Starting phenix.real_space_refine on Sat Sep 12 00:53:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5nj3_3654/09_2026/5nj3_3654.cif Found real_map, /net/cci-nas-00/data/ceres_data/5nj3_3654/09_2026/5nj3_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 { model { file = "/net/cci-nas-00/data/ceres_data/5nj3_3654/09_2026/5nj3_3654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5nj3_3654/09_2026/5nj3_3654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5nj3_3654/09_2026/5nj3_3654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5nj3_3654/09_2026/5nj3_3654.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5nj3_3654/09_2026/5nj3_3654.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5nj3_3654/09_2026/5nj3_3654.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'GLU:plan': 15, 'PHE:plan': 13, 'HIS:plan': 6, 'ASN:plan1': 16, 'ASP:plan': 13, 'ARG:plan': 13, 'TYR:plan': 7, 'GLN:plan1': 8} 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: {'GLU:plan': 15, 'PHE:plan': 13, 'HIS:plan': 6, 'ASN:plan1': 16, 'ASP:plan': 13, 'ARG:plan': 13, 'TYR:plan': 7, 'GLN:plan1': 8} 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: {'TYR:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 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: {'ARG:plan': 4, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 7, 'TYR:plan': 4, 'TRP:plan': 2, 'HIS:plan': 2} 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: {'TYR:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 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: {'ARG:plan': 4, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 7, 'TYR:plan': 4, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 174 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.99, per 1000 atoms: 0.24 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: 1.08 Conformation dependent library (CDL) restraints added in 677.4 milliseconds 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: 0.48 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: 2.49 Time building geometry restraints manager: 1.44 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: 6953 14.45 - 28.89: 367 28.89 - 43.34: 79 43.34 - 57.79: 23 57.79 - 72.23: 5 Dihedral angle restraints: 7427 sinusoidal: 1815 harmonic: 5612 Sorted by residual: dihedral pdb=" CA ASN A 601 " pdb=" C ASN A 601 " pdb=" N PRO A 602 " pdb=" CA PRO A 602 " ideal model delta harmonic sigma weight residual -180.00 -124.15 -55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ASN B 601 " pdb=" C ASN B 601 " pdb=" N PRO B 602 " pdb=" CA PRO B 602 " ideal model delta harmonic sigma weight residual -180.00 -124.17 -55.83 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA PRO A 602 " pdb=" C PRO A 602 " pdb=" N CYS A 603 " pdb=" CA CYS A 603 " ideal model delta harmonic sigma weight residual 180.00 137.89 42.11 0 5.00e+00 4.00e-02 7.09e+01 ... (remaining 7424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1892 0.094 - 0.188: 250 0.188 - 0.282: 6 0.282 - 0.376: 4 0.376 - 0.470: 4 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 596 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 596 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB ILE A 573 " pdb=" CA ILE A 573 " pdb=" CG1 ILE A 573 " pdb=" CG2 ILE A 573 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 2153 not shown) Planarity restraints: 2302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 601 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 602 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 601 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO B 602 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 602 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 602 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 576 " 0.019 2.00e-02 2.50e+03 1.82e-02 6.62e+00 pdb=" CG TYR B 576 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 576 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 576 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 576 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 576 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 576 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 576 " 0.001 2.00e-02 2.50e+03 ... (remaining 2299 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1125 2.73 - 3.27: 12461 3.27 - 3.81: 20154 3.81 - 4.36: 22516 4.36 - 4.90: 39080 Nonbonded interactions: 95336 Sorted by model distance: nonbonded pdb=" O ARG B 575 " pdb=" OG1 THR B 579 " model vdw 2.183 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.550 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 10.488 70.998 3790 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 0.