Starting phenix.real_space_refine on Sat Sep 12 14:20:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5mke_3523/09_2026/5mke_3523.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mke_3523/09_2026/5mke_3523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5mke_3523/09_2026/5mke_3523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mke_3523/09_2026/5mke_3523.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5mke_3523/09_2026/5mke_3523.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5mke_3523/09_2026/5mke_3523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5mke_3523/09_2026/5mke_3523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mke_3523/09_2026/5mke_3523.map" } resolution = 4.3 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= 0.006 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 76 5.16 5 C 10912 2.51 5 N 2508 2.21 5 O 2924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'CHS': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 96 Unusual residues: {' CA': 2, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'CHS': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 94 Unusual residues: {'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'CHS': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 94 Unusual residues: {'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 86 Unusual residues: {'CHS': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 94 Unusual residues: {'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.82, per 1000 atoms: 0.23 Number of scatterers: 16426 At special positions: 0 Unit cell: (115.14, 115.14, 101.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 76 16.00 P 4 15.00 O 2924 8.00 N 2508 7.00 C 10912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 D1003 " - " NAG D1004 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1001 " - " ASN A 305 " " NAG A1002 " - " ASN A 362 " " NAG B1001 " - " ASN B 305 " " NAG B1002 " - " ASN B 362 " " NAG C1001 " - " ASN C 305 " " NAG C1002 " - " ASN C 362 " " NAG D1001 " - " ASN D 305 " " NAG D1002 " - " ASN D 362 " " NAG D1003 " - " ASN D 375 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 375 " " NAG G 1 " - " ASN C 375 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 713.0 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB CHS A1005 " pdb=" CB CHS A1006 " pdb=" CB CHS B1005 " pdb=" CB CHS B1006 " pdb=" CB CHS C1005 " pdb=" CB CHS C1006 " pdb=" CB CHS D1005 " pdb=" CB CHS D1006 " Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 57.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 215 through 242 removed outlier: 3.727A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.769A pdb=" N MET A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.921A pdb=" N ARG A 338 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.755A pdb=" N TRP A 366 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.588A pdb=" N THR A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 498 removed outlier: 4.138A pdb=" N CYS A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 482 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 542 removed outlier: 3.960A pdb=" N ILE A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 578 removed outlier: 3.760A pdb=" N PHE A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 593 removed outlier: 3.740A pdb=" N SER A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 620 removed outlier: 3.959A pdb=" N PHE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 599 " --> pdb=" O LYS A 595 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 642 removed outlier: 3.529A pdb=" N CYS A 632 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 4.412A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 693 removed outlier: 3.731A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 679 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 242 removed outlier: 3.726A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.768A pdb=" N MET B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.920A pdb=" N ARG B 338 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 339 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.755A pdb=" N TRP B 366 " --> pdb=" O GLY B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.588A pdb=" N THR B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 498 removed outlier: 4.139A pdb=" N CYS B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS B 481 " --> pdb=" O GLU B 477 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B 490 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU B 491 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 542 removed outlier: 3.961A pdb=" N ILE B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 516 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU B 535 " --> pdb=" O ASN B 531 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 578 removed outlier: 3.761A pdb=" N PHE B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 593 removed outlier: 3.739A pdb=" N SER B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 620 removed outlier: 3.959A pdb=" N PHE B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 642 removed outlier: 3.530A pdb=" N CYS B 632 " --> pdb=" O THR B 628 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.413A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 693 removed outlier: 3.731A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 242 removed outlier: 3.726A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 255 removed outlier: 3.767A pdb=" N MET C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.921A pdb=" N ARG C 338 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C 339 " --> pdb=" O ASP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 removed outlier: 3.755A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 412 removed outlier: 3.588A pdb=" N THR C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 498 removed outlier: 4.139A pdb=" N CYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE C 479 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C 482 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 487 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 490 " --> pdb=" O TYR C 486 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU C 491 