Starting phenix.real_space_refine on Sat Sep 12 14:56:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5mkf_3524/09_2026/5mkf_3524.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mkf_3524/09_2026/5mkf_3524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5mkf_3524/09_2026/5mkf_3524.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5mkf_3524/09_2026/5mkf_3524.cif" model { file = "/net/cci-nas-00/data/ceres_data/5mkf_3524/09_2026/5mkf_3524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mkf_3524/09_2026/5mkf_3524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5mkf_3524/09_2026/5mkf_3524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mkf_3524/09_2026/5mkf_3524.map" } resolution = 4.2 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= 0.007 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 5 9.91 5 P 4 5.49 5 S 73 5.16 5 C 11006 2.51 5 N 2544 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 16620 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3962 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 469} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3959 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 469} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3959 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 469} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3959 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 469} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 170 Unusual residues: {' CA': 4, 'CHS': 2, 'NAG': 3, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 167 Unusual residues: {' CA': 1, 'CHS': 2, 'NAG': 3, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 166 Unusual residues: {'CHS': 2, 'NAG': 3, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 166 Unusual residues: {'CHS': 2, 'NAG': 3, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.33, per 1000 atoms: 0.20 Number of scatterers: 16620 At special positions: 0 Unit cell: (115.14, 115.14, 103.74, 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 5 19.99 S 73 16.00 P 4 15.00 O 2988 8.00 N 2544 7.00 C 11006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.02 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.02 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.02 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.02 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 Atom "HETATM16133 O5 NAG B1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM15963 O5 NAG A1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM16300 O5 NAG C1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM16466 O5 NAG D1001 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1001 " - " ASN A 328 " " NAG A1002 " - " ASN A 362 " " NAG A1005 " - " ASN A 299 " " NAG B1001 " - " ASN B 328 " " NAG B1002 " - " ASN B 362 " " NAG B1005 " - " ASN B 299 " " NAG C1001 " - " ASN C 328 " " NAG C1002 " - " ASN C 362 " " NAG C1005 " - " ASN C 299 " " NAG D1001 " - " ASN D 328 " " NAG D1002 " - " ASN D 362 " " NAG D1005 " - " ASN D 299 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 375 " " NAG G 1 " - " ASN C 375 " " NAG H 1 " - " ASN D 375 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 649.7 milliseconds 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB CHS A1010 " pdb=" CB CHS A1011 " pdb=" CB CHS B1010 " pdb=" CB CHS B1011 " pdb=" CB CHS C1010 " pdb=" CB CHS C1011 " pdb=" CB CHS D1010 " pdb=" CB CHS D1011 " Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 60.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 215 through 242 removed outlier: 3.917A pdb=" N SER A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 239 " --> pdb=" O CYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.507A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.566A pdb=" N TYR A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.163A pdb=" N ASP A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 398 through 413 removed outlier: 3.717A pdb=" N ALA A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 498 removed outlier: 3.632A pdb=" N ALA A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.682A pdb=" N VAL A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 527 removed outlier: 3.724A pdb=" N VAL A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 536 removed outlier: 4.078A pdb=" N VAL A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 548 through 577 removed outlier: 3.955A pdb=" N TRP A 554 " --> pdb=" O HIS A 550 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 571 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 601 removed outlier: 4.397A pdb=" N GLN A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 597 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY A 599 " --> pdb=" O LYS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 620 removed outlier: 3.657A pdb=" N TYR A 611 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 642 removed outlier: 4.623A pdb=" N PHE A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 4.080A pdb=" N GLU A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 693 removed outlier: 3.756A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 678 " --> pdb=" O ASN A 674 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 242 removed outlier: 3.651A pdb=" N GLU B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 239 " --> pdb=" O CYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.507A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.566A pdb=" N TYR B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 4.164A pdb=" N ASP B 339 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 398 through 413 removed outlier: 3.718A pdb=" N ALA B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 498 removed outlier: 3.633A pdb=" N ALA B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 3.682A pdb=" N VAL B 512 " --> pdb=" O ASN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 527 removed outlier: 3.724A pdb=" N VAL B 520 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 524 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 536 removed outlier: 4.078A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 548 through 577 removed outlier: 3.956A pdb=" N TRP B 554 " --> pdb=" O HIS B 550 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 565 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP B 570 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE B 576 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 601 removed outlier: 4.397A pdb=" N GLN B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 594 " --> pdb=" O MET B 590 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 597 " --> pdb=" O CYS B 593 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 620 removed outlier: 3.657A pdb=" N TYR B 611 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 642 removed outlier: 4.622A pdb=" N PHE B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.080A pdb=" N GLU B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 693 removed outlier: 3.757A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 678 " --> pdb=" O ASN B 674 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 684 " --> pdb=" O ILE B 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 242 removed outlier: 3.651A pdb=" N GLU C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 239 " --> pdb=" O CYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.506A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 286 through 292 removed outlier: 3.567A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 339 removed outlier: 4.164A pdb=" N ASP C 339 " --> pdb=" O ASP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 398 through 413 removed outlier: 3.717A pdb=" N ALA C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 498 removed outlier: 3.632A pdb=" N ALA C 475 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 487 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.681A pdb=" N VAL C 512 " --> pdb=" O ASN C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 527 removed outlier: 3.723A pdb=" N VAL C 520 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 524 " --> pdb=" O VAL C 520 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 536 removed outlier: 4.079A pdb=" N VAL C 532 " --> pdb=" O ARG C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 548 through 577 removed outlier: 3.955A pdb=" N TRP C 554 " --> pdb=" O HIS C 550 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 565 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 571 " --> pdb=" O PHE C 567 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE C 576 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 601 removed outlier: 4.397A pdb=" N GLN C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR C 588 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA C 594 " --> pdb=" O MET C 590 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 597 " --> pdb=" O CYS C 593 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY C 599 " --> pdb=" O LYS C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 620 removed outlier: 3.657A pdb=" N TYR C 611 " --> pdb=" O ILE C 607 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 642 removed outlier: 4.622A pdb=" N PHE C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE C 640 " --> pdb=" O GLN C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 653 removed outlier: 4.081A pdb=" N GLU C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 693 removed outlier: 3.756A pdb=" N ILE C 659 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU C 673 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 678 " --> pdb=" O ASN C 674 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 683 " --> pdb=" O ILE C 679 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 684 " --> pdb=" O ILE C 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 242 removed outlier: 3.651A pdb=" N GLU D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 239 " --> pdb=" O CYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.507A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D 257 " --> pdb=" O MET D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 286 through 292 removed outlier: 3.567A pdb=" N TYR D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 339 removed outlier: 4.164A pdb=" N ASP D 339 " --> pdb=" O ASP D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 398 through 413 removed outlier: 3.718A pdb=" N ALA D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 498 removed outlier: 3.633A pdb=" N ALA D 475 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D 487 " --> pdb=" O PHE D 483 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.682A pdb=" N VAL D 512 " --> pdb=" O ASN D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 527 removed outlier: 3.724A pdb=" N VAL D 520 " --> pdb=" O VAL D 516 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 524 " --> pdb=" O VAL D 520 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 526 " --> pdb=" O ILE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 536 removed outlier: 4.078A pdb=" N VAL D 532 " --> pdb=" O ARG D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 548 through 577 removed outlier: 3.955A pdb=" N TRP D 554 " --> pdb=" O HIS D 550 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 556 " --> pdb=" O ALA D 552 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 565 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP D 570 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 571 " --> pdb=" O PHE D 567 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE D 576 " --> pdb=" O LYS D 572 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 601 removed outlier: 4.398A pdb=" N GLN D 585 " --> pdb=" O ARG D 581 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA D 594 " --> pdb=" O MET D 590 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 597 " --> pdb=" O CYS D 593 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 620 removed outlier: 3.658A pdb=" N TYR D 611 " --> pdb=" O ILE D 607 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 642 removed outlier: 4.622A pdb=" N PHE D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE D 640 " --> pdb=" O GLN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 removed outlier: 4.080A pdb=" N GLU D 650 " --> pdb=" O PHE D 646 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 693 removed outlier: 3.757A pdb=" N ILE D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU D 673 " --> pdb=" O PHE D 669 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 678 " --> pdb=" O ASN D 674 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR D 683 " --> pdb=" O ILE D 679 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 684 " --> pdb=" O ILE D 680 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 removed outlier: 3.650A pdb=" N TYR A 391 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.651A pdb=" N TYR B 391 " --> pdb=" O GLN B 323 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 391 through 394 removed outlier: 3.650A pdb=" N TYR C 391 " --> pdb=" O GLN C 323 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 391 through 394 removed outlier: 3.650A pdb=" N TYR D 391 " --> pdb=" O GLN D 323 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2136 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: 2.04 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: 2524 1.31 - 1.43: 5050 1.43 - 1.56: 9321 1.56 - 1.68: 18 1.68 - 1.81: 110 Bond restraints: 17023 Sorted by residual: bond pdb=" O2 PX6 C1006 " pdb=" P1 PX6 C1006 " ideal model delta sigma weight residual 1.526 1.649 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O2 PX6 D1006 " pdb=" P1 PX6 D1006 " ideal model delta sigma weight residual 1.526 1.649 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" O2 PX6 B1006 " pdb=" P1 PX6 B1006 " ideal model delta sigma weight residual 1.526 1.649 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" O2 PX6 A1006 " pdb=" P1 PX6 A1006 " ideal model delta sigma weight residual 1.526 1.649 -0.123 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C4 PX6 C1006 " pdb=" O5 PX6 C1006 " ideal model delta sigma weight residual 1.325 1.414 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 17018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 22580 3.65 - 7.30: 359 7.30 - 10.95: 40 10.95 - 14.60: 4 14.60 - 18.26: 4 Bond angle restraints: 22987 Sorted by residual: angle pdb=" C2 PX6 A1006 " pdb=" C3 PX6 A1006 " pdb=" O5 PX6 A1006 " ideal model delta sigma weight residual 110.56 128.82 -18.26 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C2 PX6 D1006 " pdb=" C3 PX6 D1006 " pdb=" O5 PX6 D1006 " ideal model delta sigma weight residual 110.56 128.78 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C2 PX6 B1006 " pdb=" C3 PX6 B1006 " pdb=" O5 PX6 B1006 " ideal model delta sigma weight residual 110.56 128.73 -18.17 3.00e+00 1.11e-01 3.67e+01 angle pdb=" C2 PX6 C1006 " pdb=" C3 PX6 C1006 " pdb=" O5 PX6 C1006 " ideal model delta sigma weight residual 110.56 128.70 -18.14 3.00e+00 1.11e-01 3.66e+01 angle pdb=" O1 PX6 A1006 " pdb=" P1 PX6 A1006 " pdb=" O3 PX6 A1006 " ideal model delta sigma weight residual 114.96 100.95 14.01 3.00e+00 1.11e-01 2.18e+01 ... (remaining 22982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 9002 16.10 - 32.21: 564 32.21 - 48.31: 105 48.31 - 64.41: 52 64.41 - 80.52: 12 Dihedral angle restraints: 9735 sinusoidal: 4019 harmonic: 5716 Sorted by residual: dihedral pdb=" CA PHE B 579 " pdb=" C PHE B 579 " pdb=" N ASN B 580 " pdb=" CA ASN B 580 " ideal model delta harmonic sigma weight residual -180.00 -149.18 -30.82 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA PHE C 579 " pdb=" C PHE C 579 " pdb=" N ASN C 580 " pdb=" CA ASN C 580 " ideal model delta harmonic sigma weight residual -180.00 -149.19 -30.81 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA PHE A 579 " pdb=" C PHE A 579 " pdb=" N ASN A 580 " pdb=" CA ASN A 580 " ideal model delta harmonic sigma weight residual -180.00 -149.20 -30.80 0 5.00e+00 4.00e-02 3.79e+01 ... (remaining 9732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 2573 0.218 - 0.437: 7 0.437 - 0.655: 0 0.655 - 0.874: 4 0.874 - 1.092: 4 Chirality restraints: 2588 Sorted by residual: chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 362 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-01 2.50e+01 2.98e+01 chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.35 -1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" C1 NAG A1002 " pdb=" ND2 ASN A 362 " pdb=" C2 NAG A1002 " pdb=" O5 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.35 -1.05 2.00e-01 2.50e+01 2.77e+01 ... (remaining 2585 not shown) Planarity restraints: 2820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 375 " -0.074 2.00e-02 2.50e+03 7.47e-02 6.98e+01 pdb=" CG ASN A 375 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 375 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 375 " 0.118 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 375 " -0.054 2.00e-02 2.50e+03 5.41e-02 3.66e+01 pdb=" CG ASN D 375 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN D 375 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN D 375 " 0.083 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 375 " -0.053 2.00e-02 2.50e+03 5.24e-02 3.43e+01 pdb=" CG ASN B 375 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 375 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 375 " 0.080 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.062 2.00e-02 2.50e+03 ... (remaining 2817 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 370 2.57 - 3.15: 16821 3.15 - 3.74: 25403 3.74 - 4.32: 35719 4.32 - 4.90: 53560 Nonbonded interactions: 131873 Sorted by model distance: nonbonded pdb=" O3 NAG A1002 " pdb=" O7 NAG A1002 " model vdw 1.989 3.040 nonbonded pdb=" O3 NAG D1002 " pdb=" O7 NAG D1002 " model vdw 1.989 3.040 nonbonded pdb=" O3 NAG B1002 " pdb=" O7 NAG B1002 " model vdw 1.989 3.040 nonbonded pdb=" O3 NAG C1002 " pdb=" O7 NAG C1002 " model vdw 1.990 3.040 nonbonded pdb=" OD1 ASN B 328 " pdb=" O5 NAG B1001 " model vdw 2.037 3.040 ... (remaining 131868 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 582 or (resid 583 and (name N or name CA or na \ me C or name O or name CB )) or resid 584 through 1011)) selection = (chain 'B' and resid 215 through 1011) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.140 Find NCS groups from input model: 0.380 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 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 : 0.014 0.481 17047 Z= 0.654 Angle : 1.333 24.800 23055 Z= 0.623 Chirality : 0.073 1.092 2588 Planarity : 0.005 0.046 2804 Dihedral : 12.491 80.517 6027 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 33.61 Ramachandran Plot: Outliers : 0.84 % Allowed : 11.69 % Favored : 87.47 % Rotamer: Outliers : 0.52 % Allowed : 2.55 % Favored : 96.93 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -5.40 (0.14), residues: 1916 helix: -4.32 (0.09), residues: 856 sheet: -1.56 (0.32), residues: 200 loop : -3.17 (0.17), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 325 TYR 0.022 0.003 TYR A 391 PHE 0.020 0.003 PHE C 598 TRP 0.051 0.004 TRP D 293 HIS 0.014 0.004 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.01028 / 0.48 (17023) covalent geometry : angle 1.15715 / 0.58 (22987) SS BOND : bond 0.00815 / 0.41 ( 4) SS BOND : angle 1.69833 / 0.79 ( 8) hydrogen bonds : bond 0.34183 / 22.11 ( 740) hydrogen bonds : angle 11.33656 / 7.69 ( 2136) link_BETA1-4 : bond 0.03377 / 1.69 ( 4) link_BETA1-4 : angle 11.31906 / 5.83 ( 12) link_NAG-ASN : bond 0.28665 / 17.53 ( 16) link_NAG-ASN : angle 13.40184 / 8.24 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 501 time to evaluate : 0.570 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 TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 249 TYR cc_start: 0.9178 (t80) cc_final: 0.8214 (t80) REVERT: C 249 TYR cc_start: 0.9169 (t80) cc_final: 0.8154 (t80) REVERT: D 249 TYR cc_start: 0.9176 (t80) cc_final: 0.8182 (t80) outliers start: 9 outliers final: 5 residues processed: 505 average time/residue: 0.1127 time to fit residues: 89.6874 Evaluate side-chains 336 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 331 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 501 HIS A 508 ASN A 550 HIS ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 434 ASN B 498 HIS B 550 HIS ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN C 501 HIS C 508 ASN C 550 HIS ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN D 501 HIS D 508 ASN D 550 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.141723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107919 restraints weight = 33946.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111196 restraints weight = 20036.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113454 restraints weight = 14464.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114898 restraints weight = 11823.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115657 restraints weight = 10424.318| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17047 Z= 0.211 Angle : 0.950 20.653 23055 Z= 0.469 Chirality : 0.051 0.373 2588 Planarity : 0.005 0.033 2804 Dihedral : 11.713 59.943 2420 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.00 % Favored : 93.79 % Rotamer: Outliers : 0.52 % Allowed : 3.54 % Favored : 95.94 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.16), residues: 1916 helix: -2.88 (0.13), residues: 900 sheet: -1.34 (0.32), residues: 200 loop : -2.23 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 654 TYR 0.034 0.003 TYR C 247 PHE 0.030 0.002 PHE C 608 TRP 0.022 0.003 TRP B 293 HIS 0.004 0.001 HIS C 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (17023) covalent geometry : angle 0.85323 / 0.45 (22987) SS BOND : bond 0.01711 / 0.86 ( 4) SS BOND : angle 1.83231 / 0.85 ( 8) hydrogen bonds : bond 0.08034 / 5.17 ( 740) hydrogen bonds : angle 7.01247 / 4.80 ( 2136) link_BETA1-4 : bond 0.02297 / 1.15 ( 4) link_BETA1-4 : angle 7.28422 / 3.57 ( 12) link_NAG-ASN : bond 0.01550 / 0.85 ( 16) link_NAG-ASN : angle 8.40215 / 5.14 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 485 time to evaluate : 0.552 Fit side-chains TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 241 MET cc_start: 0.7679 (mtt) cc_final: 0.6764 (ttp) REVERT: A 249 TYR cc_start: 0.8803 (t80) cc_final: 0.8070 (t80) REVERT: A 252 MET cc_start: 0.8536 (tmm) cc_final: 0.8241 (tmm) REVERT: A 460 LEU cc_start: 0.9124 (tp) cc_final: 0.8747 (pp) REVERT: A 583 MET cc_start: 0.8584 (ptm) cc_final: 0.8356 (ptm) REVERT: B 241 MET cc_start: 0.7697 (mtt) cc_final: 0.6804 (ttp) REVERT: B 249 TYR cc_start: 0.8831 (t80) cc_final: 0.8093 (t80) REVERT: B 252 MET cc_start: 0.8631 (tmm) cc_final: 0.8375 (tmm) REVERT: B 460 LEU cc_start: 0.9117 (tp) cc_final: 0.8772 (pp) REVERT: B 666 PHE cc_start: 0.9216 (t80) cc_final: 0.8946 (t80) REVERT: C 241 MET cc_start: 0.7400 (mtp) cc_final: 0.6475 (ttp) REVERT: C 249 TYR cc_start: 0.8789 (t80) cc_final: 0.8081 (t80) REVERT: C 252 MET cc_start: 0.8525 (tmm) cc_final: 0.8242 (tmm) REVERT: C 460 LEU cc_start: 0.9123 (tp) cc_final: 0.8693 (pp) REVERT: D 241 MET cc_start: 0.7690 (mtt) cc_final: 0.6756 (ttp) REVERT: D 249 TYR cc_start: 0.8833 (t80) cc_final: 0.8096 (t80) REVERT: D 252 MET cc_start: 0.8561 (tmm) cc_final: 0.8273 (tmm) REVERT: D 460 LEU cc_start: 0.9135 (tp) cc_final: 0.8742 (pp) outliers start: 9 outliers final: 5 residues processed: 485 average time/residue: 0.1076 time to fit residues: 83.2188 Evaluate side-chains 362 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 357 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 104 optimal weight: 0.0770 chunk 173 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 48 optimal weight: 50.0000 chunk 130 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS B 501 HIS B 537 GLN C 501 HIS C 537 GLN D 501 HIS D 537 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.139496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105748 restraints weight = 34539.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109044 restraints weight = 20114.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111207 restraints weight = 14421.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.112614 restraints weight = 11785.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113382 restraints weight = 10439.297| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17047 Z= 0.231 Angle : 0.874 20.075 23055 Z= 0.428 Chirality : 0.051 0.464 2588 Planarity : 0.005 0.028 2804 Dihedral : 10.686 58.209 2420 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.10 % Favored : 92.69 % Rotamer: Outliers : 0.70 % Allowed : 5.04 % Favored : 94.26 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.17), residues: 1916 helix: -2.09 (0.15), residues: 940 sheet: -1.36 (0.34), residues: 200 loop : -2.08 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 654 TYR 0.029 0.002 TYR A 247 PHE 0.022 0.002 PHE B 608 TRP 0.037 0.003 TRP D 293 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (17023) covalent geometry : angle 0.77525 / 0.41 (22987) SS BOND : bond 0.00268 / 0.13 ( 4) SS BOND : angle 0.98694 / 0.45 ( 8) hydrogen bonds : bond 0.06071 / 3.89 ( 740) hydrogen bonds : angle 6.32961 / 4.33 ( 2136) link_BETA1-4 : bond 0.02177 / 1.09 ( 4) link_BETA1-4 : angle 6.68337 / 3.36 ( 12) link_NAG-ASN : bond 0.01493 / 0.84 ( 16) link_NAG-ASN : angle 8.21653 / 5.06 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 447 time to evaluate : 0.595 Fit side-chains TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 241 MET cc_start: 0.7304 (mtt) cc_final: 0.6402 (ttp) REVERT: A 249 TYR cc_start: 0.8710 (t80) cc_final: 0.7841 (t80) REVERT: A 513 VAL cc_start: 0.9090 (t) cc_final: 0.8860 (t) REVERT: B 241 MET cc_start: 0.7326 (mtt) cc_final: 0.6408 (ttp) REVERT: B 249 TYR cc_start: 0.8807 (t80) cc_final: 0.7985 (t80) REVERT: C 241 MET cc_start: 0.7114 (mtp) cc_final: 0.6262 (ttp) REVERT: C 249 TYR cc_start: 0.8806 (t80) cc_final: 0.7967 (t80) REVERT: C 253 MET cc_start: 0.8876 (tpp) cc_final: 0.8673 (tpp) REVERT: C 513 VAL cc_start: 0.9092 (t) cc_final: 0.8861 (t) REVERT: D 241 MET cc_start: 0.7311 (mtt) cc_final: 0.6385 (ttp) REVERT: D 249 TYR cc_start: 0.8828 (t80) cc_final: 0.7969 (t80) REVERT: D 253 MET cc_start: 0.8845 (tpp) cc_final: 0.8452 (tpp) REVERT: D 513 VAL cc_start: 0.9078 (t) cc_final: 0.8841 (t) outliers start: 12 outliers final: 4 residues processed: 447 average time/residue: 0.0983 time to fit residues: 72.4502 Evaluate side-chains 346 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 342 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 7.9990 chunk 185 optimal weight: 0.6980 chunk 168 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS A 537 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS B 501 HIS C 501 HIS ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106645 restraints weight = 34342.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109942 restraints weight = 19863.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112103 restraints weight = 14212.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113478 restraints weight = 11648.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114050 restraints weight = 10346.297| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17047 Z= 0.221 Angle : 0.855 20.120 23055 Z= 0.415 Chirality : 0.051 0.466 2588 Planarity : 0.004 0.030 2804 Dihedral : 10.315 57.603 2420 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.42 % Favored : 93.37 % Rotamer: Outliers : 0.46 % Allowed : 3.42 % Favored : 96.12 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.17), residues: 1916 helix: -1.93 (0.15), residues: 932 sheet: -1.33 (0.34), residues: 200 loop : -2.09 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 654 TYR 0.027 0.002 TYR A 247 PHE 0.030 0.002 PHE C 608 TRP 0.037 0.002 TRP D 293 HIS 0.002 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (17023) covalent geometry : angle 0.76017 / 0.39 (22987) SS BOND : bond 0.01572 / 0.79 ( 4) SS BOND : angle 1.89374 / 0.87 ( 8) hydrogen bonds : bond 0.05427 / 3.48 ( 740) hydrogen bonds : angle 6.16739 / 4.22 ( 2136) link_BETA1-4 : bond 0.02009 / 1.01 ( 4) link_BETA1-4 : angle 6.42916 / 3.25 ( 12) link_NAG-ASN : bond 0.01439 / 0.81 ( 16) link_NAG-ASN : angle 7.98825 / 4.92 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 440 time to evaluate : 0.504 Fit side-chains TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 241 MET cc_start: 0.7147 (mtt) cc_final: 0.6358 (ttp) REVERT: A 249 TYR cc_start: 0.8771 (t80) cc_final: 0.7917 (t80) REVERT: A 395 LEU cc_start: 0.8893 (mp) cc_final: 0.8315 (tp) REVERT: B 241 MET cc_start: 0.7279 (mtt) cc_final: 0.6452 (ttp) REVERT: B 249 TYR cc_start: 0.8815 (t80) cc_final: 0.7944 (t80) REVERT: B 252 MET cc_start: 0.8587 (tmm) cc_final: 0.8332 (tmm) REVERT: B 501 HIS cc_start: 0.5270 (OUTLIER) cc_final: 0.4313 (m170) REVERT: B 513 VAL cc_start: 0.9069 (t) cc_final: 0.8863 (t) REVERT: B 688 LYS cc_start: 0.8894 (tptp) cc_final: 0.8621 (mmmt) REVERT: C 241 MET cc_start: 0.7044 (mtp) cc_final: 0.6236 (ttp) REVERT: C 249 TYR cc_start: 0.8852 (t80) cc_final: 0.8051 (t80) REVERT: C 395 LEU cc_start: 0.8851 (mp) cc_final: 0.8251 (tp) REVERT: D 241 MET cc_start: 0.7118 (mtt) cc_final: 0.6309 (ttp) REVERT: D 249 TYR cc_start: 0.8829 (t80) cc_final: 0.8012 (t80) REVERT: D 395 LEU cc_start: 0.8888 (mp) cc_final: 0.8317 (tp) outliers start: 8 outliers final: 4 residues processed: 440 average time/residue: 0.0898 time to fit residues: 66.2234 Evaluate side-chains 340 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 335 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 70 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN A 501 HIS A 681 ASN B 296 GLN C 296 GLN C 501 HIS D 296 GLN D 434 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.142945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108854 restraints weight = 34264.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112118 restraints weight = 20553.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114230 restraints weight = 14959.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115616 restraints weight = 12371.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116325 restraints weight = 11018.048| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17047 Z= 0.163 Angle : 0.799 19.929 23055 Z= 0.386 Chirality : 0.048 0.436 2588 Planarity : 0.004 0.032 2804 Dihedral : 10.033 59.430 2420 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.73 % Favored : 93.06 % Rotamer: Outliers : 0.41 % Allowed : 2.09 % Favored : 97.51 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.17), residues: 1916 helix: -1.73 (0.15), residues: 932 sheet: -1.36 (0.34), residues: 200 loop : -1.99 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 654 TYR 0.044 0.002 TYR A 247 PHE 0.024 0.002 PHE C 230 TRP 0.049 0.003 TRP B 293 HIS 0.001 0.001 HIS D 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (17023) covalent geometry : angle 0.69916 / 0.36 (22987) SS BOND : bond 0.00108 / 0.05 ( 4) SS BOND : angle 1.46370 / 0.67 ( 8) hydrogen bonds : bond 0.05057 / 3.25 ( 740) hydrogen bonds : angle 5.84360 / 3.99 ( 2136) link_BETA1-4 : bond 0.01912 / 0.96 ( 4) link_BETA1-4 : angle 6.41631 / 3.24 ( 12) link_NAG-ASN : bond 0.01469 / 0.83 ( 16) link_NAG-ASN : angle 7.84957 / 4.84 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 450 time to evaluate : 0.542 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 241 MET cc_start: 0.7033 (mtt) cc_final: 0.6331 (ttp) REVERT: A 249 TYR cc_start: 0.8642 (t80) cc_final: 0.8001 (t80) REVERT: A 395 LEU cc_start: 0.8806 (mp) cc_final: 0.8216 (tp) REVERT: A 399 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7459 (ttp80) REVERT: A 436 PHE cc_start: 0.7842 (t80) cc_final: 0.7630 (t80) REVERT: B 241 MET cc_start: 0.7296 (mtt) cc_final: 0.6474 (ttp) REVERT: B 249 TYR cc_start: 0.8687 (t80) cc_final: 0.7986 (t80) REVERT: B 399 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7594 (ttp80) REVERT: B 513 VAL cc_start: 0.9035 (t) cc_final: 0.8826 (t) REVERT: B 603 MET cc_start: 0.8419 (tmm) cc_final: 0.8096 (tmm) REVERT: B 644 ILE cc_start: 0.7087 (mm) cc_final: 0.6818 (mm) REVERT: B 688 LYS cc_start: 0.8827 (tptp) cc_final: 0.8615 (mmmt) REVERT: C 241 MET cc_start: 0.7004 (mtp) cc_final: 0.6237 (ttp) REVERT: C 249 TYR cc_start: 0.8625 (t80) cc_final: 0.8055 (t80) REVERT: C 395 LEU cc_start: 0.8785 (mp) cc_final: 0.8188 (tp) REVERT: D 241 MET cc_start: 0.7161 (mtt) cc_final: 0.6415 (ttp) REVERT: D 249 TYR cc_start: 0.8650 (t80) cc_final: 0.8060 (t80) REVERT: D 399 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7434 (ttp80) outliers start: 7 outliers final: 4 residues processed: 451 average time/residue: 0.1005 time to fit residues: 73.6769 Evaluate side-chains 355 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 351 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 169 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 87 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS A 681 ASN B 498 HIS B 501 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN C 501 HIS D 501 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.142754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108747 restraints weight = 34071.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112039 restraints weight = 20435.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114148 restraints weight = 14855.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115293 restraints weight = 12260.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116307 restraints weight = 10979.109| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17047 Z= 0.179 Angle : 0.799 19.973 23055 Z= 0.386 Chirality : 0.048 0.424 2588 Planarity : 0.004 0.032 2804 Dihedral : 9.775 58.167 2420 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.42 % Favored : 93.37 % Rotamer: Outliers : 0.46 % Allowed : 2.84 % Favored : 96.70 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.17), residues: 1916 helix: -1.63 (0.15), residues: 928 sheet: -1.19 (0.36), residues: 200 loop : -1.88 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 399 TYR 0.042 0.002 TYR C 247 PHE 0.027 0.002 PHE B 608 TRP 0.030 0.002 TRP A 293 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (17023) covalent geometry : angle 0.69935 / 0.36 (22987) SS BOND : bond 0.00435 / 0.22 ( 4) SS BOND : angle 2.93272 / 1.35 ( 8) hydrogen bonds : bond 0.04648 / 2.99 ( 740) hydrogen bonds : angle 5.68999 / 3.89 ( 2136) link_BETA1-4 : bond 0.02051 / 1.03 ( 4) link_BETA1-4 : angle 6.20408 / 3.13 ( 12) link_NAG-ASN : bond 0.01479 / 0.83 ( 16) link_NAG-ASN : angle 7.80974 / 4.81 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 438 time to evaluate : 0.588 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 241 MET cc_start: 0.6992 (mtt) cc_final: 0.6271 (ttp) REVERT: A 249 TYR cc_start: 0.8727 (t80) cc_final: 0.8004 (t80) REVERT: A 370 SER cc_start: 0.8583 (t) cc_final: 0.8382 (p) REVERT: A 399 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7364 (ttp80) REVERT: A 644 ILE cc_start: 0.7260 (mm) cc_final: 0.6943 (mm) REVERT: B 241 MET cc_start: 0.7340 (mtt) cc_final: 0.6532 (ttp) REVERT: B 249 TYR cc_start: 0.8727 (t80) cc_final: 0.8095 (t80) REVERT: B 501 HIS cc_start: 0.5545 (OUTLIER) cc_final: 0.4508 (m170) REVERT: B 603 MET cc_start: 0.8427 (tmm) cc_final: 0.8126 (tmm) REVERT: B 644 ILE cc_start: 0.7153 (mm) cc_final: 0.6831 (mm) REVERT: B 688 LYS cc_start: 0.8845 (tptp) cc_final: 0.8635 (mmmt) REVERT: C 227 TYR cc_start: 0.8284 (m-80) cc_final: 0.7354 (m-10) REVERT: C 241 MET cc_start: 0.6987 (mtp) cc_final: 0.6225 (ttp) REVERT: C 249 TYR cc_start: 0.8775 (t80) cc_final: 0.8061 (t80) REVERT: C 644 ILE cc_start: 0.7232 (mm) cc_final: 0.6906 (mm) REVERT: D 241 MET cc_start: 0.7005 (mtt) cc_final: 0.6268 (ttp) REVERT: D 249 TYR cc_start: 0.8746 (t80) cc_final: 0.8013 (t80) REVERT: D 370 SER cc_start: 0.8593 (t) cc_final: 0.8386 (p) REVERT: D 399 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7387 (ttp80) REVERT: D 644 ILE cc_start: 0.7173 (mm) cc_final: 0.6871 (mm) outliers start: 8 outliers final: 4 residues processed: 438 average time/residue: 0.0961 time to fit residues: 70.1794 Evaluate side-chains 352 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 347 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 50.0000 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 169 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS A 681 ASN B 681 ASN C 501 HIS C 681 ASN D 501 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.144387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110666 restraints weight = 34030.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113916 restraints weight = 20320.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116159 restraints weight = 14737.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117349 restraints weight = 12108.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118430 restraints weight = 10796.284| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17047 Z= 0.159 Angle : 0.791 19.946 23055 Z= 0.376 Chirality : 0.047 0.399 2588 Planarity : 0.004 0.032 2804 Dihedral : 9.557 58.367 2420 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 0.41 % Allowed : 1.86 % Favored : 97.74 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.18), residues: 1916 helix: -1.50 (0.15), residues: 936 sheet: -1.07 (0.36), residues: 200 loop : -1.71 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 399 TYR 0.032 0.002 TYR C 227 PHE 0.030 0.002 PHE A 608 TRP 0.036 0.002 TRP B 293 HIS 0.001 0.000 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (17023) covalent geometry : angle 0.69259 / 0.35 (22987) SS BOND : bond 0.00081 / 0.04 ( 4) SS BOND : angle 2.38354 / 1.10 ( 8) hydrogen bonds : bond 0.04453 / 2.85 ( 740) hydrogen bonds : angle 5.56800 / 3.81 ( 2136) link_BETA1-4 : bond 0.01924 / 0.96 ( 4) link_BETA1-4 : angle 6.16268 / 3.12 ( 12) link_NAG-ASN : bond 0.01501 / 0.84 ( 16) link_NAG-ASN : angle 7.77407 / 4.78 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 449 time to evaluate : 0.606 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 TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 241 MET cc_start: 0.6934 (mtt) cc_final: 0.6278 (ttp) REVERT: A 249 TYR cc_start: 0.8685 (t80) cc_final: 0.8050 (t80) REVERT: A 399 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7368 (ttp80) REVERT: A 644 ILE cc_start: 0.7233 (mm) cc_final: 0.6876 (mm) REVERT: B 241 MET cc_start: 0.7250 (mtt) cc_final: 0.6481 (ttp) REVERT: B 249 TYR cc_start: 0.8680 (t80) cc_final: 0.8010 (t80) REVERT: B 399 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7486 (ttp80) REVERT: B 469 PHE cc_start: 0.8418 (t80) cc_final: 0.7912 (t80) REVERT: B 603 MET cc_start: 0.8421 (tmm) cc_final: 0.8119 (tmm) REVERT: B 644 ILE cc_start: 0.7127 (mm) cc_final: 0.6741 (mm) REVERT: B 688 LYS cc_start: 0.8863 (tptp) cc_final: 0.8647 (mmmt) REVERT: C 241 MET cc_start: 0.7145 (mtp) cc_final: 0.6369 (ttp) REVERT: C 249 TYR cc_start: 0.8739 (t80) cc_final: 0.8055 (t80) REVERT: C 644 ILE cc_start: 0.7222 (mm) cc_final: 0.6837 (mm) REVERT: D 241 MET cc_start: 0.7038 (mtt) cc_final: 0.6291 (ttp) REVERT: D 249 TYR cc_start: 0.8709 (t80) cc_final: 0.8008 (t80) REVERT: D 399 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7335 (ttp80) REVERT: D 644 ILE cc_start: 0.7189 (mm) cc_final: 0.6813 (mm) outliers start: 7 outliers final: 4 residues processed: 449 average time/residue: 0.0933 time to fit residues: 69.8473 Evaluate side-chains 362 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 358 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS B 498 HIS C 501 HIS D 501 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.145586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111405 restraints weight = 34164.