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.002 ARG B 426 TYR 0.044 0.005 TYR B 576 PHE 0.041 0.004 PHE D 98 TRP 0.037 0.004 TRP C 109 HIS 0.004 0.002 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.01148 / 0.50 (12858) covalent geometry : angle 1.16470 / 0.63 (17606) SS BOND : bond 0.01072 / 0.58 ( 7) SS BOND : angle 1.68298 / 0.89 ( 14) hydrogen bonds : bond 0.13336 / 10.09 ( 726) hydrogen bonds : angle 10.71992 / 7.82 ( 2082) link_BETA1-4 : bond 0.00456 / 0.24 ( 2) link_BETA1-4 : angle 4.37014 / 2.36 ( 6) link_NAG-ASN : bond 0.01234 / 0.65 ( 2) link_NAG-ASN : angle 9.49000 / 4.88 ( 6) *********************** 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 : 0.478 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: 0.8765 (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: 0.8490 (tttt) cc_final: 0.8264 (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: 0.1148 time to fit residues: 46.8808 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 : 0.463 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 40.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4045 r_free = 0.4045 target = 0.144378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.118076 restraints weight = 25845.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.115869 restraints weight = 30284.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117119 restraints weight = 26490.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117007 restraints weight = 16486.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117151 restraints weight = 17482.671| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2177 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= 0.168 Angle : 0.714 9.703 17632 Z= 0.368 Chirality : 0.045 0.232 2156 Planarity : 0.005 0.057 2300 Dihedral : 6.180 65.614 2031 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 2.39 % Allowed : 12.53 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.18), residues: 1930 helix: -0.49 (0.18), residues: 652 sheet: -0.73 (0.24), residues: 448 loop : -1.77 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 18 TYR 0.031 0.002 TYR A 645 PHE 0.023 0.002 PHE D 62 TRP 0.018 0.002 TRP A 624 HIS 0.003 0.001 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (12858) covalent geometry : angle 0.70409 / 0.37 (17606) SS BOND : bond 0.00489 / 0.30 ( 7) SS BOND : angle 1.77769 / 0.89 ( 14) hydrogen bonds : bond 0.03684 / 2.80 ( 726) hydrogen bonds : angle 6.09147 / 4.43 ( 2082) link_BETA1-4 : bond 0.00088 / 0.04 ( 2) link_BETA1-4 : angle 1.70345 / 0.81 ( 6) link_NAG-ASN : bond 0.00225 / 0.11 ( 2) link_NAG-ASN : angle 5.59890 / 3.06 ( 6) *********************** 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 243 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.481 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: B 373 PHE cc_start: 0.6340 (t80) cc_final: 0.6118 (t80) REVERT: B 477 ASP cc_start: 0.7779 (t0) cc_final: 0.7278 (m-30) REVERT: B 479 LEU cc_start: 0.8678 (mt) cc_final: 0.8470 (tp) REVERT: C 103 LYS cc_start: 0.8685 (tttt) cc_final: 0.8438 (tttp) REVERT: D 81 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7350 (pt0) REVERT: D 82 ASP cc_start: 0.8159 (m-30) cc_final: 0.7952 (m-30) REVERT: E 21 THR cc_start: 0.8202 (m) cc_final: 0.7962 (p) REVERT: E 105 THR cc_start: 0.8872 (p) cc_final: 0.8608 (t) REVERT: F 13 VAL cc_start: 0.7954 (m) cc_final: 0.7617 (p) REVERT: F 36 TYR cc_start: 0.8871 (m-80) cc_final: 0.8330 (m-80) REVERT: F 82 ASP cc_start: 0.8363 (m-30) cc_final: 0.8160 (m-30) outliers start: 21 outliers final: 9 residues processed: 228 average time/residue: 0.0900 time to fit residues: 31.9111 Evaluate side-chains 202 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 30 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 131 optimal weight: 40.0000 chunk 119 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 40.0000 chunk 170 optimal weight: 40.0000 chunk 29 optimal weight: 0.0040 chunk 149 optimal weight: 20.0000 chunk 186 optimal weight: 50.0000 chunk 180 optimal weight: 4.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3997 r_free = 0.3997 target = 0.141507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105370 restraints weight = 26591.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106901 restraints weight = 16981.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107870 restraints weight = 12899.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108432 restraints weight = 10907.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108720 restraints weight = 9886.509| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12869 Z= 0.222 Angle : 0.692 8.969 17632 Z= 0.358 Chirality : 0.046 0.252 2156 Planarity : 0.004 0.052 2300 Dihedral : 5.750 59.279 2030 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 3.53 % Allowed : 17.08 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 1930 helix: 0.57 (0.19), residues: 664 sheet: -0.34 (0.24), residues: 452 loop : -1.57 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 39 TYR 0.028 0.002 TYR A 645 PHE 0.021 0.002 PHE C 79 TRP 0.013 0.002 TRP C 109 HIS 0.002 0.001 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (12858) covalent geometry : angle 0.68401 / 0.36 (17606) SS BOND : bond 0.00893 / 0.46 ( 7) SS BOND : angle 1.64421 / 0.81 ( 14) hydrogen bonds : bond 0.03549 / 2.68 ( 726) hydrogen bonds : angle 5.32761 / 3.90 ( 2082) link_BETA1-4 : bond 0.00094 / 0.05 ( 2) link_BETA1-4 : angle 1.52606 / 0.77 ( 6) link_NAG-ASN : bond 0.00097 / 0.05 ( 2) link_NAG-ASN : angle 5.02208 / 2.68 ( 6) *********************** 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 223 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.486 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: 0.7955 (mmt180) REVERT: A 523 MET cc_start: 0.8921 (ttp) cc_final: 0.8674 (tmm) REVERT: A 541 MET cc_start: 0.7621 (mmm) cc_final: 0.7260 (mmm) REVERT: B 479 LEU cc_start: 0.8823 (mt) cc_final: 0.8314 (tp) REVERT: B 482 ARG cc_start: 0.8183 (mmm160) cc_final: 0.7762 (mmt180) REVERT: C 103 LYS cc_start: 0.8924 (tttt) cc_final: 0.8628 (tttp) REVERT: D 36 TYR cc_start: 0.8802 (m-80) cc_final: 0.8397 (m-80) REVERT: D 82 ASP cc_start: 0.8189 (m-30) cc_final: 0.7965 (m-30) REVERT: F 13 VAL cc_start: 0.8014 (m) cc_final: 0.7611 (p) REVERT: F 82 ASP cc_start: 0.8395 (m-30) cc_final: 0.8137 (m-30) outliers start: 31 outliers final: 17 residues processed: 208 average time/residue: 0.0860 time to fit residues: 28.6664 Evaluate side-chains 194 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain B residue 401 VAL 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 79 GLN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 50.0000 chunk 100 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 129 optimal weight: 40.0000 chunk 171 optimal weight: 40.0000 chunk 124 optimal weight: 40.0000 chunk 187 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 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 = 0.3960 r_free = 0.3960 target = 0.139127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104651 restraints weight = 26276.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106993 restraints weight = 17896.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106703 restraints weight = 12338.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106840 restraints weight = 11383.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106874 restraints weight = 11177.330| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 12869 Z= 0.254 Angle : 0.692 9.207 17632 Z= 0.358 Chirality : 0.046 0.248 2156 Planarity : 0.004 0.057 2300 Dihedral : 5.507 54.116 2030 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 3.99 % Allowed : 19.48 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1930 helix: 1.08 (0.20), residues: 680 sheet: -0.26 (0.24), residues: 448 loop : -1.45 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 39 TYR 0.028 0.002 TYR A 645 PHE 0.019 0.002 PHE E 79 TRP 0.012 0.002 TRP B 624 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (12858) covalent geometry : angle 0.68493 / 0.36 (17606) SS BOND : bond 0.01441 / 0.77 ( 7) SS BOND : angle 1.86917 / 1.01 ( 14) hydrogen bonds : bond 0.03531 / 2.66 ( 726) hydrogen bonds : angle 5.03467 / 3.69 ( 2082) link_BETA1-4 : bond 0.00466 / 0.23 ( 2) link_BETA1-4 : angle 1.32298 / 0.67 ( 6) link_NAG-ASN : bond 0.00067 / 0.03 ( 2) link_NAG-ASN : angle 4.66272 / 2.48 ( 6) *********************** 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 218 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.554 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: 0.7462 (pt0) cc_final: 0.7177 (pt0) REVERT: A 482 ARG cc_start: 0.8591 (mmp80) cc_final: 0.7972 (mmt180) REVERT: A 483 MET cc_start: 0.7969 (mtp) cc_final: 0.7675 (mtp) REVERT: A 539 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8642 (mm) REVERT: B 479 LEU cc_start: 0.8703 (mt) cc_final: 0.8382 (tp) REVERT: B 482 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7734 (mmt180) REVERT: B 483 MET cc_start: 0.7526 (mtp) cc_final: 0.7279 (mtp) REVERT: C 5 GLN cc_start: 0.7854 (tp40) cc_final: 0.7608 (tp40) REVERT: C 103 LYS cc_start: 0.8926 (tttt) cc_final: 0.8681 (tttp) REVERT: D 82 ASP cc_start: 0.8121 (m-30) cc_final: 0.7878 (m-30) REVERT: F 82 ASP cc_start: 0.8286 (m-30) cc_final: 0.8038 (m-30) outliers start: 35 outliers final: 21 residues processed: 203 average time/residue: 0.0857 time to fit residues: 27.7363 Evaluate side-chains 190 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 446 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 544 CYS 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 487 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 3 optimal weight: 30.0000 chunk 169 optimal weight: 0.3980 chunk 170 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 150 optimal weight: 50.0000 chunk 156 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.140657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115004 restraints weight = 26344.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.112895 restraints weight = 34399.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113902 restraints weight = 30992.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.113972 restraints weight = 17746.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114280 restraints weight = 17403.717| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12869 Z= 0.168 Angle : 0.625 8.610 17632 Z= 0.323 Chirality : 0.044 0.231 2156 Planarity : 0.004 0.055 2300 Dihedral : 5.107 54.587 2030 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 3.19 % Allowed : 19.93 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1930 helix: 1.54 (0.20), residues: 682 sheet: -0.08 (0.25), residues: 422 loop : -1.26 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 378 TYR 0.028 0.002 TYR A 645 PHE 0.016 0.002 PHE E 79 TRP 0.014 0.001 TRP B 624 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (12858) covalent geometry : angle 0.61894 / 0.32 (17606) SS BOND : bond 0.00913 / 0.49 ( 7) SS BOND : angle 1.40928 / 0.73 ( 14) hydrogen bonds : bond 0.03144 / 2.37 ( 726) hydrogen bonds : angle 4.71123 / 3.45 ( 2082) link_BETA1-4 : bond 0.00140 / 0.07 ( 2) link_BETA1-4 : angle 1.30849 / 0.65 ( 6) link_NAG-ASN : bond 0.00071 / 0.04 ( 2) link_NAG-ASN : angle 4.15136 / 2.26 ( 6) *********************** 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 219 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.367 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: A 451 GLU cc_start: 0.7414 (pt0) cc_final: 0.7135 (pt0) REVERT: A 482 ARG cc_start: 0.8495 (mmp80) cc_final: 0.8163 (mmm-85) REVERT: B 482 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7774 (mmt180) REVERT: B 511 PHE cc_start: 0.8580 (t80) cc_final: 0.8266 (t80) REVERT: C 103 LYS cc_start: 0.8979 (tttt) cc_final: 0.8725 (tttp) REVERT: D 13 VAL cc_start: 0.7648 (m) cc_final: 0.7256 (p) REVERT: D 82 ASP cc_start: 0.8112 (m-30) cc_final: 0.7891 (m-30) outliers start: 28 outliers final: 16 residues processed: 206 average time/residue: 0.0846 time to fit residues: 27.7075 Evaluate side-chains 187 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 440 SER Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 377 LEU 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 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 111 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 148 optimal weight: 40.0000 chunk 78 optimal weight: 50.0000 chunk 105 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 185 optimal weight: 40.0000 chunk 150 optimal weight: 50.0000 chunk 155 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 50.0000 chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 40.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 437 GLN B 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.137135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102325 restraints weight = 26757.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103493 restraints weight = 20278.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103559 restraints weight = 15857.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103864 restraints weight = 14309.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104004 restraints weight = 13705.865| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 12869 Z= 0.329 Angle : 0.755 9.253 17632 Z= 0.390 Chirality : 0.048 0.229 2156 Planarity : 0.005 0.055 2300 Dihedral : 5.424 51.933 2030 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 5.13 % Allowed : 22.67 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1930 helix: 1.50 (0.20), residues: 674 sheet: -0.20 (0.25), residues: 418 loop : -1.23 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 39 TYR 0.029 0.003 TYR B 645 PHE 0.025 0.002 PHE C 79 TRP 0.013 0.002 TRP C 48 HIS 0.004 0.001 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.33 (12858) covalent geometry : angle 0.74842 / 0.39 (17606) SS BOND : bond 0.00975 / 0.57 ( 7) SS BOND : angle 1.67069 / 0.92 ( 14) hydrogen bonds : bond 0.03820 / 2.86 ( 726) hydrogen bonds : angle 5.03704 / 3.70 ( 2082) link_BETA1-4 : bond 0.00092 / 0.04 ( 2) link_BETA1-4 : angle 1.41764 / 0.68 ( 6) link_NAG-ASN : bond 0.00164 / 0.08 ( 2) link_NAG-ASN : angle 4.66156 / 2.43 ( 6) *********************** 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 218 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.502 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 451 GLU cc_start: 0.7686 (pt0) cc_final: 0.7481 (pt0) REVERT: A 482 ARG cc_start: 0.8581 (mmp80) cc_final: 0.8198 (mmm-85) REVERT: B 482 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7844 (mmt180) REVERT: B 653 LYS cc_start: 0.6989 (mttt) cc_final: 0.6181 (tmmt) REVERT: C 96 CYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5880 (p) REVERT: C 103 LYS cc_start: 0.9068 (tttt) cc_final: 0.8819 (tttp) REVERT: D 31 ASN cc_start: 0.8418 (m-40) cc_final: 0.8210 (m110) REVERT: D 82 ASP cc_start: 0.8242 (m-30) cc_final: 0.7988 (m-30) outliers start: 45 outliers final: 31 residues processed: 205 average time/residue: 0.0868 time to fit residues: 28.6250 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 : 0.396 ------------------------------------------------------------------------------- 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 440 SER Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 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 440 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 65 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 117 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 125 optimal weight: 50.0000 chunk 193 optimal weight: 50.0000 chunk 150 optimal weight: 50.0000 chunk 178 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 58 optimal weight: 50.0000 chunk 164 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 GLN B 424 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 = 0.3959 r_free = 0.3959 target = 0.139154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.113449 restraints weight = 26571.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111322 restraints weight = 36844.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112330 restraints weight = 33106.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112578 restraints weight = 19542.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113519 restraints weight = 17690.013| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12869 Z= 0.192 Angle : 0.672 8.583 17632 Z= 0.348 Chirality : 0.046 0.232 2156 Planarity : 0.004 0.055 2300 Dihedral : 5.228 54.306 2030 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 4.10 % Allowed : 23.58 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1930 helix: 1.62 (0.20), residues: 696 sheet: -0.14 (0.26), residues: 402 loop : -1.15 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 39 TYR 0.026 0.002 TYR B 645 PHE 0.015 0.002 PHE E 79 TRP 0.015 0.001 TRP B 624 HIS 0.003 0.001 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (12858) covalent geometry : angle 0.66037 / 0.34 (17606) SS BOND : bond 0.00858 / 0.48 ( 7) SS BOND : angle 3.39552 / 1.84 ( 14) hydrogen bonds : bond 0.03228 / 2.43 ( 726) hydrogen bonds : angle 4.75722 / 3.48 ( 2082) link_BETA1-4 : bond 0.00036 / 0.02 ( 2) link_BETA1-4 : angle 1.36928 / 0.67 ( 6) link_NAG-ASN : bond 0.00162 / 0.08 ( 2) link_NAG-ASN : angle 4.19461 / 2.30 ( 6) *********************** 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 210 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.418 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: 0.8480 (mmp80) cc_final: 0.8189 (mmm-85) REVERT: B 482 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7693 (mmt180) REVERT: B 511 PHE cc_start: 0.8570 (t80) cc_final: 0.8288 (t80) REVERT: B 653 LYS cc_start: 0.6890 (mttt) cc_final: 0.6168 (tmmt) REVERT: C 100 TYR cc_start: 0.7492 (t80) cc_final: 0.7200 (t80) REVERT: C 103 LYS cc_start: 0.9154 (tttt) cc_final: 0.8737 (tttp) REVERT: D 82 ASP cc_start: 0.8090 (m-30) cc_final: 0.7840 (m-30) outliers start: 36 outliers final: 26 residues processed: 197 average time/residue: 0.0881 time to fit residues: 27.5836 Evaluate side-chains 193 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain 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 424 GLN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 3 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 176 optimal weight: 0.8980 chunk 125 optimal weight: 50.0000 chunk 188 optimal weight: 50.0000 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 40.0000 chunk 17 optimal weight: 50.0000 chunk 187 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 56 optimal weight: 50.0000 chunk 127 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 overall best weight: 14.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN B 424 GLN B 437 GLN B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.127102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091513 restraints weight = 27976.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092494 restraints weight = 20031.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093261 restraints weight = 16258.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093671 restraints weight = 14269.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093671 restraints weight = 13196.934| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.196 12869 Z= 1.010 Angle : 1.420 15.264 17632 Z= 0.728 Chirality : 0.073 0.372 2156 Planarity : 0.009 0.098 2300 Dihedral : 7.543 47.883 2030 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.60 % Favored : 91.09 % Rotamer: Outliers : 6.83 % Allowed : 22.10 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.18), residues: 1930 helix: -0.37 (0.19), residues: 682 sheet: -1.21 (0.24), residues: 432 loop : -2.27 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 84 TYR 0.057 0.006 TYR D 86 PHE 0.060 0.006 PHE C 79 TRP 0.045 0.006 TRP D 92 HIS 0.013 0.004 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.02320 / 1.01 (12858) covalent geometry : angle 1.40503 / 0.72 (17606) SS BOND : bond 0.01691 / 0.91 ( 7) SS BOND : angle 5.67345 / 3.11 ( 14) hydrogen bonds : bond 0.06564 / 4.89 ( 726) hydrogen bonds : angle 7.21658 / 5.30 ( 2082) link_BETA1-4 : bond 0.00342 / 0.18 ( 2) link_BETA1-4 : angle 2.52120 / 1.16 ( 6) link_NAG-ASN : bond 0.01740 / 0.87 ( 2) link_NAG-ASN : angle 7.31281 / 3.79 ( 6) *********************** 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 213 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8823 (mp) REVERT: A 539 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8655 (mm) REVERT: A 653 LYS cc_start: 0.7496 (mttt) cc_final: 0.6551 (tmmt) REVERT: B 479 LEU cc_start: 0.8807 (tp) cc_final: 0.8440 (tp) REVERT: B 653 LYS cc_start: 0.7716 (mttt) cc_final: 0.6827 (tmmt) REVERT: C 103 LYS cc_start: 0.9347 (tttt) cc_final: 0.9096 (ttmm) outliers start: 60 outliers final: 43 residues processed: 195 average time/residue: 0.0887 time to fit residues: 27.4998 Evaluate side-chains 194 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 429 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 539 LEU 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 423 ILE Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 475 LEU 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 496 MET Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 102 THR 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 22 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 18 optimal weight: 50.0000 chunk 62 optimal weight: 30.0000 chunk 136 optimal weight: 0.0870 chunk 27 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 617 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 78 GLN F 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.137467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.104609 restraints weight = 26453.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104892 restraints weight = 18914.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105331 restraints weight = 13792.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105866 restraints weight = 12409.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105948 restraints weight = 11091.298| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12869 Z= 0.159 Angle : 0.717 8.860 17632 Z= 0.371 Chirality : 0.047 0.207 2156 Planarity : 0.005 0.065 2300 Dihedral : 5.741 62.454 2030 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 2.96 % Allowed : 26.20 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.19), residues: 1930 helix: 1.09 (0.20), residues: 688 sheet: -0.55 (0.25), residues: 400 loop : -1.57 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.027 0.002 TYR A 645 PHE 0.025 0.002 PHE B 545 TRP 0.024 0.002 TRP E 35 HIS 0.002 0.001 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (12858) covalent geometry : angle 0.70743 / 0.37 (17606) SS BOND : bond 0.01365 / 0.68 ( 7) SS BOND : angle 3.11317 / 1.67 ( 14) hydrogen bonds : bond 0.03372 / 2.53 ( 726) hydrogen bonds : angle 5.31165 / 3.87 ( 2082) link_BETA1-4 : bond 0.00286 / 0.15 ( 2) link_BETA1-4 : angle 1.04064 / 0.59 ( 6) link_NAG-ASN : bond 0.00031 / 0.02 ( 2) link_NAG-ASN : angle 4.21227 / 2.30 ( 6) *********************** 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 202 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.483 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: 0.8361 (mmt-90) cc_final: 0.8027 (mmt180) REVERT: A 653 LYS cc_start: 0.7120 (mttt) cc_final: 0.6145 (tmmt) REVERT: B 511 PHE cc_start: 0.8746 (t80) cc_final: 0.8456 (t80) REVERT: B 617 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8039 (mm-40) REVERT: B 653 LYS cc_start: 0.7441 (mttt) cc_final: 0.6487 (tmmt) REVERT: C 103 LYS cc_start: 0.9155 (tttt) cc_final: 0.8902 (tttp) REVERT: D 15 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7956 (tt) REVERT: D 31 ASN cc_start: 0.8603 (m-40) cc_final: 0.8355 (m110) REVERT: D 82 ASP cc_start: 0.8144 (m-30) cc_final: 0.7805 (m-30) outliers start: 26 outliers final: 16 residues processed: 195 average time/residue: 0.0887 time to fit residues: 27.3807 Evaluate side-chains 180 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 PHE 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 423 ILE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 15 LEU 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 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 177 optimal weight: 0.0060 chunk 131 optimal weight: 40.0000 chunk 5 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 71 optimal weight: 30.0000 chunk 22 optimal weight: 50.0000 chunk 172 optimal weight: 50.0000 chunk 41 optimal weight: 3.9990 overall best weight: 7.