Starting phenix.real_space_refine on Fri Mar 15 20:24:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/03_2024/5nj3_3654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/03_2024/5nj3_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_3654/03_2024/5nj3_3654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/03_2024/5nj3_3654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/03_2024/5nj3_3654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nj3_3654/03_2024/5nj3_3654.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-dev-5265/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.17, per 1000 atoms: 0.57 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: 4.88 Conformation dependent library (CDL) restraints added in 2.6 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: 1.76 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: 4.14 Time building geometry restraints manager: 5.32 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: 7018 14.45 - 28.89: 378 28.89 - 43.34: 79 43.34 - 57.79: 31 57.79 - 72.23: 5 Dihedral angle restraints: 7511 sinusoidal: 1899 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 7508 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: 0.570 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: 3.550 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 36.070 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- 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 : 10.684 70.998 3874 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 % Allowed : 3.42 % Favored : 95.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP C 109 HIS 0.004 0.002 HIS A 457 PHE 0.041 0.004 PHE D 98 TYR 0.044 0.005 TYR B 576 ARG 0.013 0.002 ARG B 426 *********************** 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 : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ILE cc_start: 0.8766 (mt) cc_final: 0.8454 (mp) REVERT: A 488 ILE cc_start: 0.8819 (mt) cc_final: 0.8574 (mt) REVERT: A 492 ILE cc_start: 0.8264 (pt) cc_final: 0.7791 (pt) REVERT: A 624 TRP cc_start: 0.8264 (t60) cc_final: 0.7948 (t60) REVERT: B 373 PHE cc_start: 0.6918 (t80) cc_final: 0.6627 (t80) REVERT: B 479 LEU cc_start: 0.8632 (mt) cc_final: 0.8309 (tp) REVERT: B 488 ILE cc_start: 0.8732 (mt) cc_final: 0.8427 (mt) REVERT: B 617 GLN cc_start: 0.8233 (tp-100) cc_final: 0.8031 (mm-40) REVERT: C 103 LYS cc_start: 0.8489 (tttt) cc_final: 0.8265 (tttp) REVERT: E 103 LYS cc_start: 0.8906 (tttt) cc_final: 0.8391 (tttp) REVERT: E 105 THR cc_start: 0.8375 (p) cc_final: 0.8165 (t) outliers start: 6 outliers final: 1 residues processed: 283 average time/residue: 0.2497 time to fit residues: 100.2959 Evaluate side-chains 184 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9980 chunk 147 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 50 optimal weight: 5.9990 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: 0.6980 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 B 376 GLN B 424 GLN B 629 ASN C 40 GLN C 82 GLN E 40 GLN E 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12858 Z= 0.345 Angle : 0.723 9.520 17606 Z= 0.376 Chirality : 0.046 0.221 2156 Planarity : 0.005 0.069 2300 Dihedral : 6.931 63.462 2115 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 3.19 % Allowed : 12.64 % Favored : 84.17 % 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: -1.68 (0.18), residues: 1930 helix: -0.41 (0.18), residues: 656 sheet: -0.75 (0.23), residues: 452 loop : -1.84 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 624 HIS 0.003 0.001 HIS A 583 PHE 0.024 0.002 PHE D 62 TYR 0.032 0.002 TYR A 645 ARG 0.005 0.001 ARG D 18 *********************** 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 246 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 218 time to evaluate : 1.388 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: A 482 ARG cc_start: 0.8541 (mmp80) cc_final: 0.7925 (mmt180) REVERT: B 477 ASP cc_start: 0.7834 (t0) cc_final: 0.7437 (m-30) REVERT: B 479 LEU cc_start: 0.8610 (mt) cc_final: 0.8387 (tp) REVERT: B 482 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7630 (mmt180) REVERT: C 103 LYS cc_start: 0.8810 (tttt) cc_final: 0.8531 (tttp) outliers start: 28 outliers final: 11 residues processed: 227 average time/residue: 0.2002 time to fit residues: 69.5089 Evaluate side-chains 188 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 81 GLU 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: 0.8980 chunk 146 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 157 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12858 Z= 