Starting phenix.real_space_refine on Tue Nov 18 08:48:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5nj3_3654/11_2025/5nj3_3654.cif Found real_map, /net/cci-nas-00/data/ceres_data/5nj3_3654/11_2025/5nj3_3654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5nj3_3654/11_2025/5nj3_3654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5nj3_3654/11_2025/5nj3_3654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5nj3_3654/11_2025/5nj3_3654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5nj3_3654/11_2025/5nj3_3654.map" } 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-2.0-5881/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.71, per 1000 atoms: 0.29 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: 1.15 Conformation dependent library (CDL) restraints added in 696.1 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: 0.59 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: 2.47 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2150 1.31 - 1.43: 3378 1.43 - 1.56: 7254 1.56 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 12858 Sorted by residual: bond pdb=" C THR C 171 " pdb=" N PHE C 172 " ideal model delta sigma weight residual 1.339 1.180 0.160 5.57e-02 3.22e+02 8.24e+00 bond pdb=" C THR E 171 " pdb=" N PHE E 172 " ideal model delta sigma weight residual 1.339 1.180 0.160 5.57e-02 3.22e+02 8.20e+00 bond pdb=" CB GLN A 569 " pdb=" CG GLN A 569 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 7.94e+00 bond pdb=" CB GLN B 569 " pdb=" CG GLN B 569 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.71e+00 bond pdb=" C ASN A 601 " pdb=" N PRO A 602 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.02e+00 ... (remaining 12853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 16828 2.50 - 5.00: 648 5.00 - 7.49: 105 7.49 - 9.99: 19 9.99 - 12.49: 6 Bond angle restraints: 17606 Sorted by residual: angle pdb=" C PRO A 602 " pdb=" N CYS A 603 " pdb=" CA CYS A 603 " ideal model delta sigma weight residual 122.17 113.86 8.31 1.62e+00 3.81e-01 2.63e+01 angle pdb=" C PRO B 602 " pdb=" N CYS B 603 " pdb=" CA CYS B 603 " ideal model delta sigma weight residual 122.17 113.88 8.29 1.62e+00 3.81e-01 2.62e+01 angle pdb=" N PRO A 602 " pdb=" CA PRO A 602 " pdb=" C PRO A 602 " ideal model delta sigma weight residual 112.47 122.52 -10.05 2.06e+00 2.36e-01 2.38e+01 angle pdb=" N PRO B 602 " pdb=" CA PRO B 602 " pdb=" C PRO B 602 " ideal model delta sigma weight residual 112.47 122.48 -10.01 2.06e+00 2.36e-01 2.36e+01 angle pdb=" C TYR B 605 " pdb=" CA TYR B 605 " pdb=" CB TYR B 605 " ideal model delta sigma weight residual 111.48 103.98 7.50 1.59e+00 3.96e-01 2.23e+01 ... (remaining 17601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.45: 7018 14.45 - 28.89: 378 28.89 - 43.34: 79 43.34 - 57.79: 31 57.79 - 72.23: 5 Dihedral angle restraints: 7511 sinusoidal: 1899 harmonic: 5612 Sorted by residual: dihedral pdb=" CA ASN A 601 " pdb=" C ASN A 601 " pdb=" N PRO A 602 " pdb=" CA PRO A 602 " ideal model delta harmonic sigma weight residual -180.00 -124.15 -55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ASN B 601 " pdb=" C ASN B 601 " pdb=" N PRO B 602 " pdb=" CA PRO B 602 " ideal model delta harmonic sigma weight residual -180.00 -124.17 -55.83 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA PRO A 602 " pdb=" C PRO A 602 " pdb=" N CYS A 603 " pdb=" CA CYS A 603 " ideal model delta harmonic sigma weight residual 180.00 137.89 42.11 0 5.00e+00 4.00e-02 7.09e+01 ... (remaining 7508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1892 0.094 - 0.188: 250 0.188 - 0.282: 6 0.282 - 0.376: 4 0.376 - 0.470: 4 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 596 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 596 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB ILE A 573 " pdb=" CA ILE A 573 " pdb=" CG1 ILE A 573 " pdb=" CG2 ILE A 573 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 2153 not shown) Planarity restraints: 2302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 601 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 602 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 601 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO B 602 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 602 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 602 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 576 " 0.019 2.00e-02 2.50e+03 1.82e-02 6.62e+00 pdb=" CG TYR B 576 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 576 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 576 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 576 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 576 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 576 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 576 " 0.001 2.00e-02 2.50e+03 ... (remaining 2299 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1125 2.73 - 3.27: 12461 3.27 - 3.81: 20154 3.81 - 4.36: 22516 4.36 - 4.90: 39080 Nonbonded interactions: 95336 Sorted by model distance: nonbonded pdb=" O ARG B 575 " pdb=" OG1 THR B 579 " model vdw 2.183 3.040 nonbonded pdb=" O ARG A 575 " pdb=" OG1 THR A 579 " model vdw 2.184 3.040 nonbonded pdb=" O VAL A 508 " pdb=" OG1 THR A 512 " model vdw 2.264 3.040 nonbonded pdb=" O VAL B 508 " pdb=" OG1 THR B 512 " model vdw 2.264 3.040 nonbonded pdb=" O CYS A 438 " pdb=" OG SER A 441 " model vdw 2.273 3.040 ... (remaining 95331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.160 12869 Z= 0.496 Angle : 1.181 13.153 17632 Z= 0.638 Chirality : 0.064 0.470 2156 Planarity : 0.007 0.070 2300 Dihedral : 10.684 70.998 3874 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 0.68 % Allowed : 3.42 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.32 % Rama-Z 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 covalent geometry : bond 0.01148 (12858) covalent geometry : angle 1.16470 (17606) SS BOND : bond 0.01072 ( 7) SS BOND : angle 1.68298 ( 14) hydrogen bonds : bond 0.13336 ( 726) hydrogen bonds : angle 10.71992 ( 2082) link_BETA1-4 : bond 0.00456 ( 2) link_BETA1-4 : angle 4.37014 ( 6) link_NAG-ASN : bond 0.01234 ( 2) link_NAG-ASN : angle 9.49000 ( 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: 0.8766 (mt) cc_final: 0.8454 (mp) REVERT: A 488 ILE cc_start: 0.8819 (mt) cc_final: 0.8574 (mt) REVERT: A 492 ILE cc_start: 0.8264 (pt) cc_final: 0.7791 (pt) REVERT: A 624 TRP cc_start: 0.8264 (t60) cc_final: 0.7948 (t60) REVERT: B 373 PHE cc_start: 0.6918 (t80) cc_final: 0.6627 (t80) REVERT: B 479 LEU cc_start: 0.8632 (mt) cc_final: 0.8309 (tp) REVERT: B 488 ILE cc_start: 0.8732 (mt) cc_final: 0.8427 (mt) REVERT: B 617 GLN cc_start: 0.8233 (tp-100) cc_final: 0.8031 (mm-40) REVERT: C 103 LYS cc_start: 0.8489 (tttt) cc_final: 0.8265 (tttp) REVERT: E 103 LYS cc_start: 0.8906 (tttt) cc_final: 0.8391 (tttp) REVERT: E 105 THR cc_start: 0.8375 (p) cc_final: 0.8165 (t) outliers start: 6 outliers final: 1 residues processed: 283 average time/residue: 0.1236 time to fit residues: 50.0359 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 : 0.592 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 393 GLN A 424 GLN A 557 ASN B 376 GLN B 424 GLN C 40 GLN C 82 GLN D 38 GLN E 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.144150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116487 restraints weight = 25832.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.114312 restraints weight = 25983.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115338 restraints weight = 23727.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115655 restraints weight = 15317.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.115774 restraints weight = 13847.195| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2114 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= 0.175 Angle : 0.716 9.336 17632 Z= 0.369 Chirality : 0.045 0.238 2156 Planarity : 0.005 0.056 2300 Dihedral : 6.890 65.624 2115 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 2.05 % Allowed : 12.98 % Favored : 84.97 % 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: -1.82 (0.18), residues: 1930 helix: -0.65 (0.18), residues: 654 sheet: -0.79 (0.23), residues: 448 loop : -1.82 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 18 TYR 0.030 0.002 TYR A 645 PHE 0.023 0.002 PHE D 62 TRP 0.018 0.002 TRP A 624 HIS 0.002 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00389 (12858) covalent geometry : angle 0.70552 (17606) SS BOND : bond 0.00719 ( 7) SS BOND : angle 1.73041 ( 14) hydrogen bonds : bond 0.03879 ( 726) hydrogen bonds : angle 6.23893 ( 2082) link_BETA1-4 : bond 0.00295 ( 2) link_BETA1-4 : angle 2.42460 ( 6) link_NAG-ASN : bond 0.00352 ( 2) link_NAG-ASN : angle 5.71627 ( 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 236 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.493 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 518 TYR cc_start: 0.7878 (m-80) cc_final: 0.7649 (m-80) REVERT: A 541 MET cc_start: 0.7435 (mmm) cc_final: 0.6205 (mmm) REVERT: B 373 PHE cc_start: 0.6402 (t80) cc_final: 0.6171 (t80) REVERT: B 477 ASP cc_start: 0.7811 (t0) cc_final: 0.7314 (m-30) REVERT: C 103 LYS cc_start: 0.8691 (tttt) cc_final: 0.8470 (tttp) REVERT: D 81 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: D 82 ASP cc_start: 0.8143 (m-30) cc_final: 0.7939 (m-30) REVERT: E 105 THR cc_start: 0.8871 (p) cc_final: 0.8603 (t) REVERT: F 13 VAL cc_start: 0.7855 (m) cc_final: 0.7512 (p) REVERT: F 36 TYR cc_start: 0.8876 (m-80) cc_final: 0.8331 (m-80) REVERT: F 82 ASP cc_start: 0.8396 (m-30) cc_final: 0.8159 (m-30) outliers start: 18 outliers final: 8 residues processed: 224 average time/residue: 0.0983 time to fit residues: 34.0419 Evaluate side-chains 198 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 40.0000 chunk 170 optimal weight: 40.0000 chunk 29 optimal weight: 3.9990 chunk 149 optimal weight: 50.0000 chunk 186 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN B 437 GLN B 557 ASN D 38 GLN E 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.139586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113643 restraints weight = 26770.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110878 restraints weight = 37022.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112155 restraints weight = 33291.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112302 restraints weight = 19527.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112625 restraints weight = 18608.460| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 12869 Z= 0.291 Angle : 0.751 9.972 17632 Z= 0.390 Chirality : 0.048 0.263 2156 Planarity : 0.005 0.051 2300 Dihedral : 6.525 58.302 2114 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 4.44 % Allowed : 17.54 % Favored : 78.02 % 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: -0.89 (0.19), residues: 1930 helix: 0.51 (0.19), residues: 660 sheet: -0.38 (0.24), residues: 440 loop : -1.58 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 39 TYR 0.029 0.002 TYR A 645 PHE 0.025 0.003 PHE C 79 TRP 0.015 0.002 TRP C 109 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00668 (12858) covalent geometry : angle 0.74259 (17606) SS BOND : bond 0.00905 ( 7) SS BOND : angle 1.69702 ( 14) hydrogen bonds : bond 0.03862 ( 726) hydrogen bonds : angle 5.48941 ( 2082) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 2.09277 ( 6) link_NAG-ASN : bond 0.00199 ( 2) link_NAG-ASN : angle 5.42072 ( 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 231 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8589 (mmp80) cc_final: 0.7899 (mmt180) REVERT: A 518 TYR cc_start: 0.7874 (m-80) cc_final: 0.7611 (m-80) REVERT: B 373 PHE cc_start: 0.6623 (t80) cc_final: 0.6381 (t80) REVERT: B 482 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7786 (mmt180) REVERT: C 103 LYS cc_start: 0.8880 (tttt) cc_final: 0.8573 (tttp) REVERT: D 36 TYR cc_start: 0.8768 (m-80) cc_final: 0.8284 (m-80) REVERT: F 82 ASP cc_start: 0.8364 (m-30) cc_final: 0.8120 (m-30) outliers start: 39 outliers final: 22 residues processed: 210 average time/residue: 0.0906 time to fit residues: 30.1763 Evaluate side-chains 192 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 635 CYS 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 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: 2.9990 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 50.0000 chunk 100 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 129 optimal weight: 40.0000 chunk 171 optimal weight: 7.9990 chunk 124 optimal weight: 40.0000 chunk 187 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 617 GLN B 424 GLN B 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.140599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114809 restraints weight = 26048.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112627 restraints weight = 33602.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113895 restraints weight = 32250.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113915 restraints weight = 19230.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114903 restraints weight = 17545.037| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12869 Z= 0.201 Angle : 0.667 9.300 17632 Z= 0.345 Chirality : 0.046 0.242 2156 Planarity : 0.004 0.057 2300 Dihedral : 6.052 55.299 2114 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 3.19 % Allowed : 20.05 % Favored : 76.77 % 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: -0.34 (0.20), residues: 1930 helix: 1.17 (0.20), residues: 674 sheet: -0.24 (0.25), residues: 424 loop : -1.37 (0.23), residues: 832 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 0.016 0.002 PHE C 79 TRP 0.014 0.002 TRP B 624 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00463 (12858) covalent geometry : angle 0.65646 (17606) SS BOND : bond 0.00863 ( 7) SS BOND : angle 2.43156 ( 14) hydrogen bonds : bond 0.03335 ( 726) hydrogen bonds : angle 4.98888 ( 2082) link_BETA1-4 : bond 0.00152 ( 2) link_BETA1-4 : angle 1.83690 ( 6) link_NAG-ASN : bond 0.00025 ( 2) link_NAG-ASN : angle 4.93103 ( 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 223 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.488 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: 0.7529 (pt0) cc_final: 0.7103 (pt0) REVERT: A 482 ARG cc_start: 0.8459 (mmp80) cc_final: 0.7734 (mmt180) REVERT: A 492 ILE cc_start: 0.8364 (pt) cc_final: 0.8127 (pt) REVERT: B 511 PHE cc_start: 0.8563 (t80) cc_final: 0.8232 (t80) REVERT: C 5 GLN cc_start: 0.7956 (tp40) cc_final: 0.7733 (tp40) REVERT: C 103 LYS cc_start: 0.8899 (tttt) cc_final: 0.8633 (tttp) REVERT: D 36 TYR cc_start: 0.8761 (m-80) cc_final: 0.8246 (m-80) outliers start: 28 outliers final: 14 residues processed: 210 average time/residue: 0.0837 time to fit residues: 27.9872 Evaluate side-chains 186 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 424 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 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: 0.1980 chunk 170 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 150 optimal weight: 50.0000 chunk 156 optimal weight: 3.9990 chunk 122 optimal weight: 0.0040 chunk 55 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.139999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114756 restraints weight = 26375.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.112907 restraints weight = 35254.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113922 restraints weight = 35188.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114032 restraints weight = 20541.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114976 restraints weight = 18305.757| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12869 Z= 0.207 Angle : 0.664 8.230 17632 Z= 0.344 Chirality : 0.046 0.231 2156 Planarity : 0.004 0.054 2300 Dihedral : 5.889 53.916 2114 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 4.21 % Allowed : 20.62 % Favored : 75.17 % 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: -0.06 (0.20), residues: 1930 helix: 1.48 (0.20), residues: 674 sheet: -0.12 (0.25), residues: 444 loop : -1.30 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 39 TYR 0.029 0.002 TYR B 645 PHE 0.017 0.002 PHE E 79 TRP 0.013 0.001 TRP B 624 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00479 (12858) covalent geometry : angle 0.65456 (17606) SS BOND : bond 0.00691 ( 7) SS BOND : angle 2.33887 ( 14) hydrogen bonds : bond 0.03269 ( 726) hydrogen bonds : angle 4.86568 ( 2082) link_BETA1-4 : bond 0.00078 ( 2) link_BETA1-4 : angle 1.93374 ( 6) link_NAG-ASN : bond 0.00049 ( 2) link_NAG-ASN : angle 4.84084 ( 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 216 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.468 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: 0.7565 (pt0) cc_final: 0.7123 (pt0) REVERT: A 482 ARG cc_start: 0.8448 (mmp80) cc_final: 0.7720 (mmt180) REVERT: A 492 ILE cc_start: 0.8463 (pt) cc_final: 0.8201 (pt) REVERT: B 482 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7694 (mmt180) REVERT: B 511 PHE cc_start: 0.8554 (t80) cc_final: 0.8220 (t80) REVERT: C 5 GLN cc_start: 0.7958 (tp40) cc_final: 0.7596 (tp-100) REVERT: C 96 CYS cc_start: 0.6169 (OUTLIER) cc_final: 0.5939 (p) REVERT: C 103 LYS cc_start: 0.8957 (tttt) cc_final: 0.8706 (tttp) outliers start: 37 outliers final: 24 residues processed: 205 average time/residue: 0.0874 time to fit residues: 28.7051 Evaluate side-chains 197 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 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 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 405 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 96 CYS 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 96 CYS 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: 30.0000 chunk 78 optimal weight: 50.0000 chunk 105 optimal weight: 0.0980 chunk 8 optimal weight: 10.0000 chunk 185 optimal weight: 40.0000 chunk 150 optimal weight: 50.0000 chunk 155 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 50.0000 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 424 GLN B 437 GLN D 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.137690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.112522 restraints weight = 26630.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110706 restraints weight = 36802.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111916 restraints weight = 34902.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111836 restraints weight = 20822.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112753 restraints weight = 18650.371| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 12869 Z= 0.283 Angle : 0.722 8.923 17632 Z= 0.376 Chirality : 0.048 0.232 2156 Planarity : 0.005 0.056 2300 Dihedral : 6.019 53.427 2114 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer: Outliers : 5.47 % Allowed : 20.96 % Favored : 73.58 % 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: 0.00 (0.20), residues: 1930 helix: 1.57 (0.20), residues: 670 sheet: -0.19 (0.26), residues: 412 loop : -1.19 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 39 TYR 0.027 0.002 TYR A 645 PHE 0.022 0.002 PHE E 79 TRP 0.013 0.002 TRP B 624 HIS 0.003 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00655 (12858) covalent geometry : angle 0.71270 (17606) SS BOND : bond 0.00774 ( 7) SS BOND : angle 2.32272 ( 14) hydrogen bonds : bond 0.03673 ( 726) hydrogen bonds : angle 4.97343 ( 2082) link_BETA1-4 : bond 0.00155 ( 2) link_BETA1-4 : angle 1.86415 ( 6) link_NAG-ASN : bond 0.00151 ( 2) link_NAG-ASN : angle 5.07469 ( 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 222 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.414 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: 0.7613 (pt0) cc_final: 0.7259 (pt0) REVERT: A 482 ARG cc_start: 0.8479 (mmp80) cc_final: 0.7962 (mmt180) REVERT: A 483 MET cc_start: 0.7674 (mtp) cc_final: 0.7455 (mtm) REVERT: A 492 ILE cc_start: 0.8517 (pt) cc_final: 0.8263 (pt) REVERT: B 511 PHE cc_start: 0.8679 (t80) cc_final: 0.8386 (t80) REVERT: B 653 LYS cc_start: 0.6949 (mttt) cc_final: 0.6203 (tmmt) REVERT: C 96 CYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5946 (p) REVERT: C 103 LYS cc_start: 0.9124 (tttt) cc_final: 0.8842 (tttp) outliers start: 48 outliers final: 29 residues processed: 208 average time/residue: 0.0844 time to fit residues: 27.7835 Evaluate side-chains 193 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 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 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 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 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 117 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 125 optimal weight: 50.0000 chunk 193 optimal weight: 50.0000 chunk 150 optimal weight: 50.0000 chunk 178 optimal weight: 0.3980 chunk 9 optimal weight: 30.0000 chunk 58 optimal weight: 50.0000 chunk 164 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.138645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103008 restraints weight = 26616.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104467 restraints weight = 17311.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105417 restraints weight = 13248.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105890 restraints weight = 11257.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106130 restraints weight = 10293.305| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12869 Z= 0.217 Angle : 0.683 8.832 17632 Z= 0.353 Chirality : 0.046 0.241 2156 Planarity : 0.004 0.057 2300 Dihedral : 5.882 53.952 2114 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 4.67 % Allowed : 23.01 % 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: 0.08 (0.20), residues: 1930 helix: 1.63 (0.20), residues: 688 sheet: -0.19 (0.26), residues: 400 loop : -1.16 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 39 TYR 0.025 0.002 TYR B 645 PHE 0.017 0.002 PHE B 545 TRP 0.014 0.001 TRP B 624 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00505 (12858) covalent geometry : angle 0.67068 (17606) SS BOND : bond 0.00914 ( 7) SS BOND : angle 3.12097 ( 14) hydrogen bonds : bond 0.03330 ( 726) hydrogen bonds : angle 4.82181 ( 2082) link_BETA1-4 : bond 0.00357 ( 2) link_BETA1-4 : angle 1.77436 ( 6) link_NAG-ASN : bond 0.00187 ( 2) link_NAG-ASN : angle 4.84762 ( 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 214 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.515 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: 0.7617 (pt0) cc_final: 0.7220 (pt0) REVERT: A 482 ARG cc_start: 0.8434 (mmp80) cc_final: 0.8114 (mmm-85) REVERT: A 492 ILE cc_start: 0.8632 (pt) cc_final: 0.8389 (pt) REVERT: B 511 PHE cc_start: 0.8644 (t80) cc_final: 0.8250 (t80) REVERT: B 653 LYS cc_start: 0.7012 (mttt) cc_final: 0.6240 (tmmt) REVERT: C 100 TYR cc_start: 0.7549 (t80) cc_final: 0.7268 (t80) REVERT: C 103 LYS cc_start: 0.9141 (tttt) cc_final: 0.8758 (tttp) outliers start: 41 outliers final: 33 residues processed: 202 average time/residue: 0.0909 time to fit residues: 29.1492 Evaluate side-chains 202 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 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 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 429 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 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 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 176 optimal weight: 0.9980 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: 60.0000 chunk 127 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 overall best weight: 12.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 437 GLN B 376 GLN B 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.128153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093318 restraints weight = 27554.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094627 restraints weight = 19852.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094581 restraints weight = 16901.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094755 restraints weight = 14372.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.094905 restraints weight = 13915.944| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.178 12869 Z= 0.895 Angle : 1.310 23.753 17632 Z= 0.671 Chirality : 0.068 0.348 2156 Planarity : 0.008 0.079 2300 Dihedral : 7.932 55.630 2114 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.88 % Favored : 91.92 % Rotamer: Outliers : 6.95 % Allowed : 20.96 % Favored : 72.10 % 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: -1.82 (0.18), residues: 1930 helix: -0.13 (0.19), residues: 692 sheet: -1.07 (0.24), residues: 426 loop : -2.19 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG C 84 TYR 0.051 0.006 TYR E 51 PHE 0.054 0.005 PHE C 79 TRP 0.042 0.005 TRP D 92 HIS 0.011 0.003 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.02060 (12858) covalent geometry : angle 1.29555 (17606) SS BOND : bond 0.01679 ( 7) SS BOND : angle 5.08122 ( 14) hydrogen bonds : bond 0.06090 ( 726) hydrogen bonds : angle 6.91055 ( 2082) link_BETA1-4 : bond 0.00378 ( 2) link_BETA1-4 : angle 2.21781 ( 6) link_NAG-ASN : bond 0.01496 ( 2) link_NAG-ASN : angle 7.12297 ( 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: 61 poor density : 152 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.8071 (pt0) cc_final: 0.7827 (pt0) REVERT: A 471 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8870 (mp) REVERT: A 479 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8402 (tp) REVERT: A 483 MET cc_start: 0.8065 (mtp) cc_final: 0.7860 (mtp) REVERT: A 539 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8618 (mm) REVERT: A 653 LYS cc_start: 0.7431 (mttt) cc_final: 0.6568 (tmtt) REVERT: B 477 ASP cc_start: 0.8420 (t0) cc_final: 0.7375 (m-30) REVERT: B 483 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7789 (mtp) REVERT: B 653 LYS cc_start: 0.7715 (mttt) cc_final: 0.6833 (tmmt) REVERT: C 103 LYS cc_start: 0.9331 (tttt) cc_final: 0.9058 (ttmm) REVERT: F 82 ASP cc_start: 0.8444 (m-30) cc_final: 0.8120 (m-30) outliers start: 61 outliers final: 47 residues processed: 196 average time/residue: 0.0855 time to fit residues: 26.8092 Evaluate side-chains 198 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 479 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 429 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 483 MET 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 523 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 559 THR 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 33 LEU 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: 10.0000 chunk 57 optimal weight: 40.0000 chunk 89 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 18 optimal weight: 50.0000 chunk 62 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.136340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103512 restraints weight = 26342.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103249 restraints weight = 18165.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103865 restraints weight = 14010.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104168 restraints weight = 12388.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104276 restraints weight = 12007.260| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12869 Z= 0.185 Angle : 0.715 9.464 17632 Z= 0.371 Chirality : 0.047 0.213 2156 Planarity : 0.005 0.060 2300 Dihedral : 6.479 60.220 2114 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 3.53 % Allowed : 24.49 % Favored : 71.98 % 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: -0.58 (0.19), residues: 1930 helix: 1.09 (0.20), residues: 700 sheet: -0.61 (0.25), residues: 400 loop : -1.56 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 482 TYR 0.026 0.002 TYR A 645 PHE 0.017 0.002 PHE A 545 TRP 0.019 0.002 TRP B 624 HIS 0.003 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00422 (12858) covalent geometry : angle 0.70435 (17606) SS BOND : bond 0.01148 ( 7) SS BOND : angle 3.07225 ( 14) hydrogen bonds : bond 0.03481 ( 726) hydrogen bonds : angle 5.32888 ( 2082) link_BETA1-4 : bond 0.00194 ( 2) link_BETA1-4 : angle 1.51394 ( 6) link_NAG-ASN : bond 0.00238 ( 2) link_NAG-ASN : angle 4.83655 ( 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 198 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.8671 (tp) cc_final: 0.8438 (tp) REVERT: A 482 ARG cc_start: 0.8345 (mmt-90) cc_final: 0.7949 (mmt180) REVERT: A 492 ILE cc_start: 0.8668 (pt) cc_final: 0.8415 (pt) REVERT: A 653 LYS cc_start: 0.7158 (mttt) cc_final: 0.6175 (tmmt) REVERT: B 477 ASP cc_start: 0.8205 (t0) cc_final: 0.7242 (m-30) REVERT: B 511 PHE cc_start: 0.8761 (t80) cc_final: 0.8385 (t80) REVERT: B 653 LYS cc_start: 0.7495 (mttt) cc_final: 0.6500 (tmmt) REVERT: C 27 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.8068 (t80) REVERT: C 103 LYS cc_start: 0.9169 (tttt) cc_final: 0.8898 (tttp) outliers start: 31 outliers final: 21 residues processed: 189 average time/residue: 0.0906 time to fit residues: 27.2072 Evaluate side-chains 182 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 177 optimal weight: 0.1980 chunk 131 optimal weight: 40.0000 chunk 5 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 155 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 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: 1.9990 overall best weight: 7.