Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 18:01:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/07_2023/5nj3_3654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/07_2023/5nj3_3654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/07_2023/5nj3_3654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/07_2023/5nj3_3654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/07_2023/5nj3_3654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/07_2023/5nj3_3654.pdb" } resolution = 3.78 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7982 2.51 5 N 2226 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 426": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 65": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 12662 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 3599 Classifications: {'peptide': 561} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'PTRANS': 19, 'TRANS': 541} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 791 Unresolved non-hydrogen angles: 1007 Unresolved non-hydrogen dihedrals: 645 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 16, 'ASP:plan': 13, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 401 Chain: "B" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 3599 Classifications: {'peptide': 561} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'PTRANS': 19, 'TRANS': 541} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 791 Unresolved non-hydrogen angles: 1007 Unresolved non-hydrogen dihedrals: 645 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 16, 'ASP:plan': 13, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 401 Chain: "C" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1374 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 192} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1330 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 199} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 174 Chain: "E" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1374 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 192} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "F" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1330 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 199} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 174 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.61, per 1000 atoms: 0.52 Number of scatterers: 12662 At special positions: 0 Unit cell: (96.627, 158.967, 154.811, 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 50 16.00 O 2404 8.00 N 2226 7.00 C 7982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.05 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 2.1 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 24 sheets defined 39.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 85 through 95 Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.473A pdb=" N ASN A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.911A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.995A pdb=" N ALA A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.801A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 4.479A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.534A pdb=" N GLY A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 391 removed outlier: 3.616A pdb=" N LEU A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 413 removed outlier: 4.023A pdb=" N SER A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 422 through 441 removed outlier: 3.526A pdb=" N GLY A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 435 " --> pdb=" O PHE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.739A pdb=" N LEU A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 448 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 502 through 529 Processing helix chain 'A' and resid 533 through 550 removed outlier: 4.282A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.324A pdb=" N VAL A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A 557 " --> pdb=" O GLY A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 557' Processing helix chain 'A' and resid 558 through 561 removed outlier: 3.777A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 558 through 561' Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.507A pdb=" N LEU A 568 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.899A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.582A pdb=" N PHE A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 582 through 587' Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 623 through 652 removed outlier: 3.773A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 116 through 121 removed outlier: 4.473A pdb=" N ASN B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.911A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 removed outlier: 3.995A pdb=" N ALA B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.801A pdb=" N ASN B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 4.479A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 removed outlier: 3.534A pdb=" N GLY B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 3.615A pdb=" N LEU B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 413 removed outlier: 4.023A pdb=" N SER B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 422 through 441 removed outlier: 3.525A pdb=" N GLY B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 435 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.739A pdb=" N LEU B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 448 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL B 450 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 502 through 529 Processing helix chain 'B' and resid 533 through 550 removed outlier: 4.281A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 4.323A pdb=" N VAL B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 557' Processing helix chain 'B' and resid 558 through 561 removed outlier: 3.777A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 558 through 561' Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.507A pdb=" N LEU B 568 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 582 removed outlier: 