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114783 restraints weight = 20221.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117057 restraints weight = 14562.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118579 restraints weight = 11899.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119317 restraints weight = 10481.465| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17047 Z= 0.148 Angle : 0.783 19.920 23055 Z= 0.372 Chirality : 0.047 0.373 2588 Planarity : 0.004 0.033 2804 Dihedral : 9.359 57.965 2420 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.90 % Favored : 93.89 % Rotamer: Outliers : 0.41 % Allowed : 1.80 % Favored : 97.80 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.18), residues: 1916 helix: -1.43 (0.15), residues: 964 sheet: -0.91 (0.37), residues: 200 loop : -1.72 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 399 TYR 0.045 0.002 TYR D 247 PHE 0.033 0.002 PHE B 608 TRP 0.028 0.002 TRP D 293 HIS 0.002 0.000 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (17023) covalent geometry : angle 0.68526 / 0.35 (22987) SS BOND : bond 0.00168 / 0.08 ( 4) SS BOND : angle 1.88646 / 0.87 ( 8) hydrogen bonds : bond 0.04271 / 2.72 ( 740) hydrogen bonds : angle 5.44789 / 3.73 ( 2136) link_BETA1-4 : bond 0.01970 / 0.99 ( 4) link_BETA1-4 : angle 5.99573 / 3.03 ( 12) link_NAG-ASN : bond 0.01499 / 0.84 ( 16) link_NAG-ASN : angle 7.73159 / 4.75 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 444 time to evaluate : 0.613 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 TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 241 MET cc_start: 0.7037 (mtt) cc_final: 0.6338 (ttp) REVERT: A 249 TYR cc_start: 0.8716 (t80) cc_final: 0.8109 (t80) REVERT: A 255 GLN cc_start: 0.9048 (mt0) cc_final: 0.7979 (tm-30) REVERT: A 399 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7381 (ttp80) REVERT: A 644 ILE cc_start: 0.7292 (mm) cc_final: 0.6956 (mm) REVERT: B 241 MET cc_start: 0.7113 (mtt) cc_final: 0.6360 (ttp) REVERT: B 249 TYR cc_start: 0.8699 (t80) cc_final: 0.8082 (t80) REVERT: B 370 SER cc_start: 0.8478 (t) cc_final: 0.8228 (p) REVERT: B 469 PHE cc_start: 0.8429 (t80) cc_final: 0.7910 (t80) REVERT: B 608 PHE cc_start: 0.9073 (t80) cc_final: 0.8844 (t80) REVERT: B 644 ILE cc_start: 0.7126 (mm) cc_final: 0.6720 (mm) REVERT: B 688 LYS cc_start: 0.8807 (tptp) cc_final: 0.8600 (mmmt) REVERT: C 241 MET cc_start: 0.7092 (mtp) cc_final: 0.6353 (ttp) REVERT: C 249 TYR cc_start: 0.8640 (t80) cc_final: 0.8082 (t80) REVERT: C 395 LEU cc_start: 0.8809 (mp) cc_final: 0.8225 (tp) REVERT: C 644 ILE cc_start: 0.7221 (mm) cc_final: 0.6854 (mm) REVERT: D 241 MET cc_start: 0.7030 (mtt) cc_final: 0.6292 (ttp) REVERT: D 249 TYR cc_start: 0.8650 (t80) cc_final: 0.8054 (t80) REVERT: D 370 SER cc_start: 0.8364 (t) cc_final: 0.8099 (p) REVERT: D 395 LEU cc_start: 0.8804 (mp) cc_final: 0.8228 (tp) REVERT: D 399 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7301 (ttp80) REVERT: D 644 ILE cc_start: 0.7165 (mm) cc_final: 0.6813 (mm) outliers start: 7 outliers final: 4 residues processed: 444 average time/residue: 0.0948 time to fit residues: 69.8852 Evaluate side-chains 370 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 366 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 181 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS A 547 ASN B 305 ASN B 498 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 GLN ** 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 = 0.3952 r_free = 0.3952 target = 0.148330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114096 restraints weight = 33619.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117392 restraints weight = 20634.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119640 restraints weight = 15173.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121061 restraints weight = 12537.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121779 restraints weight = 11158.811| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17047 Z= 0.133 Angle : 0.787 19.845 23055 Z= 0.368 Chirality : 0.046 0.374 2588 Planarity : 0.004 0.035 2804 Dihedral : 9.155 57.946 2420 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.64 % Favored : 94.15 % Rotamer: Outliers : 0.35 % Allowed : 0.75 % Favored : 98.90 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.18), residues: 1916 helix: -1.23 (0.15), residues: 960 sheet: -0.66 (0.38), residues: 200 loop : -1.68 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 399 TYR 0.040 0.002 TYR D 247 PHE 0.040 0.002 PHE D 608 TRP 0.033 0.002 TRP B 293 HIS 0.001 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (17023) covalent geometry : angle 0.68668 / 0.35 (22987) SS BOND : bond 0.00029 / 0.01 ( 4) SS BOND : angle 1.75538 / 0.81 ( 8) hydrogen bonds : bond 0.04074 / 2.60 ( 740) hydrogen bonds : angle 5.25327 / 3.61 ( 2136) link_BETA1-4 : bond 0.02015 / 1.01 ( 4) link_BETA1-4 : angle 5.92030 / 3.00 ( 12) link_NAG-ASN : bond 0.01497 / 0.84 ( 16) link_NAG-ASN : angle 7.91664 / 4.84 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 454 time to evaluate : 0.560 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 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 TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 241 MET cc_start: 0.7006 (mtt) cc_final: 0.6338 (ttp) REVERT: A 249 TYR cc_start: 0.8605 (t80) cc_final: 0.8100 (t80) REVERT: A 255 GLN cc_start: 0.9027 (mt0) cc_final: 0.7974 (tm-30) REVERT: A 399 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7521 (ttp80) REVERT: A 644 ILE cc_start: 0.7278 (mm) cc_final: 0.6989 (mm) REVERT: B 241 MET cc_start: 0.6994 (mtt) cc_final: 0.6348 (ttp) REVERT: B 249 TYR cc_start: 0.8582 (t80) cc_final: 0.8025 (t80) REVERT: B 370 SER cc_start: 0.8297 (t) cc_final: 0.8068 (p) REVERT: B 469 PHE cc_start: 0.8451 (t80) cc_final: 0.7958 (t80) REVERT: B 514 ILE cc_start: 0.9226 (mp) cc_final: 0.9014 (tt) REVERT: B 603 MET