta sigma weight residual 1.458 1.380 0.078 1.00e-02 1.00e+04 6.12e+01 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 85.18 - 95.35: 16 95.35 - 105.53: 508 105.53 - 115.70: 12276 115.70 - 125.87: 14068 125.87 - 136.05: 380 Bond angle restraints: 27248 Sorted by residual: angle pdb=" N LEU B 612 " pdb=" CA LEU B 612 " pdb=" C LEU B 612 " ideal model delta sigma weight residual 111.04 136.05 -25.01 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU C 612 " pdb=" CA LEU C 612 " pdb=" C LEU C 612 " ideal model delta sigma weight residual 111.04 136.03 -24.99 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU A 612 " pdb=" CA LEU A 612 " pdb=" C LEU A 612 " ideal model delta sigma weight residual 111.04 136.02 -24.98 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU D 612 " pdb=" CA LEU D 612 " pdb=" C LEU D 612 " ideal model delta sigma weight residual 111.04 136.01 -24.97 1.55e+00 4.16e-01 2.59e+02 angle pdb=" N LEU C 354 " pdb=" CA LEU C 354 " pdb=" C LEU C 354 " ideal model delta sigma weight residual 108.99 85.57 23.42 1.57e+00 4.06e-01 2.23e+02 ... (remaining 27243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 11120 15.24 - 30.47: 652 30.47 - 45.71: 144 45.71 - 60.94: 8 60.94 - 76.18: 12 Dihedral angle restraints: 11936 sinusoidal: 4780 harmonic: 7156 Sorted by residual: dihedral pdb=" N TRP C 613 " pdb=" C TRP C 613 " pdb=" CA TRP C 613 " pdb=" CB TRP C 613 " ideal model delta harmonic sigma weight residual 122.80 92.84 29.96 0 2.50e+00 1.60e-01 1.44e+02 dihedral pdb=" N TRP D 613 " pdb=" C TRP D 613 " pdb=" CA TRP D 613 " pdb=" CB TRP D 613 " ideal model delta harmonic sigma weight residual 122.80 92.84 29.96 0 2.50e+00 1.60e-01 1.44e+02 dihedral pdb=" N TRP A 613 " pdb=" C TRP A 613 " pdb=" CA TRP A 613 " pdb=" CB TRP A 613 " ideal model delta harmonic sigma weight residual 122.80 92.86 29.94 0 2.50e+00 1.60e-01 1.43e+02 ... (remaining 11933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 3036 0.199 - 0.397: 48 0.397 - 0.596: 4 0.596 - 0.795: 8 0.795 - 0.993: 4 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CA LEU C 612 " pdb=" N LEU C 612 " pdb=" C LEU C 612 " pdb=" CB LEU C 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA LEU B 612 " pdb=" N LEU B 612 " pdb=" C LEU B 612 " pdb=" CB LEU B 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA LEU A 612 " pdb=" N LEU A 612 " pdb=" C LEU A 612 " pdb=" CB LEU A 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 ... (remaining 3097 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 285 " -0.052 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER B 285 " 0.211 2.00e-02 2.50e+03 pdb=" O SER B 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP B 286 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 285 " -0.053 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER D 285 " 0.211 2.00e-02 2.50e+03 pdb=" O SER D 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP D 286 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 285 " -0.052 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER A 285 " 0.210 2.00e-02 2.50e+03 pdb=" O SER A 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP A 286 " -0.071 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 79 2.50 - 3.10: 13170 3.10 - 3.70: 30008 3.70 - 4.30: 44383 4.30 - 4.90: 71847 Nonbonded interactions: 159487 Sorted by model distance: nonbonded pdb=" O SER B 285 " pdb=" CD1 TRP B 286 " model vdw 1.899 3.260 nonbonded pdb=" O SER D 285 " pdb=" CD1 TRP D 286 " model vdw 1.899 3.260 nonbonded pdb=" O SER A 285 " pdb=" CD1 TRP A 286 " model vdw 1.900 3.260 nonbonded pdb=" O SER C 285 " pdb=" CD1 TRP C 286 " model vdw 1.900 3.260 nonbonded pdb=" N GLN A 230 " pdb=" OE1 GLN A 230 " model vdw 2.096 2.520 ... (remaining 159482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12660 2.51 5 N 3320 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.270 Check model and map are aligned: 0.290 Process input model: 48.770 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 69.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.012 0.145 20064 Z= 0.791 Angle : 1.528 25.188 27248 Z= 0.875 Chirality : 0.087 0.993 3100 Planarity : 0.009 0.122 3460 Dihedral : 10.643 76.176 7312 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.89 % Favored : 92.79 % Rotamer Outliers : 0.57 % Cbeta Deviations : 1.21 % 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: -5.75 (0.12), residues: 2440 helix: -3.98 (0.07), residues: 1428 sheet: -3.16 (0.62), residues: 64 loop : -3.31 (0.17), residues: 948 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 607 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 616 average time/residue: 1.3181 time to fit residues: 910.0464 Evaluate side-chains 353 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 349 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 3 average time/residue: 0.2784 time to fit residues: 3.5668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 0.0970 chunk 116 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: