Starting phenix.real_space_refine on Wed Jul 30 19:07:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5nj3_3654/07_2025/5nj3_3654.cif Found real_map, /net/cci-nas-00/data/ceres_data/5nj3_3654/07_2025/5nj3_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/cci-nas-00/data/ceres_data/5nj3_3654/07_2025/5nj3_3654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5nj3_3654/07_2025/5nj3_3654.map" model { file = "/net/cci-nas-00/data/ceres_data/5nj3_3654/07_2025/5nj3_3654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5nj3_3654/07_2025/5nj3_3654.cif" } 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. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.77, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 2.95 Conformation dependent library (CDL) restraints added in 1.8 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: 1.96 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: 4.85 Time building geometry restraints manager: 3.53 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: 0.00 - 2.50: 16828 2.50 - 5.00: 648 5.00 - 7.49: 105 7.49 - 9.99: 19 9.99 - 12.49: 6 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 3.040 nonbonded pdb=" O ARG A 575 " pdb=" OG1 THR A 579 " model vdw 2.184 3.040 nonbonded pdb=" O VAL A 508 " pdb=" OG1 THR A 512 " model vdw 2.264 3.040 nonbonded pdb=" O VAL B 508 " pdb=" OG1 THR B 512 " model vdw 2.264 3.040 nonbonded pdb=" O CYS A 438 " pdb=" OG SER A 441 " model vdw 2.273 3.040 ... (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 Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.600 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- 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 12869 Z= 0.496 Angle : 1.181 13.153 17632 Z= 0.638 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01234 ( 2) link_NAG-ASN : angle 9.49000 ( 6) link_BETA1-4 : bond 0.00456 ( 2) link_BETA1-4 : angle 4.37014 ( 6) hydrogen bonds : bond 0.13336 ( 726) hydrogen bonds : angle 10.71992 ( 2082) SS BOND : bond 0.01072 ( 7) SS BOND : angle 1.68298 ( 14) covalent geometry : bond 0.01148 (12858) covalent geometry : angle 1.16470 (17606) *********************** 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 to be fit. rotamer outliers: 6 poor density : 279 time to evaluate : 1.345 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: 0.2504 time to fit residues: 100.7741 Evaluate side-chains 184 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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: 0.8980 chunk 147 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 50.0000 chunk 152 optimal weight: 50.0000 chunk 58 optimal weight: 40.0000 chunk 92 optimal weight: 0.0470 chunk 113 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 overall best weight: 2.3482 ------------------------------------------------------------------------------- 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 A 557 ASN B 376 GLN B 424 GLN C 40 GLN C 82 GLN D 38 GLN E 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.142703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116800 restraints weight = 25867.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.114898 restraints weight = 32021.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116318 restraints weight = 28310.074| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12869 Z= 0.224 Angle : 0.750 9.616 17632 Z= 0.387 Chirality : 0.047 0.247 2156 Planarity : 0.005 0.063 2300 Dihedral : 6.895 64.146 2115 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 2.73 % Allowed : 12.41 % Favored : 84.85 % 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: -1.75 (0.18), residues: 1930 helix: -0.56 (0.18), residues: 656 sheet: -0.77 (0.23), residues: 452 loop : -1.79 (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 B 375 PHE 0.025 0.002 PHE D 62 TYR 0.031 0.002 TYR A 645 ARG 0.005 0.001 ARG D 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 2) link_NAG-ASN : angle 5.64612 ( 6) link_BETA1-4 : bond 0.00403 ( 2) link_BETA1-4 : angle 2.33397 ( 6) hydrogen bonds : bond 0.03927 ( 726) hydrogen bonds : angle 6.12914 ( 2082) SS BOND : bond 0.00532 ( 7) SS BOND : angle 1.98983 ( 14) covalent geometry : bond 0.00509 (12858) covalent geometry : angle 0.73954 (17606) *********************** 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 242 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 1.306 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: 0.8633 (mmp80) cc_final: 0.7979 (mmt180) REVERT: A 518 TYR cc_start: 0.7869 (m-80) cc_final: 0.7564 (m-80) REVERT: B 477 ASP cc_start: 0.7828 (t0) cc_final: 0.7383 (m-30) REVERT: B 479 LEU cc_start: 0.8681 (mt) cc_final: 0.8393 (tp) REVERT: C 103 LYS cc_start: 0.8790 (tttt) cc_final: 0.8503 (tttp) REVERT: D 81 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: D 82 ASP cc_start: 0.8166 (m-30) cc_final: 0.7964 (m-30) REVERT: F 13 VAL cc_start: 0.7957 (m) cc_final: 0.7583 (p) REVERT: F 36 TYR cc_start: 0.8885 (m-80) cc_final: 0.8358 (m-80) REVERT: F 82 ASP cc_start: 0.8402 (m-30) cc_final: 0.8171 (m-30) outliers start: 24 outliers final: 10 residues processed: 226 average time/residue: 0.2197 time to fit residues: 76.8542 Evaluate side-chains 188 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 491 CYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 106 ILE 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 130 optimal weight: 2.9990 chunk 7 optimal weight: 50.0000 chunk 169 optimal weight: 0.3980 chunk 138 optimal weight: 5.9990 chunk 59 optimal weight: 30.0000 chunk 181 optimal weight: 1.9990 chunk 18 optimal weight: 50.0000 chunk 4 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN B 557 ASN D 38 GLN E 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.142044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115429 restraints weight = 26181.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.112497 restraints weight = 32036.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113814 restraints weight = 29967.762| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12869 Z= 0.190 Angle : 0.661 8.591 17632 Z= 0.343 Chirality : 0.045 0.237 2156 Planarity : 0.004 0.055 2300 Dihedral : 6.234 59.428 2114 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 2.85 % Allowed : 16.74 % Favored : 80.41 % 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: -0.79 (0.19), residues: 1930 helix: 0.64 (0.20), residues: 658 sheet: -0.39 (0.24), residues: 448 loop : -1.55 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 624 HIS 0.002 0.001 HIS A 583 PHE 0.018 0.002 PHE B 432 TYR 0.028 0.002 TYR A 645 ARG 0.004 0.001 ARG C 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 2) link_NAG-ASN : angle 5.08149 ( 6) link_BETA1-4 : bond 0.00096 ( 2) link_BETA1-4 : angle 2.11115 ( 6) hydrogen bonds : bond 0.03403 ( 726) hydrogen bonds : angle 5.31970 ( 2082) SS BOND : bond 0.00885 ( 7) SS BOND : angle 1.88988 ( 14) covalent geometry : bond 0.00434 (12858) covalent geometry : angle 0.65102 (17606) *********************** 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 218 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.337 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 482 ARG cc_start: 0.8648 (mmp80) cc_final: 0.8028 (mmt180) REVERT: B 479 LEU cc_start: 0.8773 (mt) cc_final: 0.8305 (tp) REVERT: B 482 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7761 (mmt180) REVERT: C 103 LYS cc_start: 0.8872 (tttt) cc_final: 0.8579 (tttp) REVERT: D 36 TYR cc_start: 0.8708 (m-80) cc_final: 0.8290 (m-80) REVERT: D 82 ASP cc_start: 0.8192 (m-30) cc_final: 0.7984 (m-30) REVERT: F 13 VAL cc_start: 0.8088 (m) cc_final: 0.7677 (p) REVERT: F 82 ASP cc_start: 0.8373 (m-30) cc_final: 0.8143 (m-30) outliers start: 25 outliers final: 14 residues processed: 208 average time/residue: 0.2083 time to fit residues: 67.1885 Evaluate side-chains 193 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 635 CYS 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 59 THR 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 132 optimal weight: 0.0570 chunk 75 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 168 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 50.0000 chunk 129 optimal weight: 40.0000 chunk 85 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.139183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113128 restraints weight = 26062.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110828 restraints weight = 33504.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111862 restraints weight = 31951.978| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 12869 Z= 0.245 Angle : 0.694 9.538 17632 Z= 0.359 Chirality : 0.047 0.249 2156 Planarity : 0.005 0.056 2300 Dihedral : 6.036 54.085 2114 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 3.87 % Allowed : 18.11 % Favored : 78.02 % 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: -0.36 (0.20), residues: 1930 helix: 1.14 (0.20), residues: 678 sheet: -0.26 (0.24), residues: 444 loop : -1.41 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 624 HIS 0.002 0.001 HIS A 583 PHE 0.020 0.002 PHE C 79 TYR 0.029 0.002 TYR A 645 ARG 0.007 0.001 ARG C 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 4.94012 ( 6) link_BETA1-4 : bond 0.00085 ( 2) link_BETA1-4 : angle 1.89531 ( 6) hydrogen bonds : bond 0.03587 ( 726) hydrogen bonds : angle 5.01936 ( 2082) SS BOND : bond 0.00857 ( 7) SS BOND : angle 1.61440 ( 14) covalent geometry : bond 0.00569 (12858) covalent geometry : angle 0.68613 (17606) *********************** 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 220 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 1.853 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 451 GLU cc_start: 0.7524 (pt0) cc_final: 0.7272 (pt0) REVERT: A 482 ARG cc_start: 0.8663 (mmp80) cc_final: 0.8076 (mmt180) REVERT: A 492 ILE cc_start: 0.8435 (pt) cc_final: 0.8147 (pt) REVERT: B 479 LEU cc_start: 0.8699 (mt) cc_final: 0.8331 (tp) REVERT: B 482 ARG cc_start: 0.8275 (mmm160) cc_final: 0.7792 (mmt180) REVERT: B 483 MET cc_start: 0.7534 (mtp) cc_final: 0.7296 (mtp) REVERT: B 511 PHE cc_start: 0.8680 (t80) cc_final: 0.8367 (t80) REVERT: C 5 GLN cc_start: 0.7850 (tp40) cc_final: 0.7569 (tp40) REVERT: C 103 LYS cc_start: 0.8953 (tttt) cc_final: 0.8659 (tttp) outliers start: 34 outliers final: 19 residues processed: 206 average time/residue: 0.2348 time to fit residues: 76.3273 Evaluate side-chains 186 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 487 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 11 LEU 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 104 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 129 optimal weight: 30.0000 chunk 79 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 96 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 73 optimal weight: 50.0000 chunk 188 optimal weight: 50.0000 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 617 GLN B 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.136350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103610 restraints weight = 26695.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102438 restraints weight = 19668.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102423 restraints weight = 17923.338| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 12869 Z= 0.363 Angle : 0.792 9.831 17632 Z= 0.412 Chirality : 0.050 0.256 2156 Planarity : 0.005 0.054 2300 Dihedral : 6.342 53.087 2114 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 5.13 % Allowed : 20.39 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.05 % 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: -0.32 (0.20), residues: 1930 helix: 1.31 (0.20), residues: 662 sheet: -0.38 (0.25), residues: 418 loop : -1.35 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 109 HIS 0.004 0.001 HIS A 583 PHE 0.027 0.003 PHE E 79 TYR 0.032 0.003 TYR B 645 ARG 0.004 0.001 ARG B 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 2) link_NAG-ASN : angle 5.39208 ( 6) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 1.92521 ( 6) hydrogen bonds : bond 0.03914 ( 726) hydrogen bonds : angle 5.22352 ( 2082) SS BOND : bond 0.01112 ( 7) SS BOND : angle 2.39809 ( 14) covalent geometry : bond 0.00835 (12858) covalent geometry : angle 0.78276 (17606) *********************** 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 217 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ILE cc_start: 0.8563 (pt) cc_final: 0.8309 (pt) REVERT: B 479 LEU cc_start: 0.8854 (mt) cc_final: 0.8486 (tp) REVERT: B 653 LYS cc_start: 0.7067 (mttt) cc_final: 0.6259 (tmmt) REVERT: C 96 CYS cc_start: 0.6396 (OUTLIER) cc_final: 0.6121 (p) REVERT: C 103 LYS cc_start: 0.9039 (tttt) cc_final: 0.8773 (tttp) outliers start: 45 outliers final: 32 residues processed: 204 average time/residue: 0.2388 time to fit residues: 78.0324 Evaluate side-chains 196 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 419 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 424 GLN 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 11 LEU 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 96 CYS 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 18 LEU Chi-restraints excluded: chain E residue 22 CYS 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 Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 152 optimal weight: 50.0000 chunk 169 optimal weight: 0.0020 chunk 193 optimal weight: 50.0000 chunk 20 optimal weight: 50.0000 chunk 83 optimal weight: 0.0370 chunk 21 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8072 ------------------------------------------------------------------------------- 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 D 31 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.141087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115728 restraints weight = 26452.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113531 restraints weight = 36352.