0.172 Angle : 0.594 8.579 17606 Z= 0.309 Chirality : 0.043 0.185 2156 Planarity : 0.004 0.067 2300 Dihedral : 6.160 59.810 2114 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 1.82 % Allowed : 18.22 % Favored : 79.95 % 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: -0.68 (0.19), residues: 1930 helix: 0.75 (0.19), residues: 662 sheet: -0.33 (0.24), residues: 448 loop : -1.49 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 35 HIS 0.001 0.000 HIS A 630 PHE 0.015 0.001 PHE F 62 TYR 0.028 0.001 TYR A 645 ARG 0.003 0.000 ARG D 18 *********************** 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 227 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8507 (mmp80) cc_final: 0.7804 (mmt180) REVERT: B 479 LEU cc_start: 0.8616 (mt) cc_final: 0.8304 (tp) REVERT: B 511 PHE cc_start: 0.8408 (t80) cc_final: 0.8118 (t80) REVERT: C 5 GLN cc_start: 0.7593 (tp40) cc_final: 0.7262 (tp-100) REVERT: C 103 LYS cc_start: 0.8746 (tttt) cc_final: 0.8540 (tttp) REVERT: F 13 VAL cc_start: 0.8124 (m) cc_final: 0.7677 (p) outliers start: 16 outliers final: 8 residues processed: 217 average time/residue: 0.1918 time to fit residues: 65.3126 Evaluate side-chains 193 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 81 LEU 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: 6.9990 chunk 91 optimal weight: 7.9990 chunk 19 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 167 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.099 12858 Z= 0.685 Angle : 0.860 10.328 17606 Z= 0.450 Chirality : 0.052 0.265 2156 Planarity : 0.005 0.057 2300 Dihedral : 6.736 59.752 2114 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.94 % Rotamer: Outliers : 5.35 % Allowed : 20.05 % Favored : 74.60 % 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: -0.76 (0.19), residues: 1930 helix: 0.80 (0.20), residues: 664 sheet: -0.44 (0.24), residues: 444 loop : -1.60 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 109 HIS 0.006 0.001 HIS B 583 PHE 0.034 0.003 PHE C 79 TYR 0.031 0.003 TYR E 94 ARG 0.008 0.001 ARG C 39 *********************** 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 217 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 170 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 TRP cc_start: 0.7891 (t-100) cc_final: 0.7688 (t-100) REVERT: A 482 ARG cc_start: 0.8510 (mmp80) cc_final: 0.7839 (mmt180) REVERT: B 451 GLU cc_start: 0.7540 (pt0) cc_final: 0.7335 (pt0) REVERT: C 103 LYS cc_start: 0.9011 (tttt) cc_final: 0.8795 (tttp) REVERT: D 31 ASN cc_start: 0.8466 (m-40) cc_final: 0.8234 (m110) outliers start: 47 outliers final: 31 residues processed: 201 average time/residue: 0.1839 time to fit residues: 58.2543 Evaluate side-chains 191 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 2 optimal weight: 50.0000 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 50.0000 chunk 160 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 95 optimal weight: 0.6980 chunk 168 optimal weight: 40.0000 chunk 47 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12858 Z= 0.256 Angle : 0.639 8.330 17606 Z= 0.334 Chirality : 0.045 0.227 2156 Planarity : 0.004 0.056 2300 Dihedral : 6.133 59.843 2114 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 4.67 % Allowed : 20.96 % Favored : 74.37 % 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: -0.20 (0.19), residues: 1930 helix: 1.40 (0.20), residues: 668 sheet: -0.19 (0.24), residues: 436 loop : -1.39 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 35 HIS 0.002 0.001 HIS A 583 PHE 0.021 0.002 PHE A 545 TYR 0.028 0.002 TYR A 645 ARG 0.003 0.000 ARG C 39 *********************** 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 221 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8375 (mmp80) cc_final: 0.7900 (mmt180) REVERT: A 541 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7265 (tpp) REVERT: B 451 GLU cc_start: 0.7453 (pt0) cc_final: 0.7177 (pt0) REVERT: B 511 PHE cc_start: 0.8498 (t80) cc_final: 0.8215 (t80) REVERT: C 103 LYS cc_start: 0.8878 (tttt) cc_final: 0.8607 (tttp) outliers start: 41 outliers final: 21 residues processed: 206 average time/residue: 0.1917 time to fit residues: 62.1077 Evaluate side-chains 190 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 17 ASP 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: 40.0000 chunk 37 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 98 optimal weight: 1.