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 542 removed outlier: 3.960A pdb=" N ILE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 516 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 538 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 578 removed outlier: 3.760A pdb=" N PHE C 568 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C 574 " --> pdb=" O TRP C 570 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 removed outlier: 3.739A pdb=" N SER C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR C 588 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 591 " --> pdb=" O SER C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 620 removed outlier: 3.959A pdb=" N PHE C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C 599 " --> pdb=" O LYS C 595 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 602 " --> pdb=" O PHE C 598 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 642 removed outlier: 3.530A pdb=" N CYS C 632 " --> pdb=" O THR C 628 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 640 " --> pdb=" O GLN C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 653 removed outlier: 4.412A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 693 removed outlier: 3.731A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 673 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE C 679 " --> pdb=" O MET C 675 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 683 " --> pdb=" O ILE C 679 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 242 removed outlier: 3.726A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 255 removed outlier: 3.767A pdb=" N MET D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.921A pdb=" N ARG D 338 " --> pdb=" O GLN D 335 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP D 339 " --> pdb=" O ASP D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 removed outlier: 3.755A pdb=" N TRP D 366 " --> pdb=" O GLY D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.588A pdb=" N THR D 402 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL D 406 " --> pdb=" O THR D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 498 removed outlier: 4.139A pdb=" N CYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS D 481 " --> pdb=" O GLU D 477 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE D 482 " --> pdb=" O ILE D 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 487 " --> pdb=" O PHE D 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 490 " --> pdb=" O TYR D 486 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU D 491 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 542 removed outlier: 3.961A pdb=" N ILE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 516 " --> pdb=" O VAL D 512 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE D 526 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU D 535 " --> pdb=" O ASN D 531 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 538 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 578 removed outlier: 3.761A pdb=" N PHE D 568 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE D 574 " --> pdb=" O TRP D 570 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 593 removed outlier: 3.739A pdb=" N SER D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 620 removed outlier: 3.959A pdb=" N PHE D 598 " --> pdb=" O ALA D 594 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D 602 " --> pdb=" O PHE D 598 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 642 removed outlier: 3.530A pdb=" N CYS D 632 " --> pdb=" O THR D 628 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE D 640 " --> pdb=" O GLN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 removed outlier: 4.413A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 650 " --> pdb=" O PHE D 646 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN D 653 " --> pdb=" O ILE D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 693 removed outlier: 3.731A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU D 673 " --> pdb=" O PHE D 669 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE D 679 " --> pdb=" O MET D 675 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 683 " --> pdb=" O ILE D 679 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.571A pdb=" N ASP A 425 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.571A pdb=" N ASP A 425 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 458 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 393 through 394 removed outlier: 3.570A pdb=" N ASP B 425 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 393 through 394 removed outlier: 3.570A pdb=" N ASP B 425 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 458 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 393 through 394 removed outlier: 3.571A pdb=" N ASP C 425 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 393 through 394 removed outlier: 3.571A pdb=" N ASP C 425 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 458 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 393 through 394 removed outlier: 3.570A pdb=" N ASP D 425 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 393 through 394 removed outlier: 3.570A pdb=" N ASP D 425 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 458 " --> pdb=" O VAL D 438 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1971 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: 2.41 Time building geometry restraints manager: 2.03 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: 2492 1.31 - 1.43: 5007 1.43 - 1.56: 9192 1.56 - 1.68: 21 1.68 - 1.81: 116 Bond restraints: 16828 Sorted by residual: bond pdb=" O2 PX6 B1007 " pdb=" P1 PX6 B1007 " ideal model delta sigma weight residual 1.526 1.650 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" O2 PX6 D1007 " pdb=" P1 PX6 D1007 " ideal model delta sigma weight residual 1.526 1.650 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" O2 PX6 A1007 " pdb=" P1 PX6 A1007 " ideal model delta sigma weight residual 1.526 1.650 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O2 PX6 C1007 " pdb=" P1 PX6 C1007 " ideal model delta sigma weight residual 1.526 1.649 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C4 PX6 B1007 " pdb=" O5 PX6 B1007 " ideal model delta sigma weight residual 1.325 1.416 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 16823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 22292 4.00 - 7.99: 384 7.99 - 11.99: 24 11.99 - 15.98: 8 15.98 - 19.98: 4 Bond angle restraints: 22712 Sorted by residual: angle pdb=" C ALA A 384 " pdb=" N THR A 385 " pdb=" CA THR A 385 " ideal model delta sigma weight residual 121.70 134.60 -12.90 1.80e+00 3.09e-01 5.14e+01 angle pdb=" C ALA C 384 " pdb=" N THR C 385 " pdb=" CA THR C 385 " ideal model delta sigma weight residual 121.70 134.55 -12.85 1.80e+00 3.09e-01 5.09e+01 angle pdb=" C ALA B 384 " pdb=" N THR B 385 " pdb=" CA THR B 385 " ideal model delta sigma weight residual 121.70 134.53 -12.83 1.80e+00 3.09e-01 5.08e+01 angle pdb=" C ALA D 384 " pdb=" N THR D 385 " pdb=" CA THR D 385 " ideal model delta sigma weight residual 121.70 134.50 -12.80 1.80e+00 3.09e-01 5.06e+01 angle pdb=" C2 PX6 B1007 " pdb=" C3 PX6 B1007 " pdb=" O5 PX6 B1007 " ideal model delta sigma weight residual 110.56 130.54 -19.98 3.00e+00 1.11e-01 4.44e+01 ... (remaining 22707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 8866 16.82 - 33.63: 556 33.63 - 50.45: 129 50.45 - 67.27: 69 67.27 - 84.08: 16 Dihedral angle restraints: 9636 sinusoidal: 3996 harmonic: 5640 Sorted by residual: dihedral pdb=" CA SER D 627 " pdb=" C SER D 627 " pdb=" N THR D 628 " pdb=" CA THR D 628 " ideal model delta harmonic sigma weight residual 180.00 137.07 42.93 0 5.00e+00 4.00e-02 7.37e+01 dihedral pdb=" CA SER C 627 " pdb=" C SER C 627 " pdb=" N THR C 628 " pdb=" CA THR C 628 " ideal model delta harmonic sigma weight residual 180.00 137.07 42.93 0 5.00e+00 4.00e-02 7.37e+01 dihedral pdb=" CA SER A 627 " pdb=" C SER A 627 " pdb=" N THR A 628 " pdb=" CA THR A 628 " ideal model delta harmonic sigma weight residual 180.00 137.09 42.91 0 5.00e+00 4.00e-02 7.37e+01 ... (remaining 9633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2061 0.080 - 0.160: 404 0.160 - 0.240: 69 0.240 - 0.321: 6 0.321 - 0.401: 8 Chirality restraints: 2548 Sorted by residual: chirality pdb=" C1 NAG D1004 " pdb=" O4 NAG D1003 " pdb=" C2 NAG D1004 " pdb=" O5 NAG D1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 4.01e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-02 2.50e+03 3.52e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-02 2.50e+03 3.24e+02 ... (remaining 2545 not shown) Planarity restraints: 2776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 362 " 0.088 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN C 362 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 362 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 362 " -0.140 2.00e-02 2.50e+03 pdb=" C1 NAG C1002 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 362 " -0.088 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN A 362 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 362 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 362 " 0.140 2.00e-02 2.50e+03 pdb=" C1 NAG A1002 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 362 " -0.088 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN D 362 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN D 362 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN D 362 " 0.140 2.00e-02 2.50e+03 pdb=" C1 NAG D1002 " -0.116 2.00e-02 2.50e+03 ... (remaining 2773 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 262 2.43 - 3.04: 13590 3.04 - 3.66: 26230 3.66 - 4.28: 39292 4.28 - 4.90: 57482 Nonbonded interactions: 136856 Sorted by model distance: nonbonded pdb=" CD1 LEU B 573 " pdb=" CD1 ILE C 606 " model vdw 1.806 3.880 nonbonded pdb=" CD1 LEU A 573 " pdb=" CD1 ILE B 606 " model vdw 1.829 3.880 nonbonded pdb=" O PHE D 310 " pdb=" OE1 GLU D 312 " model vdw 1.847 3.040 nonbonded pdb=" CD1 LEU C 573 " pdb=" CD1 ILE D 606 " model vdw 1.871 3.880 nonbonded pdb=" CD1 ILE A 606 " pdb=" CD1 LEU D 573 " model vdw 1.909 3.880 ... (remaining 136851 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 215 through 1002 or resid 1010)) selection = (chain 'B' and (resid 215 through 1002 or resid 1010)) selection = (chain 'C' and (resid 215 through 1002 or resid 1010)) selection = (chain 'D' and (resid 215 through 1002 or resid 1008)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 14.750 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 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 : 0.010 0.124 16844 Z= 0.473 Angle : 1.313 19.981 22760 Z= 0.650 Chirality : 0.068 0.401 2548 Planarity : 0.007 0.074 2764 Dihedral : 13.564 84.082 5988 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 56.95 Ramachandran Plot: Outliers : 0.48 % Allowed : 18.47 % Favored : 81.05 % Rotamer: Outliers : 0.82 % Allowed : 1.75 % Favored : 97.44 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 1.08 % 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: -5.74 (0.14), residues: 1884 helix: -4.86 (0.07), residues: 852 sheet: -3.20 (0.28), residues: 196 loop : -2.57 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 397 TYR 0.029 0.004 TYR A 248 PHE 0.032 0.004 PHE A 445 TRP 0.046 0.005 TRP D 366 HIS 0.010 0.003 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00988 / 0.47 (16828) covalent geometry : angle 1.27678 / 0.64 (22712) hydrogen bonds : bond 0.40427 / 25.67 ( 685) hydrogen bonds : angle 11.52365 / 7.79 ( 1971) link_BETA1-4 : bond 0.10394 / 5.21 ( 4) link_BETA1-4 : angle 7.72521 / 3.78 ( 12) link_NAG-ASN : bond 0.02356 / 1.27 ( 12) link_NAG-ASN : angle 6.42694 / 3.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 563 time to evaluate : 0.544 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: 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: 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 309 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5470 (mm) REVERT: A 313 ASN cc_start: 0.7196 (m-40) cc_final: 0.6806 (m110) REVERT: A 324 LEU cc_start: 0.8403 (mt) cc_final: 0.8140 (mp) REVERT: A 358 PHE cc_start: 0.7193 (t80) cc_final: 0.6980 (t80) REVERT: A 460 LEU cc_start: 0.8672 (tp) cc_final: 0.8434 (tp) REVERT: A 663 THR cc_start: 0.9005 (p) cc_final: 0.8584 (p) REVERT: A 676 PHE cc_start: 0.7792 (m-10) cc_final: 0.7232 (m-80) REVERT: B 283 THR cc_start: 0.8882 (p) cc_final: 0.8618 (p) REVERT: B 309 ILE cc_start: 0.5893 (OUTLIER) cc_final: 0.5551 (mm) REVERT: B 313 ASN cc_start: 0.7208 (m-40) cc_final: 0.6843 (m110) REVERT: B 324 LEU cc_start: 0.8129 (mt) cc_final: 0.7894 (mp) REVERT: B 460 LEU cc_start: 0.8710 (tp) cc_final: 0.8329 (tp) REVERT: B 504 ARG cc_start: 0.4800 (tpt90) cc_final: 0.2593 (ttp80) REVERT: B 663 THR cc_start: 0.9174 (p) cc_final: 0.8765 (p) REVERT: B 676 PHE cc_start: 0.7720 (m-10) cc_final: 0.7272 (m-80) REVERT: B 683 THR cc_start: 0.7541 (p) cc_final: 0.7279 (t) REVERT: C 313 ASN cc_start: 0.7196 (m-40) cc_final: 0.6855 (m110) REVERT: C 324 LEU cc_start: 0.8298 (mt) cc_final: 0.7974 (mp) REVERT: C 358 PHE cc_start: 0.7072 (t80) cc_final: 0.6833 (t80) REVERT: C 460 LEU cc_start: 0.8651 (tp) cc_final: 0.8398 (tp) REVERT: C 663 THR cc_start: 0.9048 (p) cc_final: 0.8677 (p) REVERT: C 676 PHE cc_start: 0.7806 (m-10) cc_final: 0.7242 (m-80) REVERT: D 313 ASN cc_start: 0.6894 (m-40) cc_final: 0.6673 (m110) REVERT: D 324 LEU cc_start: 0.8365 (mt) cc_final: 0.8053 (mp) REVERT: D 358 PHE cc_start: 0.7084 (t80) cc_final: 0.6859 (t80) REVERT: D 663 THR cc_start: 0.9078 (p) cc_final: 0.8682 (p) REVERT: D 676 PHE cc_start: 0.7782 (m-10) cc_final: 0.7067 (m-80) REVERT: D 683 THR cc_start: 0.7608 (p) cc_final: 0.7347 (t) outliers start: 14 outliers final: 7 residues processed: 577 average time/residue: 0.1145 time to fit residues: 102.9188 Evaluate side-chains 379 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 370 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 GLN A 458 GLN A 498 HIS A 550 HIS A 555 GLN A 613 GLN A 622 GLN B 434 ASN B 458 GLN B 498 HIS B 550 HIS ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 653 ASN C 458 GLN C 498 HIS C 550 HIS C 555 GLN C 613 GLN C 622 GLN D 458 GLN D 498 HIS D 550 HIS D 555 GLN D 613 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.164905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.134785 restraints weight = 38210.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.138621 restraints weight = 24168.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.140575 restraints weight = 17253.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.142907 restraints weight = 14064.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.143849 restraints weight = 11968.269| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16844 Z= 0.256 Angle : 1.002 12.833 22760 Z= 0.532 Chirality : 0.057 0.250 2548 Planarity : 0.008 0.080 2764 Dihedral : 13.783 59.688 2392 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 1.11 % Allowed : 4.66 % Favored : 94.23 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.16), residues: 1884 helix: -2.89 (0.13), residues: 896 sheet: -3.12 (0.32), residues: 188 loop : -2.99 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 320 TYR 0.026 0.003 TYR C 227 PHE 0.031 0.003 PHE B 480 TRP 0.037 0.004 TRP C 280 HIS 0.006 0.002 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 (16828) covalent geometry : angle 0.98675 / 0.53 (22712) hydrogen bonds : bond 0.09308 / 5.89 ( 685) hydrogen bonds : angle 7.47227 / 5.05 ( 1971) link_BETA1-4 : bond 0.00839 / 0.42 ( 4) link_BETA1-4 : angle 4.62896 / 2.15 ( 12) link_NAG-ASN : bond 0.00767 / 0.46 ( 12) link_NAG-ASN : angle 3.61607 / 2.10 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 498 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 280 TRP cc_start: 0.7908 (m-10) cc_final: 0.7519 (m-10) REVERT: A 282 PHE cc_start: 0.8066 (t80) cc_final: 0.7859 (t80) REVERT: A 341 ILE cc_start: 0.1923 (pt) cc_final: 0.1639 (pt) REVERT: A 345 TYR cc_start: 0.7332 (m-80) cc_final: 0.7040 (m-10) REVERT: A 358 PHE cc_start: 0.6680 (t80) cc_final: 0.6450 (t80) REVERT: A 414 TRP cc_start: 0.7045 (m-90) cc_final: 0.5697 (m-90) REVERT: A 439 VAL cc_start: 0.7748 (t) cc_final: 0.7107 (t) REVERT: A 501 HIS cc_start: 0.6013 (t-90) cc_final: 0.5082 (m170) REVERT: A 567 PHE cc_start: 0.8510 (t80) cc_final: 0.8277 (t80) REVERT: A 616 TYR cc_start: 0.7088 (t80) cc_final: 0.6882 (t80) REVERT: A 631 GLU cc_start: 0.8306 (tt0) cc_final: 0.7936 (tt0) REVERT: A 676 PHE cc_start: 0.7964 (m-10) cc_final: 0.7689 (m-80) REVERT: B 241 MET cc_start: 0.7118 (ptp) cc_final: 0.6631 (ttp) REVERT: B 432 ASN cc_start: 0.8242 (m-40) cc_final: 0.8034 (m110) REVERT: B 501 HIS cc_start: 0.5772 (t-90) cc_final: 0.5033 (m170) REVERT: B 653 ASN cc_start: 0.7511 (m-40) cc_final: 0.7222 (m-40) REVERT: B 656 LEU cc_start: 0.8800 (tt) cc_final: 0.8578 (tt) REVERT: C 324 LEU cc_start: 0.8446 (mt) cc_final: 0.8231 (mp) REVERT: C 341 ILE cc_start: 0.1851 (pt) cc_final: 0.1567 (pt) REVERT: C 345 TYR cc_start: 0.7343 (m-80) cc_final: 0.7023 (m-10) REVERT: C 358 PHE cc_start: 0.6401 (t80) cc_final: 0.6180 (t80) REVERT: C 414 TRP cc_start: 0.6987 (m-90) cc_final: 0.5574 (m-90) REVERT: C 501 HIS cc_start: 0.6047 (t-90) cc_final: 0.5049 (m170) REVERT: C 631 GLU cc_start: 0.8246 (tt0) cc_final: 0.7883 (tt0) REVERT: C 633 ILE cc_start: 0.9095 (tp) cc_final: 0.8733 (tp) REVERT: C 676 PHE cc_start: 0.7873 (m-10) cc_final: 0.7659 (m-80) REVERT: D 241 MET cc_start: 0.7061 (ptp) cc_final: 0.6650 (ttp) REVERT: D 324 LEU cc_start: 0.8421 (mt) cc_final: 0.8183 (mp) REVERT: D 358 PHE cc_start: 0.6549 (t80) cc_final: 0.6343 (t80) REVERT: D 501 HIS cc_start: 0.6064 (t-90) cc_final: 0.5132 (m170) REVERT: D 631 GLU cc_start: 0.8218 (tt0) cc_final: 0.7826 (tt0) REVERT: D 633 ILE cc_start: 0.9070 (tp) cc_final: 0.8726 (tp) REVERT: D 676 PHE cc_start: 0.8004 (m-10) cc_final: 0.7590 (m-80) outliers start: 19 outliers final: 9 residues processed: 512 average time/residue: 0.1075 time to fit residues: 89.3478 Evaluate side-chains 399 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 390 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 GLN A 613 GLN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 613 GLN D 613 GLN D 622 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.167447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.138165 restraints weight = 38225.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.141695 restraints weight = 25968.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.143194 restraints weight = 19290.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.145047 restraints weight = 16233.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.146950 restraints weight = 13828.845| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16844 Z= 0.219 Angle : 0.886 13.958 22760 Z= 0.467 Chirality : 0.052 0.213 2548 Planarity : 0.006 0.067 2764 Dihedral : 13.199 59.691 2392 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.82 % Allowed : 4.72 % Favored : 94.46 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.97 (0.17), residues: 1884 helix: -2.16 (0.15), residues: 892 sheet: -2.97 (0.35), residues: 184 loop : -3.00 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 327 TYR 0.022 0.002 TYR C 227 PHE 0.028 0.002 PHE A 669 TRP 0.054 0.003 TRP C 280 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (16828) covalent geometry : angle 0.87341 / 0.47 (22712) hydrogen bonds : bond 0.07494 / 4.78 ( 685) hydrogen bonds : angle 6.81298 / 4.63 ( 1971) link_BETA1-4 : bond 0.00495 / 0.25 ( 4) link_BETA1-4 : angle 4.46259 / 2.07 ( 12) link_NAG-ASN : bond 0.00587 / 0.32 ( 12) link_NAG-ASN : angle 2.80048 / 1.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 493 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 252 MET cc_start: 0.8292 (ptt) cc_final: 0.8088 (ptt) REVERT: A 269 ASN cc_start: 0.8369 (p0) cc_final: 0.8125 (p0) REVERT: A 341 ILE cc_start: 0.1612 (pt) cc_final: 0.1236 (pt) REVERT: A 345 TYR cc_start: 0.7484 (m-80) cc_final: 0.7162 (m-10) REVERT: A 501 HIS cc_start: 0.5894 (t-90) cc_final: 0.5072 (m170) REVERT: A 590 MET cc_start: 0.4120 (tmm) cc_final: 0.3796 (tmm) REVERT: A 621 THR cc_start: 0.8420 (p) cc_final: 0.8188 (t) REVERT: B 269 ASN cc_start: 0.8007 (p0) cc_final: 0.7709 (p0) REVERT: B 501 HIS cc_start: 0.5753 (t-90) cc_final: 0.5115 (m170) REVERT: B 571 ILE cc_start: 0.9175 (pt) cc_final: 0.8970 (pt) REVERT: B 667 PHE cc_start: 0.7942 (t80) cc_final: 0.7728 (t80) REVERT: C 252 MET cc_start: 0.8185 (ptt) cc_final: 0.7979 (ptt) REVERT: C 269 ASN cc_start: 0.8410 (p0) cc_final: 0.8148 (p0) REVERT: C 341 ILE cc_start: 0.2031 (pt) cc_final: 0.1810 (pt) REVERT: C 414 TRP cc_start: 0.7014 (m-90) cc_final: 0.5982 (m-90) REVERT: C 426 PHE cc_start: 0.7476 (p90) cc_final: 0.7132 (p90) REVERT: C 501 HIS cc_start: 0.5774 (t-90) cc_final: 0.5037 (m170) REVERT: C 556 ILE cc_start: 0.9295 (mt) cc_final: 0.8580 (mt) REVERT: C 560 ASN cc_start: 0.8794 (m-40) cc_final: 0.8130 (m-40) REVERT: D 269 ASN cc_start: 0.8470 (p0) cc_final: 0.8176 (p0) REVERT: D 501 HIS cc_start: 0.5876 (t-90) cc_final: 0.5074 (m170) REVERT: D 590 MET cc_start: 0.3945 (tmm) cc_final: 0.3506 (tmm) outliers start: 14 outliers final: 9 residues processed: 502 average time/residue: 0.1065 time to fit residues: 87.6018 Evaluate side-chains 383 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 374 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN A 622 GLN B 613 GLN C 613 GLN C 622 GLN D 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.164585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.134369 restraints weight = 37945.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.138176 restraints weight = 25120.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140422 restraints weight = 18365.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.142107 restraints weight = 14808.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.142938 restraints weight = 12801.750| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16844 Z= 0.244 Angle : 0.888 14.063 22760 Z= 0.466 Chirality : 0.055 0.373 2548 Planarity : 0.006 0.067 2764 Dihedral : 12.837 59.141 2392 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 0.12 % Allowed : 4.55 % Favored : 95.34 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -3.70 (0.18), residues: 1884 helix: -1.97 (0.15), residues: 900 sheet: -3.01 (0.35), residues: 184 loop : -2.78 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 320 TYR 0.018 0.002 TYR C 227 PHE 0.037 0.003 PHE A 605 TRP 0.052 0.003 TRP C 280 HIS 0.006 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 (16828) covalent geometry : angle 0.87291 / 0.46 (22712) hydrogen bonds : bond 0.06452 / 4.13 ( 685) hydrogen bonds : angle 6.46659 / 4.38 ( 1971) link_BETA1-4 : bond 0.00532 / 0.27 ( 4) link_BETA1-4 : angle 4.09784 / 1.91 ( 12) link_NAG-ASN : bond 0.00461 / 0.27 ( 12) link_NAG-ASN : angle 3.56259 / 1.93 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 438 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 269 ASN cc_start: 0.8456 (p0) cc_final: 0.8215 (p0) REVERT: A 295 MET cc_start: 0.7509 (mtm) cc_final: 0.7151 (mpp) REVERT: A 345 TYR cc_start: 0.7426 (m-80) cc_final: 0.7202 (m-10) REVERT: A 501 HIS cc_start: 0.5933 (t-90) cc_final: 0.5099 (m170) REVERT: A 590 MET cc_start: 0.4246 (tmm) cc_final: 0.3829 (tmm) REVERT: A 603 MET cc_start: 0.8167 (ptm) cc_final: 0.7907 (ptp) REVERT: A 616 TYR cc_start: 0.7079 (t80) cc_final: 0.6774 (t80) REVERT: A 621 THR cc_start: 0.8636 (p) cc_final: 0.8372 (t) REVERT: B 241 MET cc_start: 0.7135 (ptp) cc_final: 0.5781 (ttt) REVERT: B 324 LEU cc_start: 0.8427 (mt) cc_final: 0.8068 (mp) REVERT: B 501 HIS cc_start: 0.5684 (t-90) cc_final: 0.5027 (m170) REVERT: B 590 MET cc_start: 0.3919 (tmm) cc_final: 0.3531 (tmm) REVERT: B 621 THR cc_start: 0.8588 (p) cc_final: 0.8313 (t) REVERT: C 241 MET cc_start: 0.7190 (ptp) cc_final: 0.5642 (ttt) REVERT: C 269 ASN cc_start: 0.8499 (p0) cc_final: 0.8230 (p0) REVERT: C 295 MET cc_start: 0.7265 (mtm) cc_final: 0.7064 (mpp) REVERT: C 501 HIS cc_start: 0.5940 (t-90) cc_final: 0.5101 (m170) REVERT: C 556 ILE cc_start: 0.9164 (mt) cc_final: 0.8946 (mt) REVERT: C 557 GLN cc_start: 0.8473 (mt0) cc_final: 0.8118 (mt0) REVERT: C 590 MET cc_start: 0.3962 (tmm) cc_final: 0.3475 (tmm) REVERT: C 675 MET cc_start: 0.7497 (mmm) cc_final: 0.7148 (mmm) REVERT: D 241 MET cc_start: 0.7020 (ptp) cc_final: 0.5791 (ttt) REVERT: D 269 ASN cc_start: 0.8498 (p0) cc_final: 0.8264 (p0) REVERT: D 501 HIS cc_start: 0.5982 (t-90) cc_final: 0.5128 (m170) REVERT: D 590 MET cc_start: 0.3906 (tmm) cc_final: 0.3396 (tmm) REVERT: D 624 ASP cc_start: 0.7555 (m-30) cc_final: 0.7185 (m-30) outliers start: 2 outliers final: 2 residues processed: 440 average time/residue: 0.1085 time to fit residues: 77.5978 Evaluate side-chains 355 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 353 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 613 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 622 GLN D 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.169352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.139318 restraints weight = 37530.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.143147 restraints weight = 24248.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145479 restraints weight = 17589.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.147686 restraints weight = 14196.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.148457 restraints weight = 11869.372| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16844 Z= 0.184 Angle : 0.840 12.840 22760 Z= 0.437 Chirality : 0.051 0.222 2548 Planarity : 0.005 0.061 2764 Dihedral : 12.474 59.967 2392 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.39 (0.18), residues: 1884 helix: -1.73 (0.16), residues: 900 sheet: -2.79 (0.37), residues: 184 loop : -2.62 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 440 TYR 0.057 0.002 TYR C 227 PHE 0.034 0.002 PHE B 485 TRP 0.044 0.002 TRP B 280 HIS 0.005 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (16828) covalent geometry : angle 0.83043 / 0.44 (22712) hydrogen bonds : bond 0.05714 / 3.68 ( 685) hydrogen bonds : angle 6.10291 / 4.12 ( 1971) link_BETA1-4 : bond 0.00558 / 0.28 ( 4) link_BETA1-4 : angle 3.66450 / 1.71 ( 12) link_NAG-ASN : bond 0.00639 / 0.38 ( 12) link_NAG-ASN : angle 2.51604 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 269 ASN cc_start: 0.8383 (p0) cc_final: 0.8169 (p0) REVERT: A 295 MET cc_start: 0.7274 (mtm) cc_final: 0.7062 (mpp) REVERT: A 501 HIS cc_start: 0.5856 (t-90) cc_final: 0.5063 (m170) REVERT: A 590 MET cc_start: 0.4395 (tmm) cc_final: 0.3791 (tmm) REVERT: A 633 ILE cc_start: 0.8894 (tp) cc_final: 0.8581 (tp) REVERT: B 241 MET cc_start: 0.7225 (ptp) cc_final: 0.5739 (ttt) REVERT: B 324 LEU cc_start: 0.8289 (mt) cc_final: 0.8082 (mp) REVERT: B 460 LEU cc_start: 0.7922 (tp) cc_final: 0.7714 (tp) REVERT: B 501 HIS cc_start: 0.5594 (t-90) cc_final: 0.4945 (m90) REVERT: B 590 MET cc_start: 0.3916 (tmm) cc_final: 0.3611 (tmm) REVERT: C 269 ASN cc_start: 0.8399 (p0) cc_final: 0.8129 (p0) REVERT: C 501 HIS cc_start: 0.5841 (t-90) cc_final: 0.5044 (m170) REVERT: C 557 GLN cc_start: 0.8400 (mt0) cc_final: 0.7999 (mt0) REVERT: C 590 MET cc_start: 0.4005 (tmm) cc_final: 0.3330 (tmm) REVERT: C 616 TYR cc_start: 0.7013 (t80) cc_final: 0.6795 (t80) REVERT: C 621 THR cc_start: 0.8361 (p) cc_final: 0.8143 (t) REVERT: C 633 ILE cc_start: 0.8828 (tp) cc_final: 0.8520 (tp) REVERT: D 269 ASN cc_start: 0.8417 (p0) cc_final: 0.8159 (p0) REVERT: D 501 HIS cc_start: 0.5834 (t-90) cc_final: 0.5081 (m170) REVERT: D 590 MET cc_start: 0.4059 (tmm) cc_final: 0.3354 (tmm) REVERT: D 621 THR cc_start: 0.8331 (p) cc_final: 0.8127 (t) REVERT: D 633 ILE cc_start: 0.8890 (tp) cc_final: 0.8604 (tp) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.1105 time to fit residues: 81.7241 Evaluate side-chains 359 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 130 optimal weight: 0.0370 chunk 60 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 overall best weight: 4.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 GLN B 555 GLN B 622 GLN C 557 GLN C 622 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.164054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.133139 restraints weight = 38002.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.137012 restraints weight = 24935.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.139082 restraints weight = 18087.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.141258 restraints weight = 14871.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.141788 restraints weight = 12532.118| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16844 Z= 0.226 Angle : 0.847 13.816 22760 Z= 0.446 Chirality : 0.052 0.223 2548 Planarity : 0.005 0.065 2764 Dihedral : 12.478 59.903 2392 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.75 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 4.55 % Twisted General : 0.22 % 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: -3.32 (0.18), residues: 1884 helix: -1.67 (0.16), residues: 904 sheet: -2.82 (0.36), residues: 176 loop : -2.59 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 320 TYR 0.020 0.002 TYR C 227 PHE 0.029 0.003 PHE D 669 TRP 0.026 0.003 TRP C 280 HIS 0.006 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (16828) covalent geometry : angle 0.83980 / 0.45 (22712) hydrogen bonds : bond 0.05401 / 3.49 ( 685) hydrogen bonds : angle 5.92029 / 4.01 ( 1971) link_BETA1-4 : bond 0.00800 / 0.41 ( 4) link_BETA1-4 : angle 3.39431 / 1.62 ( 12) link_NAG-ASN : bond 0.00459 / 0.26 ( 12) link_NAG-ASN : angle 2.07485 / 1.17 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 501 HIS cc_start: 0.5907 (t-90) cc_final: 0.5092 (m170) REVERT: A 590 MET cc_start: 0.3928 (tmm) cc_final: 0.3611 (tmm) REVERT: A 633 ILE cc_start: 0.8794 (tp) cc_final: 0.8527 (tp) REVERT: B 501 HIS cc_start: 0.5718 (t-90) cc_final: 0.4975 (m90) REVERT: B 590 MET cc_start: 0.3998 (tmm) cc_final: 0.3600 (tmm) REVERT: B 608 PHE cc_start: 0.7776 (t80) cc_final: 0.5997 (t80) REVERT: C 269 ASN cc_start: 0.8477 (p0) cc_final: 0.8213 (p0) REVERT: C 501 HIS cc_start: 0.5864 (t-90) cc_final: 0.5056 (m170) REVERT: C 590 MET cc_start: 0.4070 (tmm) cc_final: 0.3618 (tmm) REVERT: C 616 TYR cc_start: 0.7000 (t80) cc_final: 0.6774 (t80) REVERT: C 633 ILE cc_start: 0.8793 (tp) cc_final: 0.8494 (tp) REVERT: D 244 SER cc_start: 0.8274 (p) cc_final: 0.8068 (m) REVERT: D 269 ASN cc_start: 0.8407 (p0) cc_final: 0.8103 (p0) REVERT: D 501 HIS cc_start: 0.5940 (t-90) cc_final: 0.5100 (m170) REVERT: D 590 MET cc_start: 0.3908 (tmm) cc_final: 0.3559 (tmm) REVERT: D 633 ILE cc_start: 0.8836 (tp) cc_final: 0.8559 (tp) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.1062 time to fit residues: 76.7946 Evaluate side-chains 361 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 622 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.164209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.133223 restraints weight = 38022.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137081 restraints weight = 25014.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.139003 restraints weight = 18187.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.141391 restraints weight = 15098.