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115053 restraints weight = 32567.112| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12869 Z= 0.123 Angle : 0.630 9.568 17632 Z= 0.326 Chirality : 0.044 0.265 2156 Planarity : 0.004 0.057 2300 Dihedral : 5.761 55.945 2114 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 2.73 % Allowed : 23.01 % Favored : 74.26 % 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: 0.17 (0.20), residues: 1930 helix: 1.76 (0.20), residues: 672 sheet: -0.12 (0.25), residues: 426 loop : -1.13 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 35 HIS 0.001 0.001 HIS A 583 PHE 0.018 0.002 PHE B 545 TYR 0.025 0.002 TYR B 645 ARG 0.004 0.001 ARG C 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 2) link_NAG-ASN : angle 4.53484 ( 6) link_BETA1-4 : bond 0.00232 ( 2) link_BETA1-4 : angle 1.74682 ( 6) hydrogen bonds : bond 0.02993 ( 726) hydrogen bonds : angle 4.66630 ( 2082) SS BOND : bond 0.00852 ( 7) SS BOND : angle 2.93466 ( 14) covalent geometry : bond 0.00275 (12858) covalent geometry : angle 0.61849 (17606) *********************** 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 210 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.469 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 492 ILE cc_start: 0.8602 (pt) cc_final: 0.8355 (pt) REVERT: A 541 MET cc_start: 0.7581 (mmm) cc_final: 0.7364 (tpp) REVERT: B 479 LEU cc_start: 0.8812 (mt) cc_final: 0.8608 (tp) REVERT: B 482 ARG cc_start: 0.8263 (mmt-90) cc_final: 0.7868 (mmt180) REVERT: B 511 PHE cc_start: 0.8536 (t80) cc_final: 0.8270 (t80) REVERT: B 534 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7822 (p) REVERT: C 103 LYS cc_start: 0.9082 (tttt) cc_final: 0.8746 (tttp) REVERT: D 13 VAL cc_start: 0.7739 (m) cc_final: 0.7391 (p) outliers start: 24 outliers final: 17 residues processed: 202 average time/residue: 0.1996 time to fit residues: 63.7695 Evaluate side-chains 189 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 441 SER 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 423 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 LEU 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 E residue 82 GLN Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 30 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 165 optimal weight: 40.0000 chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.134203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098881 restraints weight = 26919.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100064 restraints weight = 20534.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100396 restraints weight = 14841.263| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.099 12869 Z= 0.460 Angle : 0.876 9.519 17632 Z= 0.454 Chirality : 0.053 0.251 2156 Planarity : 0.006 0.052 2300 Dihedral : 6.573 52.484 2114 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.37 % Rotamer: Outliers : 5.58 % Allowed : 21.98 % Favored : 72.44 % 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: -0.46 (0.20), residues: 1930 helix: 1.11 (0.20), residues: 692 sheet: -0.42 (0.25), residues: 398 loop : -1.44 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 92 HIS 0.005 0.001 HIS B 583 PHE 0.032 0.003 PHE E 79 TYR 0.028 0.003 TYR B 645 ARG 0.005 0.001 ARG B 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 2) link_NAG-ASN : angle 5.65005 ( 6) link_BETA1-4 : bond 0.00118 ( 2) link_BETA1-4 : angle 1.94780 ( 6) hydrogen bonds : bond 0.04317 ( 726) hydrogen bonds : angle 5.43578 ( 2082) SS BOND : bond 0.01248 ( 7) SS BOND : angle 3.77837 ( 14) covalent geometry : bond 0.01063 (12858) covalent geometry : angle 0.86360 (17606) *********************** 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 215 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 479 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8676 (tp) REVERT: A 653 LYS cc_start: 0.7114 (mttt) cc_final: 0.6106 (tmmt) REVERT: B 458 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7306 (tt0) REVERT: B 479 LEU cc_start: 0.8896 (mt) cc_final: 0.8480 (tp) REVERT: B 653 LYS cc_start: 0.7399 (mttt) cc_final: 0.6463 (tmmt) REVERT: C 96 CYS cc_start: 0.6411 (OUTLIER) cc_final: 0.6121 (p) REVERT: C 103 LYS cc_start: 0.9210 (tttt) cc_final: 0.8955 (tttp) REVERT: D 31 ASN cc_start: 0.8579 (m-40) cc_final: 0.8375 (m110) REVERT: D 36 TYR cc_start: 0.8871 (m-80) cc_final: 0.8417 (m-80) outliers start: 49 outliers final: 29 residues processed: 199 average time/residue: 0.2279 time to fit residues: 71.1996 Evaluate side-chains 197 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 419 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 523 MET 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 484 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 11 LEU 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 96 CYS Chi-restraints excluded: chain D residue 3 VAL 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 F residue 3 VAL Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 172 optimal weight: 20.0000 chunk 152 optimal weight: 40.0000 chunk 175 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 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 437 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.139417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107067 restraints weight = 26284.