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 GLN B 437 GLN B 617 GLN ** 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 = 0.3845 r_free = 0.3845 target = 0.130997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096371 restraints weight = 27360.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097753 restraints weight = 19324.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097698 restraints weight = 15841.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098281 restraints weight = 13618.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.098507 restraints weight = 12691.762| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.121 12869 Z= 0.547 Angle : 0.955 10.909 17632 Z= 0.495 Chirality : 0.055 0.253 2156 Planarity : 0.006 0.071 2300 Dihedral : 6.264 52.319 2030 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 3.42 % Allowed : 25.17 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.19), residues: 1930 helix: 0.59 (0.19), residues: 702 sheet: -0.75 (0.25), residues: 400 loop : -1.91 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 465 TYR 0.030 0.004 TYR A 464 PHE 0.034 0.003 PHE E 79 TRP 0.027 0.003 TRP D 92 HIS 0.006 0.002 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.01265 / 0.55 (12858) covalent geometry : angle 0.94177 / 0.49 (17606) SS BOND : bond 0.01423 / 0.79 ( 7) SS BOND : angle 4.40638 / 2.34 ( 14) hydrogen bonds : bond 0.04569 / 3.42 ( 726) hydrogen bonds : angle 5.88201 / 4.29 ( 2082) link_BETA1-4 : bond 0.00051 / 0.03 ( 2) link_BETA1-4 : angle 1.60844 / 0.78 ( 6) link_NAG-ASN : bond 0.00718 / 0.36 ( 2) link_NAG-ASN : angle 5.28533 / 2.79 ( 6) ********************** 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 189 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8517 (mmt-90) cc_final: 0.8109 (mmt180) REVERT: A 653 LYS cc_start: 0.7435 (mttt) cc_final: 0.6348 (tmmt) REVERT: B 479 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8445 (tp) REVERT: B 653 LYS cc_start: 0.7591 (mttt) cc_final: 0.6750 (tmmt) REVERT: C 103 LYS cc_start: 0.9281 (tttt) cc_final: 0.9023 (tttp) REVERT: D 79 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8545 (tm-30) REVERT: D 82 ASP cc_start: 0.8274 (m-30) cc_final: 0.7988 (m-30) REVERT: F 36 TYR cc_start: 0.8967 (m-80) cc_final: 0.8459 (m-80) outliers start: 30 outliers final: 24 residues processed: 181 average time/residue: 0.0863 time to fit residues: 24.9571 Evaluate side-chains 181 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 PHE 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 429 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 559 THR 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 104 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 138 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 58 optimal weight: 50.0000 chunk 26 optimal weight: 50.0000 chunk 67 optimal weight: 20.0000 chunk 172 optimal weight: 50.0000 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN A 437 GLN B 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.137079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104133 restraints weight = 26538.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104469 restraints weight = 17954.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104649 restraints weight = 14363.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105324 restraints weight = 12819.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105337 restraints weight = 11464.563| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12869 Z= 0.157 Angle : 0.685 9.629 17632 Z= 0.354 Chirality : 0.045 0.198 2156 Planarity : 0.005 0.058 2300 Dihedral : 5.437 61.290 2030 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 2.16 % Allowed : 26.42 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1930 helix: 1.31 (0.20), residues: 702 sheet: -0.50 (0.26), residues: 402 loop : -1.45 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.023 0.002 TYR A 464 PHE 0.014 0.002 PHE A 545 TRP 0.023 0.002 TRP C 35 HIS 0.003 0.001 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (12858) covalent geometry : angle 0.67559 / 0.35 (17606) SS BOND : bond 0.00756 / 0.46 ( 7) SS BOND : angle 2.97879 / 1.57 ( 14) hydrogen bonds : bond 0.03224 / 2.42 ( 726) hydrogen bonds : angle 5.02413 / 3.66 ( 2082) link_BETA1-4 : bond 0.00072 / 0.04 ( 2) link_BETA1-4 : angle 1.41137 / 0.73 ( 6) link_NAG-ASN : bond 0.00061 / 0.03 ( 2) link_NAG-ASN : angle 4.16003 / 2.31 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.06 seconds wall clock time: 35 minutes 5.69 seconds (2105.69 seconds total)