cc_start: 0.8371 (tmm) cc_final: 0.8082 (tmm) REVERT: B 644 ILE cc_start: 0.7125 (mm) cc_final: 0.6836 (mm) REVERT: C 239 TYR cc_start: 0.8436 (t80) cc_final: 0.8104 (t80) REVERT: C 241 MET cc_start: 0.7060 (mtp) cc_final: 0.6310 (ttp) REVERT: C 249 TYR cc_start: 0.8551 (t80) cc_final: 0.8065 (t80) REVERT: C 644 ILE cc_start: 0.7228 (mm) cc_final: 0.6933 (mm) REVERT: D 241 MET cc_start: 0.6968 (mtt) cc_final: 0.6308 (ttp) REVERT: D 249 TYR cc_start: 0.8563 (t80) cc_final: 0.8056 (t80) REVERT: D 255 GLN cc_start: 0.8981 (mt0) cc_final: 0.7969 (tm-30) REVERT: D 370 SER cc_start: 0.8252 (t) cc_final: 0.8017 (p) REVERT: D 399 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7495 (ttp80) REVERT: D 644 ILE cc_start: 0.7216 (mm) cc_final: 0.6927 (mm) outliers start: 6 outliers final: 4 residues processed: 454 average time/residue: 0.0959 time to fit residues: 72.0612 Evaluate side-chains 359 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 355 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 114 optimal weight: 9.9990 chunk 141 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 48 optimal weight: 50.0000 chunk 122 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 313 ASN B 498 HIS B 501 HIS C 501 HIS D 501 HIS ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114347 restraints weight = 33622.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117878 restraints weight = 19868.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120274 restraints weight = 14224.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121787 restraints weight = 11550.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122767 restraints weight = 10176.963| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17047 Z= 0.134 Angle : 0.785 19.913 23055 Z= 0.366 Chirality : 0.046 0.408 2588 Planarity : 0.004 0.032 2804 Dihedral : 9.028 57.266 2420 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.27 % Favored : 94.52 % Rotamer: Outliers : 0.41 % Allowed : 0.52 % Favored : 99.07 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.18), residues: 1916 helix: -1.16 (0.16), residues: 960 sheet: -0.49 (0.39), residues: 196 loop : -1.70 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 399 TYR 0.037 0.002 TYR D 247 PHE 0.033 0.002 PHE D 608 TRP 0.029 0.002 TRP D 293 HIS 0.001 0.000 HIS D 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (17023) covalent geometry : angle 0.68081 / 0.34 (22987) SS BOND : bond 0.00019 / 0.01 ( 4) SS BOND : angle 1.66514 / 0.77 ( 8) hydrogen bonds : bond 0.04087 / 2.57 ( 740) hydrogen bonds : angle 5.20792 / 3.57 ( 2136) link_BETA1-4 : bond 0.02005 / 1.00 ( 4) link_BETA1-4 : angle 5.78649 / 2.92 ( 12) link_NAG-ASN : bond 0.01437 / 0.78 ( 16) link_NAG-ASN : angle 8.05887 / 5.07 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 442 time to evaluate : 0.585 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 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 TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. REVERT: A 239 TYR cc_start: 0.8370 (t80) cc_final: 0.8070 (t80) REVERT: A 241 MET cc_start: 0.6969 (mtt) cc_final: 0.6340 (ttp) REVERT: A 249 TYR cc_start: 0.8620 (t80) cc_final: 0.8039 (t80) REVERT: A 255 GLN cc_start: 0.8988 (mt0) cc_final: 0.7902 (tm-30) REVERT: A 295 MET cc_start: 0.7040 (mmt) cc_final: 0.6725 (mmt) REVERT: A 399 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7488 (ttp80) REVERT: A 644 ILE cc_start: 0.7269 (mm) cc_final: 0.6987 (mm) REVERT: B 241 MET cc_start: 0.7055 (mtt) cc_final: 0.6395 (ttp) REVERT: B 249 TYR cc_start: 0.8618 (t80) cc_final: 0.8040 (t80) REVERT: B 469 PHE cc_start: 0.8420 (t80) cc_final: 0.7959 (t80) REVERT: B 590 MET cc_start: 0.5794 (mmm) cc_final: 0.5573 (tpp) REVERT: B 603 MET cc_start: 0.8301 (tmm) cc_final: 0.8018 (tmm) REVERT: B 644 ILE cc_start: 0.7045 (mm) cc_final: 0.6751 (mm) REVERT: C 239 TYR cc_start: 0.8408 (t80) cc_final: 0.8094 (t80) REVERT: C 241 MET cc_start: 0.7038 (mtp) cc_final: 0.6301 (ttp) REVERT: C 249 TYR cc_start: 0.8632 (t80) cc_final: 0.8107 (t80) REVERT: C 608 PHE cc_start: 0.8883 (t80) cc_final: 0.8642 (t80) REVERT: C 644 ILE cc_start: 0.7162 (mm) cc_final: 0.6857 (mm) REVERT: D 239 TYR cc_start: 0.8373 (t80) cc_final: 0.8047 (t80) REVERT: D 241 MET cc_start: 0.7030 (mtt) cc_final: 0.6267 (ttp) REVERT: D 249 TYR cc_start: 0.8629 (t80) cc_final: 0.8103 (t80) REVERT: D 399 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7452 (ttp80) REVERT: D 644 ILE cc_start: 0.7079 (mm) cc_final: 0.6789 (mm) outliers start: 7 outliers final: 4 residues processed: 442 average time/residue: 0.0925 time to fit residues: 68.2926 Evaluate side-chains 367 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 363 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 60 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 159 optimal weight: 0.0770 chunk 191 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 498 HIS B 501 HIS C 501 HIS ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113571 restraints weight = 33675.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116919 restraints weight = 20382.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119170 restraints weight = 14836.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120648 restraints weight = 12189.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121564 restraints weight = 10799.882| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17047 Z= 0.149 Angle : 0.778 19.979 23055 Z= 0.366 Chirality : 0.045 0.392 2588 Planarity : 0.004 0.045 2804 Dihedral : 8.983 56.361 2420 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.27 % Favored : 94.52 % Rotamer: Outliers : 0.35 % Allowed : 0.93 % Favored : 98.72 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.18), residues: 1916 helix: -1.08 (0.16), residues: 960 sheet: -0.38 (0.38), residues: 200 loop : -1.72 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 399 TYR 0.036 0.002 TYR B 247 PHE 0.028 0.002 PHE A 608 TRP 0.061 0.002 TRP B 293 HIS 0.002 0.001 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (17023) covalent geometry : angle 0.67667 / 0.34 (22987) SS BOND : bond 0.00063 / 0.03 ( 4) SS BOND : angle 1.65359 / 0.76 ( 8) hydrogen bonds : bond 0.04002 / 2.53 ( 740) hydrogen bonds : angle 5.20132 / 3.58 ( 2136) link_BETA1-4 : bond 0.01988 / 1.00 ( 4) link_BETA1-4 : angle 5.66875 / 2.86 ( 12) link_NAG-ASN : bond 0.01455 / 0.80 ( 16) link_NAG-ASN : angle 7.94468 / 4.94 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.70 seconds wall clock time: 46 minutes 2.45 seconds (2762.45 seconds total)