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096220 restraints weight = 27333.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097605 restraints weight = 19892.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097734 restraints weight = 15997.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098172 restraints weight = 13595.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098402 restraints weight = 12951.193| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.012 0.117 12869 Z= 0.534 Angle : 0.962 11.340 17632 Z= 0.498 Chirality : 0.055 0.256 2156 Planarity : 0.006 0.066 2300 Dihedral : 6.958 52.373 2114 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.46 % Favored : 92.44 % Rotamer: Outliers : 3.42 % Allowed : 25.28 % Favored : 71.30 % 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: -1.13 (0.19), residues: 1930 helix: 0.58 (0.20), residues: 702 sheet: -0.78 (0.25), residues: 400 loop : -1.89 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 84 TYR 0.030 0.004 TYR D 86 PHE 0.035 0.003 PHE E 79 TRP 0.024 0.003 TRP D 92 HIS 0.006 0.002 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.01236 (12858) covalent geometry : angle 0.95068 (17606) SS BOND : bond 0.01273 ( 7) SS BOND : angle 3.77956 ( 14) hydrogen bonds : bond 0.04604 ( 726) hydrogen bonds : angle 5.93330 ( 2082) link_BETA1-4 : bond 0.00273 ( 2) link_BETA1-4 : angle 1.85858 ( 6) link_NAG-ASN : bond 0.00759 ( 2) link_NAG-ASN : angle 5.75779 ( 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 192 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8509 (mmt-90) cc_final: 0.8105 (mmm-85) REVERT: A 653 LYS cc_start: 0.7439 (mttt) cc_final: 0.6416 (tmmt) REVERT: B 477 ASP cc_start: 0.8266 (t0) cc_final: 0.7311 (m-30) REVERT: B 653 LYS cc_start: 0.7798 (mttt) cc_final: 0.6791 (tmmt) REVERT: C 27 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8144 (t80) REVERT: C 103 LYS cc_start: 0.9274 (tttt) cc_final: 0.9002 (tttp) REVERT: D 79 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8607 (tm-30) outliers start: 30 outliers final: 23 residues processed: 185 average time/residue: 0.0888 time to fit residues: 26.1719 Evaluate side-chains 183 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 27 PHE 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 81 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 138 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 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: 30.0000 chunk 37 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN C 40 GLN D 38 GLN E 40 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 = 0.3940 r_free = 0.3940 target = 0.138060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105319 restraints weight = 26312.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105286 restraints weight = 18366.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105799 restraints weight = 14046.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106544 restraints weight = 12329.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.106498 restraints weight = 11543.862| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12869 Z= 0.140 Angle : 0.685 11.211 17632 Z= 0.352 Chirality : 0.045 0.211 2156 Planarity : 0.005 0.054 2300 Dihedral : 6.030 61.243 2114 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 2.16 % Allowed : 26.65 % Favored : 71.18 % 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: -0.24 (0.20), residues: 1930 helix: 1.48 (0.20), residues: 702 sheet: -0.48 (0.25), residues: 404 loop : -1.44 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 482 TYR 0.025 0.002 TYR B 645 PHE 0.022 0.002 PHE A 545 TRP 0.024 0.002 TRP E 35 HIS 0.002 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00319 (12858) covalent geometry : angle 0.67544 (17606) SS BOND : bond 0.00687 ( 7) SS BOND : angle 2.67801 ( 14) hydrogen bonds : bond 0.03132 ( 726) hydrogen bonds : angle 4.97172 ( 2082) link_BETA1-4 : bond 0.00102 ( 2) link_BETA1-4 : angle 1.52836 ( 6) link_NAG-ASN : bond 0.00009 ( 2) link_NAG-ASN : angle 4.54971 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1925.55 seconds wall clock time: 33 minutes 58.71 seconds (2038.71 seconds total)