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.107383 restraints weight = 16748.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107576 restraints weight = 13411.574| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12869 Z= 0.129 Angle : 0.640 9.208 17632 Z= 0.331 Chirality : 0.044 0.219 2156 Planarity : 0.004 0.051 2300 Dihedral : 5.743 56.563 2114 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 2.73 % Allowed : 25.63 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.05 % 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: 0.15 (0.20), residues: 1930 helix: 1.72 (0.20), residues: 690 sheet: -0.23 (0.25), residues: 424 loop : -1.13 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 35 HIS 0.003 0.001 HIS B 583 PHE 0.025 0.002 PHE B 545 TYR 0.026 0.002 TYR B 645 ARG 0.002 0.001 ARG A 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 2) link_NAG-ASN : angle 4.53501 ( 6) link_BETA1-4 : bond 0.00326 ( 2) link_BETA1-4 : angle 1.52623 ( 6) hydrogen bonds : bond 0.03000 ( 726) hydrogen bonds : angle 4.67415 ( 2082) SS BOND : bond 0.00732 ( 7) SS BOND : angle 2.54893 ( 14) covalent geometry : bond 0.00293 (12858) covalent geometry : angle 0.63045 (17606) *********************** 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 197 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.431 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: 0.8578 (mmt-90) cc_final: 0.8180 (mmm-85) REVERT: A 492 ILE cc_start: 0.8592 (pt) cc_final: 0.8342 (pt) REVERT: B 458 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7320 (tt0) REVERT: B 479 LEU cc_start: 0.8887 (mt) cc_final: 0.8493 (tp) REVERT: B 511 PHE cc_start: 0.8605 (t80) cc_final: 0.8288 (t80) REVERT: B 534 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7815 (p) REVERT: B 653 LYS cc_start: 0.7085 (mttt) cc_final: 0.6326 (tmmt) REVERT: C 103 LYS cc_start: 0.9123 (tttt) cc_final: 0.8750 (ttmm) REVERT: D 31 ASN cc_start: 0.8491 (m-40) cc_final: 0.8275 (m110) outliers start: 24 outliers final: 15 residues processed: 188 average time/residue: 0.2024 time to fit residues: 59.0442 Evaluate side-chains 183 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 441 SER 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 405 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 534 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 173 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 19 optimal weight: 40.0000 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 143 optimal weight: 30.0000 chunk 130 optimal weight: 50.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.131655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097630 restraints weight = 27013.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097873 restraints weight = 18866.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098111 restraints weight = 15664.994| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.118 12869 Z= 0.544 Angle : 0.957 10.389 17632 Z= 0.496 Chirality : 0.055 0.272 2156 Planarity : 0.006 0.056 2300 Dihedral : 6.680 52.449 2114 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.94 % Favored : 92.95 % Rotamer: Outliers : 4.67 % Allowed : 23.69 % Favored : 71.64 % 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: -0.68 (0.19), residues: 1930 helix: 0.97 (0.20), residues: 690 sheet: -0.67 (0.25), residues: 412 loop : -1.54 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 92 HIS 0.007 0.002 HIS B 583 PHE 0.035 0.003 PHE C 79 TYR 0.028 0.004 TYR C 51 ARG 0.005 0.001 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 2) link_NAG-ASN : angle 5.79817 ( 6) link_BETA1-4 : bond 0.00308 ( 2) link_BETA1-4 : angle 1.84084 ( 6) hydrogen bonds : bond 0.04590 ( 726) hydrogen bonds : angle 5.66550 ( 2082) SS BOND : bond 0.01256 ( 7) SS BOND : angle 3.76702 ( 14) covalent geometry : bond 0.01251 (12858) covalent geometry : angle 0.94548 (17606) *********************** 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 200 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 653 LYS cc_start: 0.7157 (mttt) cc_final: 0.6164 (tmmt) REVERT: B 458 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7306 (tt0) REVERT: B 479 LEU cc_start: 0.8950 (mt) cc_final: 0.8704 (tp) REVERT: B 653 LYS cc_start: 0.7491 (mttt) cc_final: 0.6600 (tmmt) REVERT: C 103 LYS cc_start: 0.9261 (tttt) cc_final: 0.9007 (tttp) REVERT: D 36 TYR cc_start: 0.8951 (m-80) cc_final: 0.8528 (m-80) REVERT: D 79 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8356 (tm-30) outliers start: 41 outliers final: 31 residues processed: 185 average time/residue: 0.2306 time to fit residues: 67.1531 Evaluate side-chains 187 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 419 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 491 CYS 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 423 ILE Chi-restraints