3.899A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.582A pdb=" N PHE B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 587' Processing helix chain 'B' and resid 610 through 618 Processing helix chain 'B' and resid 623 through 652 removed outlier: 3.774A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 71 removed outlier: 4.812A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.461A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 242 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 78 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 71 removed outlier: 4.813A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.462A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASN B 76 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE B 242 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 78 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.608A pdb=" N THR C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.222A pdb=" N ARG C 39 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.501A pdb=" N TYR C 108 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 127 through 130 removed outlier: 3.987A pdb=" N GLY C 145 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS C 146 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 127 through 130 removed outlier: 3.987A pdb=" N GLY C 145 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS C 146 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 157 through 160 removed outlier: 4.011A pdb=" N CYS C 201 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS C 214 " --> pdb=" O CYS C 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.140A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 45 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.575A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB6, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.608A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.222A pdb=" N ARG E 39 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.501A pdb=" N TYR E 108 " --> pdb=" O THR E 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 127 through 130 removed outlier: 3.989A pdb=" N GLY E 145 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS E 146 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR E 181 " --> pdb=" O GLY E 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 130 removed outlier: 3.989A pdb=" N GLY E 145 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS E 146 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR E 181 " --> pdb=" O GLY E 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 157 through 160 removed outlier: 4.010A pdb=" N CYS E 201 " --> pdb=" O LYS E 214 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS E 214 " --> pdb=" O CYS E 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.140A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.575A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 153 through 154 754 hydrogen bonds defined for protein. 2082 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: 5.35 Time building geometry restraints manager: 5.48 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: 2150 1.31 - 1.43: 3378 1.43 - 1.56: 7254 1.56 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 12858 Sorted by residual: bond pdb=" C THR C 171 " pdb=" N PHE C 172 " ideal model delta sigma weight residual 1.339 1.180 0.160 5.57e-02 3.22e+02 8.24e+00 bond pdb=" C THR E 171 " pdb=" N PHE E 172 " ideal model delta sigma weight residual 1.339 1.180 0.160 5.57e-02 3.22e+02 8.20e+00 bond pdb=" CB GLN A 569 " pdb=" CG GLN A 569 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 7.94e+00 bond pdb=" CB GLN B 569 " pdb=" CG GLN B 569 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.71e+00 bond pdb=" C ASN A 601 " pdb=" N PRO A 602 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.02e+00 ... (remaining 12853 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.71: 245 105.71 - 113.25: 6955 113.25 - 120.79: 5963 120.79 - 128.33: 4365 128.33 - 135.87: 78 Bond angle restraints: 17606 Sorted by residual: angle pdb=" C PRO A 602 " pdb=" N CYS A 603 " pdb=" CA CYS A 603 " ideal model delta sigma weight residual 122.17 113.86 8.31 1.62e+00 3.81e-01 2.63e+01 angle pdb=" C PRO B 602 " pdb=" N CYS B 603 " pdb=" CA CYS B 603 " ideal model delta sigma weight residual 122.17 113.88 8.29 1.62e+00 3.81e-01 2.62e+01 angle pdb=" N PRO A 602 " pdb=" CA PRO A 602 " pdb=" C PRO A 602 " ideal model delta sigma weight residual 112.47 122.52 -10.05 2.06e+00 2.36e-01 2.38e+01 angle pdb=" N PRO B 602 " pdb=" CA PRO B 602 " pdb=" C PRO B 602 " ideal model delta sigma weight residual 112.47 122.48 -10.01 2.06e+00 2.36e-01 2.36e+01 angle pdb=" C TYR B 605 " pdb=" CA TYR B 605 " pdb=" CB TYR B 605 " ideal model delta sigma weight residual 111.48 103.98 7.50 1.59e+00 3.96e-01 2.23e+01 ... (remaining 17601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.45: 6953 14.45 - 28.89: 367 28.89 - 43.34: 79 43.34 - 57.79: 23 57.79 - 72.23: 5 Dihedral angle restraints: 7427 sinusoidal: 1815 harmonic: 5612 Sorted by residual: dihedral pdb=" CA ASN A 601 " pdb=" C ASN A 601 " pdb=" N PRO A 602 " pdb=" CA PRO A 602 " ideal model delta harmonic sigma weight residual -180.00 -124.15 -55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ASN B 601 " pdb=" C ASN B 601 " pdb=" N PRO B 602 " pdb=" CA PRO B 602 " ideal model delta harmonic sigma weight residual -180.00 -124.17 -55.83 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA PRO A 602 " pdb=" C PRO A 602 " pdb=" N CYS A 603 " pdb=" CA CYS A 603 " ideal model delta harmonic sigma weight residual 180.00 137.89 42.11 0 5.00e+00 4.00e-02 7.09e+01 ... (remaining 7424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1892 0.094 - 0.188: 250 0.188 - 0.282: 6 0.282 - 0.376: 4 0.376 - 0.470: 4 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 596 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 596 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB ILE A 573 " pdb=" CA ILE A 573 " pdb=" CG1 ILE A 573 " pdb=" CG2 ILE A 573 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 2153 not shown) Planarity restraints: 