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.141586 restraints weight = 12527.307| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16844 Z= 0.232 Angle : 0.885 13.299 22760 Z= 0.460 Chirality : 0.055 0.450 2548 Planarity : 0.005 0.061 2764 Dihedral : 12.498 59.581 2392 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.29 (0.18), residues: 1884 helix: -1.66 (0.16), residues: 900 sheet: -2.69 (0.38), residues: 176 loop : -2.57 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 251 TYR 0.028 0.002 TYR C 227 PHE 0.035 0.003 PHE B 669 TRP 0.038 0.003 TRP A 570 HIS 0.006 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (16828) covalent geometry : angle 0.86591 / 0.46 (22712) hydrogen bonds : bond 0.05385 / 3.49 ( 685) hydrogen bonds : angle 5.91215 / 3.99 ( 1971) link_BETA1-4 : bond 0.00443 / 0.22 ( 4) link_BETA1-4 : angle 3.25988 / 1.54 ( 12) link_NAG-ASN : bond 0.00616 / 0.35 ( 12) link_NAG-ASN : angle 4.35822 / 2.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 252 MET cc_start: 0.8487 (ptt) cc_final: 0.8153 (ptt) REVERT: A 501 HIS cc_start: 0.5932 (t-90) cc_final: 0.5083 (m170) REVERT: A 590 MET cc_start: 0.4031 (tmm) cc_final: 0.3665 (tmm) REVERT: A 633 ILE cc_start: 0.8772 (tp) cc_final: 0.8444 (tp) REVERT: B 501 HIS cc_start: 0.5677 (t-90) cc_final: 0.4955 (m170) REVERT: B 504 ARG cc_start: 0.4228 (tpt90) cc_final: 0.3258 (ptt-90) REVERT: B 590 MET cc_start: 0.4118 (tmm) cc_final: 0.3686 (tmm) REVERT: B 667 PHE cc_start: 0.8123 (t80) cc_final: 0.7782 (t80) REVERT: C 269 ASN cc_start: 0.8430 (p0) cc_final: 0.8106 (p0) REVERT: C 414 TRP cc_start: 0.7617 (m-90) cc_final: 0.7192 (m-90) REVERT: C 501 HIS cc_start: 0.5885 (t-90) cc_final: 0.5069 (m170) REVERT: C 590 MET cc_start: 0.4322 (tmm) cc_final: 0.3858 (tmm) REVERT: C 633 ILE cc_start: 0.8842 (tp) cc_final: 0.8544 (tp) REVERT: D 313 ASN cc_start: 0.8730 (t0) cc_final: 0.8422 (t0) REVERT: D 414 TRP cc_start: 0.7552 (m-90) cc_final: 0.7108 (m-90) REVERT: D 501 HIS cc_start: 0.5944 (t-90) cc_final: 0.5093 (m170) REVERT: D 590 MET cc_start: 0.4037 (tmm) cc_final: 0.3631 (tmm) REVERT: D 633 ILE cc_start: 0.8809 (tp) cc_final: 0.8510 (tp) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1060 time to fit residues: 78.0937 Evaluate side-chains 358 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 110 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 178 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.168192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137425 restraints weight = 39424.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.141536 restraints weight = 25723.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.143582 restraints weight = 18680.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.146138 restraints weight = 15372.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.147189 restraints weight = 12571.583| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16844 Z= 0.176 Angle : 0.830 12.617 22760 Z= 0.431 Chirality : 0.052 0.339 2548 Planarity : 0.005 0.061 2764 Dihedral : 12.110 59.805 2392 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.24 (0.19), residues: 1884 helix: -1.71 (0.15), residues: 928 sheet: -2.78 (0.38), residues: 176 loop : -2.38 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 399 TYR 0.047 0.002 TYR D 227 PHE 0.035 0.002 PHE A 669 TRP 0.026 0.002 TRP A 570 HIS 0.004 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (16828) covalent geometry : angle 0.82008 / 0.43 (22712) hydrogen bonds : bond 0.04898 / 3.19 ( 685) hydrogen bonds : angle 5.74275 / 3.87 ( 1971) link_BETA1-4 : bond 0.00502 / 0.25 ( 4) link_BETA1-4 : angle 3.07013 / 1.44 ( 12) link_NAG-ASN : bond 0.00518 / 0.30 ( 12) link_NAG-ASN : angle 2.90247 / 1.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 262 VAL cc_start: 0.7543 (m) cc_final: 0.7256 (p) REVERT: A 313 ASN cc_start: 0.8196 (t0) cc_final: 0.7904 (t0) REVERT: A 501 HIS cc_start: 0.5899 (t-90) cc_final: 0.5046 (m170) REVERT: A 633 ILE cc_start: 0.8675 (tp) cc_final: 0.8364 (tp) REVERT: B 313 ASN cc_start: 0.8283 (t0) cc_final: 0.7907 (t0) REVERT: B 414 TRP cc_start: 0.7192 (m-90) cc_final: 0.6785 (m-90) REVERT: B 501 HIS cc_start: 0.5674 (t-90) cc_final: 0.4927 (m90) REVERT: B 504 ARG cc_start: 0.4103 (tpt90) cc_final: 0.2995 (ptt-90) REVERT: B 590 MET cc_start: 0.4149 (tmm) cc_final: 0.3752 (tmm) REVERT: B 633 ILE cc_start: 0.8476 (tp) cc_final: 0.8076 (tp) REVERT: C 269 ASN cc_start: 0.8299 (p0) cc_final: 0.8046 (p0) REVERT: C 414 TRP cc_start: 0.7406 (m-90) cc_final: 0.7074 (m-90) REVERT: C 501 HIS cc_start: 0.5834 (t-90) cc_final: 0.4999 (m170) REVERT: C 590 MET cc_start: 0.4119 (tmm) cc_final: 0.3632 (tmm) REVERT: C 633 ILE cc_start: 0.8697 (tp) cc_final: 0.8390 (tp) REVERT: D 313 ASN cc_start: 0.8752 (t0) cc_final: 0.8319 (t0) REVERT: D 414 TRP cc_start: 0.7154 (m-90) cc_final: 0.6921 (m-90) REVERT: D 501 HIS cc_start: 0.5872 (t-90) cc_final: 0.5071 (m170) REVERT: D 590 MET cc_start: 0.3905 (tmm) cc_final: 0.3686 (tmm) REVERT: D 633 ILE cc_start: 0.8722 (tp) cc_final: 0.8437 (tp) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1057 time to fit residues: 78.3514 Evaluate side-chains 363 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 173 optimal weight: 0.0670 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN B 555 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN D 434 ASN D 622 GLN ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.170385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.139665 restraints weight = 39733.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.143684 restraints weight = 25833.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.145768 restraints weight = 18619.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.148508 restraints weight = 15346.