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 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: 0.7982 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 12858 Z= 0.491 Angle : 0.738 10.132 17606 Z= 0.385 Chirality : 0.049 0.229 2156 Planarity : 0.005 0.052 2300 Dihedral : 6.297 59.716 2114 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 5.69 % Allowed : 22.44 % Favored : 71.87 % 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: -0.33 (0.19), residues: 1930 helix: 1.33 (0.20), residues: 672 sheet: -0.29 (0.26), residues: 396 loop : -1.44 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 92 HIS 0.003 0.001 HIS A 583 PHE 0.024 0.002 PHE C 79 TYR 0.027 0.002 TYR A 645 ARG 0.003 0.001 ARG B 465 *********************** 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 217 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 167 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 TRP cc_start: 0.7846 (t-100) cc_final: 0.7472 (t-100) REVERT: A 458 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7279 (tt0) REVERT: A 463 TYR cc_start: 0.8531 (m-80) cc_final: 0.8300 (m-80) REVERT: A 483 MET cc_start: 0.7606 (mtp) cc_final: 0.7382 (mtp) REVERT: B 451 GLU cc_start: 0.7641 (pt0) cc_final: 0.7421 (pt0) REVERT: B 653 LYS cc_start: 0.7149 (mttt) cc_final: 0.6299 (tmmt) REVERT: D 31 ASN cc_start: 0.8445 (m-40) cc_final: 0.8212 (m110) outliers start: 50 outliers final: 35 residues processed: 201 average time/residue: 0.1881 time to fit residues: 59.7720 Evaluate side-chains 199 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 65 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 0.9980 chunk 21 optimal weight: 50.0000 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 186 optimal weight: 40.0000 chunk 117 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN B 424 GLN B 437 GLN B 557 ASN B 569 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12858 Z= 0.173 Angle : 0.595 10.506 17606 Z= 0.309 Chirality : 0.044 0.189 2156 Planarity : 0.004 0.056 2300 Dihedral : 5.713 59.751 2114 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 3.53 % Allowed : 24.03 % Favored : 72.44 % 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: 0.24 (0.20), residues: 1930 helix: 1.76 (0.20), residues: 684 sheet: -0.16 (0.26), residues: 414 loop : -1.03 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 35 HIS 0.002 0.001 HIS A 583 PHE 0.013 0.001 PHE B 578 TYR 0.026 0.001 TYR A 645 ARG 0.002 0.000 ARG A 383 *********************** 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 217 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.470 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: A 379 TRP cc_start: 0.7833 (t-100) cc_final: 0.7462 (t-100) REVERT: A 482 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7980 (mmt180) REVERT: B 451 GLU cc_start: 0.7604 (pt0) cc_final: 0.7263 (pt0) REVERT: B 511 PHE cc_start: 0.8432 (t80) cc_final: 0.8179 (t80) REVERT: B 653 LYS cc_start: 0.7002 (mttt) cc_final: 0.6161 (tmmt) REVERT: D 13 VAL cc_start: 0.7630 (m) cc_final: 0.7298 (p) outliers start: 31 outliers final: 22 residues processed: 207 average time/residue: 0.1944 time to fit residues: 62.8601 Evaluate side-chains 196 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 3 VAL 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: 8.9990 chunk 56 optimal weight: 50.0000 chunk 36 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 30.0000 chunk 92 optimal weight: 0.8980 chunk 17 optimal weight: 60.0000 chunk 146 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 chunk 179 optimal weight: 7.9990 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 12858 Z= 0.649 Angle : 0.836 8.918 17606 Z= 0.435 Chirality : 0.052 0.257 2156 Planarity : 0.005 0.052 2300 Dihedral : 6.435 58.648 2114 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.94 % Favored : 92.95 % Rotamer: Outliers : 4.44 % Allowed : 24.15 % Favored : 71.41 % 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: -0.38 (0.20), residues: 1930 helix: 1.34 (0.20), residues: 676 sheet: -0.37 (0.25), residues: 418 loop : -1.53 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 92 HIS 0.005 0.001 HIS A 583 PHE 0.031 0.003 PHE C 79 TYR 0.028 0.003 TYR B 645 ARG 0.004 0.001 ARG B 465 *********************** 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 206 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 TRP cc_start: 0.7888 (t-100) cc_final: 0.7419 (t-100) REVERT: A 471 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 483 MET cc_start: 0.7484 (mtp) cc_final: 0.7250 (mtp) REVERT: A 653 LYS cc_start: 0.7126 (mttt) cc_final: 0.6149 (tmmt) REVERT: B 451 GLU cc_start: 0.7794 (pt0) cc_final: 0.7529 (pt0) REVERT: B 653 LYS cc_start: 0.7384 (mttt) cc_final: 0.6444 (tmmt) outliers start: 39 outliers final: 31 residues processed: 196 average time/residue: 0.1916 time to fit residues: 59.1080 Evaluate side-chains 195 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 42 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 75 optimal weight: 50.0000 chunk 136 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 569 GLN B 424 GLN B 437 GLN B 569 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12858 Z= 0.181 Angle : 0.619 9.714 17606 Z= 0.321 Chirality : 0.044 0.194 2156 Planarity : 0.004 0.053 2300 Dihedral : 5.704 58.676 2114 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.35 % Favored : 95.54 % Rotamer: Outliers : 3.76 % Allowed : 24.49 % Favored : 71.75 % 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: 0.28 (0.20), residues: 1930 helix: 1.89 (0.20), residues: 686 sheet: -0.16 (0.26), residues: 400 loop : -1.08 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 35 HIS 0.002 0.001 HIS A 583 PHE 0.016 0.002 PHE A 545 TYR 0.025 0.002 TYR A 645 ARG 0.004 0.001 ARG A 482 *********************** 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 201 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 TRP cc_start: 0.7890 (t-100) cc_final: 0.7483 (t-100) REVERT: A 482 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7486 (mmt180) REVERT: B 451 GLU cc_start: 0.7801 (pt0) cc_final: 0.7504 (pt0) REVERT: B 492 ILE cc_start: 0.8491 (pt) cc_final: 0.8219 (pt) REVERT: B 511 PHE cc_start: 0.8457 (t80) cc_final: 0.8200 (t80) REVERT: B 653 LYS cc_start: 0.7150 (mttt) cc_final: 0.6264 (tmmt) REVERT: F 70 ASP cc_start: 0.7816 (p0) cc_final: 0.7581 (p0) outliers start: 33 outliers final: 24 residues processed: 193 average time/residue: 0.1867 time to fit residues: 56.8538 Evaluate side-chains 188 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 65 THR 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: 5.9990 chunk 128 optimal weight: 0.1980 chunk 193 optimal weight: 50.0000 chunk 177 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12858 Z= 0.338 Angle : 0.667 11.012 17606 Z= 0.348 Chirality : 0.046 0.302 2156 Planarity : 0.004 0.051 2300 Dihedral : 5.787 58.783 2114 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.94 % Rotamer: Outliers : 2.96 % Allowed : 24.94 % Favored : 72.10 % 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: 0.22 (0.20), residues: 1930 helix: 1.85 (0.20), residues: 688 sheet: -0.22 (0.26), residues: 404 loop : -1.13 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 48 HIS 0.002 0.001 HIS A 583 PHE 0.018 0.002 PHE E 79 TYR 0.025 0.002 TYR A 645 ARG 0.005 0.001 ARG B 482 ********************** 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 196 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 TRP cc_start: 0.7903 (t-100) cc_final: 0.7462 (t-100) REVERT: A 482 ARG cc_start: 0.8248 (mmt-90) cc_final: 0.7825 (mmt180) REVERT: B 451 GLU cc_start: 0.7879 (pt0) cc_final: 0.7615 (pt0) REVERT: B 511 PHE cc_start: 0.8584 (t80) cc_final: 0.8337 (t80) REVERT: B 653 LYS cc_start: 0.7364 (mttt) cc_final: 0.6436 (tmmt) REVERT: F 70 ASP cc_start: 0.7925 (p0) cc_final: 0.7653 (p0) outliers start: 26 outliers final: 25 residues processed: 189 average time/residue: 0.1862 time to fit residues: 55.8373 Evaluate side-chains 193 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 0.2980 chunk 22 optimal weight: 50.0000 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 19 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 569 GLN B 437 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.140555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106928 restraints weight = 25801.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108459 restraints weight = 16705.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109360 restraints weight = 12674.018| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12858 Z= 0.162 Angle : 0.610 9.800 17606 Z= 0.316 Chirality : 0.044 0.262 2156 Planarity : 0.004 0.052 2300 Dihedral : 5.513 59.652 2114 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.80 % Rotamer: Outliers : 2.51 % Allowed : 25.63 % Favored : 71.87 % 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: 0.51 (0.20), residues: 1930 helix: 2.08 (0.21), residues: 686 sheet: -0.03 (0.27), residues: 398 loop : -0.94 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 35 HIS 0.002 0.001 HIS A 583 PHE 0.016 0.002 PHE B 373 TYR 0.033 0.002 TYR B 645 ARG 0.005 0.000 ARG B 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.94 seconds wall clock time: 43 minutes 17.34 seconds (2597.34 seconds total)