excluded: chain B residue 450 VAL 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 B residue 569 GLN 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 79 GLN 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 F residue 3 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 68 optimal weight: 40.0000 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 50.0000 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 0.7980 chunk 80 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 6 optimal weight: 30.0000 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 437 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN D 31 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.138940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.106439 restraints weight = 26241.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105826 restraints weight = 18159.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106488 restraints weight = 15012.015| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12869 Z= 0.130 Angle : 0.665 11.529 17632 Z= 0.344 Chirality : 0.045 0.251 2156 Planarity : 0.004 0.050 2300 Dihedral : 5.813 57.419 2114 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 2.28 % Allowed : 26.42 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.05 % 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: 0.13 (0.20), residues: 1930 helix: 1.75 (0.20), residues: 688 sheet: -0.29 (0.26), residues: 402 loop : -1.13 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 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 C 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 2) link_NAG-ASN : angle 4.58962 ( 6) link_BETA1-4 : bond 0.00358 ( 2) link_BETA1-4 : angle 1.61573 ( 6) hydrogen bonds : bond 0.03073 ( 726) hydrogen bonds : angle 4.74652 ( 2082) SS BOND : bond 0.00773 ( 7) SS BOND : angle 2.35472 ( 14) covalent geometry : bond 0.00292 (12858) covalent geometry : angle 0.65597 (17606) ********************** 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 to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.419 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: 0.8493 (mmt-90) cc_final: 0.8146 (mmm-85) REVERT: A 492 ILE cc_start: 0.8724 (pt) cc_final: 0.8459 (pt) REVERT: A 540 LEU cc_start: 0.9137 (tp) cc_final: 0.8892 (tt) REVERT: A 653 LYS cc_start: 0.7027 (mttt) cc_final: 0.6071 (tmmt) REVERT: B 458 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7314 (tt0) REVERT: B 479 LEU cc_start: 0.8918 (mt) cc_final: 0.8467 (tp) REVERT: B 511 PHE cc_start: 0.8804 (t80) cc_final: 0.8480 (t80) REVERT: B 548 MET cc_start: 0.8620 (ttm) cc_final: 0.8248 (mtm) REVERT: B 653 LYS cc_start: 0.7200 (mttt) cc_final: 0.6408 (tmmt) REVERT: C 103 LYS cc_start: 0.9161 (tttt) cc_final: 0.8757 (ttmm) REVERT: D 70 ASP cc_start: 0.7818 (p0) cc_final: 0.7598 (p0) REVERT: F 70 ASP cc_start: 0.7964 (p0) cc_final: 0.7730 (p0) outliers start: 20 outliers final: 16 residues processed: 190 average time/residue: 0.2081 time to fit residues: 62.1280 Evaluate side-chains 185 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 441 SER 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 489 PHE Chi-restraints excluded: chain B residue 569 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 104 optimal weight: 0.6980 chunk 17 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN F 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.139062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106237 restraints weight = 26119.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.106387 restraints weight = 17119.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106968 restraints weight = 13262.036| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12869 Z= 0.131 Angle : 0.635 7.689 17632 Z= 0.331 Chirality : 0.045 0.265 2156 Planarity : 0.004 0.047 2300 Dihedral : 5.402 52.476 2114 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.34 % Rotamer: Outliers : 2.16 % Allowed : 26.31 % Favored : 71.53 % 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: 0.34 (0.20), residues: 1930 helix: 1.94 (0.20), residues: 692 sheet: -0.18 (0.25), residues: 428 loop : -1.05 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 35 HIS 0.001 0.000 HIS A 583 PHE 0.013 0.001 PHE B 432 TYR 0.024 0.002 TYR A 645 ARG 0.004 0.001 ARG D 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 2) link_NAG-ASN : angle 4.49352 ( 6) link_BETA1-4 : bond 0.00100 ( 2) link_BETA1-4 : angle 1.86882 ( 6) hydrogen bonds : bond 0.02951 ( 726) hydrogen bonds : angle 4.50622 ( 2082) SS BOND : bond 0.00802 ( 7) SS BOND : angle 1.99830 ( 14) covalent geometry : bond 0.00300 (12858) covalent geometry : angle 0.62671 (17606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3931.21 seconds wall clock time: 71 minutes 11.89 seconds (4271.89 seconds total)