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.148400 restraints weight = 12800.158| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16844 Z= 0.170 Angle : 0.811 14.025 22760 Z= 0.422 Chirality : 0.051 0.276 2548 Planarity : 0.005 0.045 2764 Dihedral : 11.798 59.929 2392 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.12 % Allowed : 0.64 % Favored : 99.24 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.19 (0.19), residues: 1884 helix: -1.67 (0.15), residues: 960 sheet: -3.02 (0.36), residues: 184 loop : -2.28 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 355 TYR 0.042 0.002 TYR A 227 PHE 0.023 0.002 PHE D 669 TRP 0.024 0.002 TRP A 570 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (16828) covalent geometry : angle 0.80398 / 0.42 (22712) hydrogen bonds : bond 0.04688 / 3.06 ( 685) hydrogen bonds : angle 5.61584 / 3.80 ( 1971) link_BETA1-4 : bond 0.00620 / 0.31 ( 4) link_BETA1-4 : angle 2.88487 / 1.36 ( 12) link_NAG-ASN : bond 0.00464 / 0.26 ( 12) link_NAG-ASN : angle 2.39252 / 1.29 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 435 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 262 VAL cc_start: 0.7443 (m) cc_final: 0.7155 (p) REVERT: A 414 TRP cc_start: 0.7130 (m-90) cc_final: 0.6811 (m-90) REVERT: A 501 HIS cc_start: 0.5883 (t-90) cc_final: 0.5033 (m170) REVERT: A 633 ILE cc_start: 0.8616 (tp) cc_final: 0.8327 (tp) REVERT: A 676 PHE cc_start: 0.7685 (p90) cc_final: 0.7162 (p90) REVERT: B 227 TYR cc_start: 0.8333 (m-80) cc_final: 0.7991 (m-80) REVERT: B 313 ASN cc_start: 0.8452 (t0) cc_final: 0.8086 (t0) REVERT: B 414 TRP cc_start: 0.7069 (m-90) cc_final: 0.6841 (m-90) REVERT: B 501 HIS cc_start: 0.5707 (t-90) cc_final: 0.4951 (m90) REVERT: B 590 MET cc_start: 0.4125 (tmm) cc_final: 0.3730 (tmm) REVERT: B 633 ILE cc_start: 0.8209 (tp) cc_final: 0.7847 (tp) REVERT: C 223 GLU cc_start: 0.7847 (tt0) cc_final: 0.7479 (mm-30) REVERT: C 269 ASN cc_start: 0.8228 (p0) cc_final: 0.7974 (p0) REVERT: C 501 HIS cc_start: 0.5873 (t-90) cc_final: 0.4996 (m170) REVERT: C 590 MET cc_start: 0.3986 (tmm) cc_final: 0.3774 (tmm) REVERT: C 633 ILE cc_start: 0.8649 (tp) cc_final: 0.8369 (tp) REVERT: D 313 ASN cc_start: 0.8657 (t0) cc_final: 0.8275 (t0) REVERT: D 501 HIS cc_start: 0.5857 (t-90) cc_final: 0.5032 (m170) REVERT: D 633 ILE cc_start: 0.8635 (tp) cc_final: 0.8398 (tp) outliers start: 2 outliers final: 0 residues processed: 435 average time/residue: 0.1065 time to fit residues: 75.4868 Evaluate side-chains 352 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 97 optimal weight: 0.3980 chunk 119 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.167559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.137037 restraints weight = 39950.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.141036 restraints weight = 26209.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.142848 restraints weight = 18978.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.144483 restraints weight = 15843.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.147142 restraints weight = 13527.278| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16844 Z= 0.210 Angle : 0.849 13.018 22760 Z= 0.441 Chirality : 0.052 0.275 2548 Planarity : 0.005 0.046 2764 Dihedral : 11.823 59.038 2392 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.10 (0.18), residues: 1884 helix: -1.51 (0.15), residues: 948 sheet: -2.96 (0.37), residues: 184 loop : -2.38 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 251 TYR 0.045 0.002 TYR B 227 PHE 0.025 0.002 PHE A 669 TRP 0.029 0.003 TRP A 570 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (16828) covalent geometry : angle 0.84204 / 0.44 (22712) hydrogen bonds : bond 0.04837 / 3.15 ( 685) hydrogen bonds : angle 5.62537 / 3.79 ( 1971) link_BETA1-4 : bond 0.00513 / 0.26 ( 4) link_BETA1-4 : angle 2.90188 / 1.37 ( 12) link_NAG-ASN : bond 0.00535 / 0.30 ( 12) link_NAG-ASN : angle 2.35481 / 1.27 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 262 VAL cc_start: 0.7169 (m) cc_final: 0.6926 (p) REVERT: A 414 TRP cc_start: 0.7130 (m-90) cc_final: 0.6898 (m-90) REVERT: A 501 HIS cc_start: 0.6065 (t-90) cc_final: 0.5134 (m170) REVERT: A 633 ILE cc_start: 0.8706 (tp) cc_final: 0.8432 (tp) REVERT: A 676 PHE cc_start: 0.7745 (p90) cc_final: 0.6976 (p90) REVERT: B 313 ASN cc_start: 0.8298 (t0) cc_final: 0.8005 (t0) REVERT: B 414 TRP cc_start: 0.7205 (m-90) cc_final: 0.6989 (m-90) REVERT: B 501 HIS cc_start: 0.5922 (t-90) cc_final: 0.5033 (m170) REVERT: B 590 MET cc_start: 0.4118 (tmm) cc_final: 0.3722 (tmm) REVERT: B 633 ILE cc_start: 0.8276 (tp) cc_final: 0.7987 (tp) REVERT: C 501 HIS cc_start: 0.6007 (t-90) cc_final: 0.5079 (m170) REVERT: C 590 MET cc_start: 0.4244 (tmm) cc_final: 0.3989 (tmm) REVERT: C 633 ILE cc_start: 0.8701 (tp) cc_final: 0.8437 (tp) REVERT: D 501 HIS cc_start: 0.6037 (t-90) cc_final: 0.5142 (m170) REVERT: D 633 ILE cc_start: 0.8690 (tp) cc_final: 0.8453 (tp) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.1030 time to fit residues: 69.0253 Evaluate side-chains 337 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 166 optimal weight: 9.9990 chunk 121 optimal weight: 0.0270 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 ASN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN B 555 GLN B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.171608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.141087 restraints weight = 39810.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.145231 restraints weight = 26061.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.147256 restraints weight = 18859.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.149450 restraints weight = 15514.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.151832 restraints weight = 12899.515| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16844 Z= 0.163 Angle : 0.806 11.150 22760 Z= 0.416 Chirality : 0.050 0.249 2548 Planarity : 0.004 0.045 2764 Dihedral : 11.519 59.665 2392 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % 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: -3.11 (0.18), residues: 1884 helix: -1.52 (0.15), residues: 984 sheet: -2.49 (0.41), residues: 164 loop : -2.56 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 251 TYR 0.033 0.002 TYR B 227 PHE 0.036 0.002 PHE C 669 TRP 0.019 0.002 TRP A 570 HIS 0.003 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16828) covalent geometry : angle 0.79922 / 0.42 (22712) hydrogen bonds : bond 0.04474 / 2.91 ( 685) hydrogen bonds : angle 5.51528 / 3.71 ( 1971) link_BETA1-4 : bond 0.00481 / 0.24 ( 4) link_BETA1-4 : angle 2.74527 / 1.30 ( 12) link_NAG-ASN : bond 0.00462 / 0.26 ( 12) link_NAG-ASN : angle 2.18734 / 1.20 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2855.20 seconds wall clock time: 50 minutes 22.94 seconds (3022.94 seconds total)