2302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 601 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 602 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 601 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO B 602 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 602 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 602 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 576 " 0.019 2.00e-02 2.50e+03 1.82e-02 6.62e+00 pdb=" CG TYR B 576 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 576 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 576 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 576 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 576 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 576 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 576 " 0.001 2.00e-02 2.50e+03 ... (remaining 2299 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1125 2.73 - 3.27: 12461 3.27 - 3.81: 20154 3.81 - 4.36: 22516 4.36 - 4.90: 39080 Nonbonded interactions: 95336 Sorted by model distance: nonbonded pdb=" O ARG B 575 " pdb=" OG1 THR B 579 " model vdw 2.183 2.440 nonbonded pdb=" O ARG A 575 " pdb=" OG1 THR A 579 " model vdw 2.184 2.440 nonbonded pdb=" O VAL A 508 " pdb=" OG1 THR A 512 " model vdw 2.264 2.440 nonbonded pdb=" O VAL B 508 " pdb=" OG1 THR B 512 " model vdw 2.264 2.440 nonbonded pdb=" O CYS A 438 " pdb=" OG SER A 441 " model vdw 2.273 2.440 ... (remaining 95331 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' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.080 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 36.120 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.011 0.160 12858 Z= 0.737 Angle : 1.165 12.489 17606 Z= 0.634 Chirality : 0.064 0.470 2156 Planarity : 0.007 0.070 2300 Dihedral : 10.488 70.998 3790 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.32 % 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: -3.80 (0.16), residues: 1930 helix: -3.06 (0.12), residues: 646 sheet: -1.42 (0.23), residues: 454 loop : -2.56 (0.20), residues: 830 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 1.519 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: 6 outliers final: 1 residues processed: 283 average time/residue: 0.2525 time to fit residues: 101.3314 Evaluate side-chains 180 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1040 time to fit residues: 2.0628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 147 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 50 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 50.0000 chunk 152 optimal weight: 50.0000 chunk 58 optimal weight: 50.0000 chunk 92 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 393 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN B 424 GLN B 629 ASN C 40 GLN C 82 GLN E 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 12858 Z= 0.351 Angle : 0.723 9.281 17606 Z= 0.377 Chirality : 0.046 0.231 2156 Planarity : 0.005 0.065 2300 Dihedral : 6.200 63.628 2030 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.81 (0.18), residues: 1930 helix: -0.59 (0.18), residues: 662 sheet: -0.79 (0.23), residues: 452 loop : -1.86 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 210 time to evaluate : 1.484 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 outliers start: 31 outliers final: 10 residues processed: 218 average time/residue: 0.2061 time to fit residues: 69.7111 Evaluate side-chains 182 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1162 time to fit residues: 3.9680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 146 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 157 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 617 GLN B 424 GLN E 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12858 Z= 0.203 Angle : 0.610 8.470 17606 Z= 0.316 Chirality : 0.044 0.191 2156 Planarity : 0.004 0.062 2300 Dihedral : 5.469 58.876 2030 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.70 (0.19), residues: 1930 helix: 0.74 (0.20), residues: 658 sheet: -0.37 (0.24), residues: 448 loop : -1.48 (0.23), residues: 824 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 207 time to evaluate : 1.460 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: 17 outliers final: 8 residues processed: 219 average time/residue: 0.1935 time to fit residues: 65.9268 Evaluate side-chains 191 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1171 time to fit residues: 3.7300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 19 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 118 optimal weight: 0.0010 chunk 177 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 167 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 629 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.087 12858 Z= 0.529 Angle : 0.789 8.754 17606 Z= 0.411 Chirality : 0.050 0.250 2156 Planarity : 0.005 0.056 2300 Dihedral : 5.831 46.653 2030 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.06 % Favored : 93.83 % Rotamer Outliers : 4.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.61 (0.19), residues: 1930 helix: 0.94 (0.20), residues: 664 sheet: -0.37 (0.24), residues: 444 loop : -1.54 (0.22), residues: 822 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 200 average time/residue: 0.1993 time to fit residues: 62.8303 Evaluate side-chains 183 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1143 time to fit residues: 6.6966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 50.0000 chunk 139 optimal weight: 0.5980 chunk 77 optimal weight: 50.0000 chunk 160 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 95 optimal weight: 0.9980 chunk 168 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 436 ASN A 569 GLN B 557 ASN B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 12858 Z= 0.180 Angle : 0.616 8.683 17606 Z= 0.320 Chirality : 0.044 0.233 2156 Planarity : 0.004 0.058 2300 Dihedral : 5.202 46.672 2030 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.85 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.11 % 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: -0.03 (0.20), residues: 1930 helix: 1.55 (0.20), residues: 674 sheet: -0.12 (0.24), residues: 446 loop : -1.32 (0.23), residues: 810 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 208 average time/residue: 0.2023 time to fit residues: 66.1957 Evaluate side-chains 185 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.431 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1292 time to fit residues: 4.7028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 30.0000 chunk 168 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 62 optimal weight: 50.0000 chunk 98 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN D 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.120 12858 Z= 0.741 Angle : 0.920 9.133 17606 Z= 0.478 Chirality : 0.054 0.285 2156 Planarity : 0.006 0.065 2300 Dihedral : 6.209 40.446 2030 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.10 % Favored : 92.80 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.22 % 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: -0.85 (0.19), residues: 1930 helix: 0.80 (0.20), residues: 686 sheet: -0.44 (0.26), residues: 390 loop : -1.78 (0.21), residues: 854 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 185 average time/residue: 0.1964 time to fit residues: 57.4391 Evaluate side-chains 179 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1121 time to fit residues: 7.0800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 0.9990 chunk 21 optimal weight: 50.0000 chunk 106 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 186 optimal weight: 40.0000 chunk 117 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12858 Z= 0.186 Angle : 0.637 9.773 17606 Z= 0.331 Chirality : 0.044 0.188 2156 Planarity : 0.004 0.050 2300 Dihedral : 5.226 47.212 2030 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.80 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.06 (0.20), residues: 1930 helix: 1.58 (0.20), residues: 682 sheet: -0.19 (0.26), residues: 388 loop : -1.32 (0.22), residues: 860 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 177 average time/residue: 0.2037 time to fit residues: 56.9237 Evaluate side-chains 168 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1348 time to fit residues: 2.7270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 50.0000 chunk 111 optimal weight: 0.4980 chunk 56 optimal weight: 60.0000 chunk 36 optimal weight: 0.0010 chunk 118 optimal weight: 0.8980 chunk 127 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 60.0000 chunk 146 optimal weight: 30.0000 chunk 170 optimal weight: 30.0000 chunk 179 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 569 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12858 Z= 0.185 Angle : 0.598 9.864 17606 Z= 0.312 Chirality : 0.043 0.194 2156 Planarity : 0.004 0.051 2300 Dihedral : 4.825 42.818 2030 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.92 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.27 (0.20), residues: 1930 helix: 1.85 (0.20), residues: 688 sheet: -0.18 (0.26), residues: 400 loop : -1.05 (0.23), residues: 842 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 188 average time/residue: 0.1948 time to fit residues: 58.1779 Evaluate side-chains 173 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 169 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1358 time to fit residues: 2.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 136 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 12858 Z= 0.283 Angle : 0.645 11.219 17606 Z= 0.338 Chirality : 0.045 0.289 2156 Planarity : 0.004 0.049 2300 Dihedral : 4.862 40.584 2030 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.61 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.27 (0.20), residues: 1930 helix: 1.83 (0.20), residues: 692 sheet: -0.10 (0.26), residues: 412 loop : -1.10 (0.23), residues: 826 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 172 average time/residue: 0.1982 time to fit residues: 53.8541 Evaluate side-chains 164 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1253 time to fit residues: 3.0113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 50.0000 chunk 112 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 128 optimal weight: 0.0570 chunk 193 optimal weight: 50.0000 chunk 177 optimal weight: 0.0040 chunk 153 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 overall best weight: 0.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN B 437 GLN B 569 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12858 Z= 0.160 Angle : 0.597 8.308 17606 Z= 0.311 Chirality : 0.044 0.276 2156 Planarity : 0.004 0.051 2300 Dihedral : 4.527 39.297 2030 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.57 (0.20), residues: 1930 helix: 2.05 (0.21), residues: 692 sheet: 0.15 (0.26), residues: 410 loop : -0.95 (0.23), residues: 828 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.492 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 outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.1960 time to fit residues: 59.1439 Evaluate side-chains 179 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.478 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1195 time to fit residues: 2.0887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 1.9990 chunk 47 optimal weight: 0.0060 chunk 141 optimal weight: 0.3980 chunk 22 optimal weight: 50.0000 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 19 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.141545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107631 restraints weight = 25998.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.108988 restraints weight = 16816.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109875 restraints weight = 13017.527| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12858 Z= 0.171 Angle : 0.590 9.102 17606 Z= 0.308 Chirality : 0.044 0.290 2156 Planarity : 0.004 0.049 2300 Dihedral : 4.388 35.594 2030 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.73 (0.20), residues: 1930 helix: 2.20 (0.21), residues: 694 sheet: 0.18 (0.25), residues: 438 loop : -0.87 (0.23), residues: 798 =============================================================================== Job complete usr+sys time: 2276.80 seconds wall clock time: 42 minutes 13.12 seconds (2533.12 seconds total)