Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 03:27:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524_ligands.cif 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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/04_2023/5mkf_3524_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 496": "NH1" <-> "NH2" Residue "D ARG 654": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/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: {'TRANS': 1, None: 11} Not linked: pdbres="NAG A1001 " pdbres="NAG A1002 " Not linked: pdbres="NAG A1002 " pdbres="NAG A1005 " Not linked: pdbres="NAG A1005 " pdbres="PX6 A1006 " Not linked: pdbres="PX6 A1006 " pdbres="PLM A1007 " Not linked: pdbres="PLM A1007 " pdbres="PLM A1008 " ... (remaining 6 not shown) Chain breaks: 1 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: {'TRANS': 1, None: 8} Not linked: pdbres="NAG B1001 " pdbres="NAG B1002 " Not linked: pdbres="NAG B1002 " pdbres="NAG B1005 " Not linked: pdbres="NAG B1005 " pdbres="PX6 B1006 " Not linked: pdbres="PX6 B1006 " pdbres="PLM B1007 " Not linked: pdbres="PLM B1007 " pdbres="PLM B1008 " ... (remaining 3 not shown) Chain breaks: 1 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: {'TRANS': 1, None: 7} Not linked: pdbres="NAG C1001 " pdbres="NAG C1002 " Not linked: pdbres="NAG C1002 " pdbres="NAG C1005 " Not linked: pdbres="NAG C1005 " pdbres="PX6 C1006 " Not linked: pdbres="PX6 C1006 " pdbres="PLM C1007 " Not linked: pdbres="PLM C1007 " pdbres="PLM C1008 " ... (remaining 2 not shown) Chain breaks: 1 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: {'TRANS': 1, None: 7} Not linked: pdbres="NAG D1001 " pdbres="NAG D1002 " Not linked: pdbres="NAG D1002 " pdbres="NAG D1005 " Not linked: pdbres="NAG D1005 " pdbres="PX6 D1006 " Not linked: pdbres="PX6 D1006 " pdbres="PLM D1007 " Not linked: pdbres="PLM D1007 " pdbres="PLM D1008 " ... (remaining 2 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.37, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 7.70 Conformation dependent library (CDL) restraints added in 2.3 seconds 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 52.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 216 through 241 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 244 through 257 removed outlier: 4.194A pdb=" N TYR A 247 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG A 251 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 252 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 254 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 256 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 335 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 399 through 412 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 470 through 497 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 506 through 511 Processing helix chain 'A' and resid 513 through 535 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) removed outlier: 4.805A pdb=" N ASN A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 541 No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 549 through 575 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) Processing helix chain 'A' and resid 582 through 600 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 602 through 619 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 629 through 641 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 646 through 652 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 656 through 693 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 241 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 244 through 257 removed outlier: 4.194A pdb=" N TYR B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B 251 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 252 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 254 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 256 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 335 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 399 through 412 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 470 through 497 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 506 through 511 Processing helix chain 'B' and resid 513 through 535 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) removed outlier: 4.806A pdb=" N ASN B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 541 No H-bonds generated for 'chain 'B' and resid 538 through 541' Processing helix chain 'B' and resid 549 through 575 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) Processing helix chain 'B' and resid 582 through 600 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 602 through 619 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 629 through 641 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 646 through 652 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 656 through 693 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 241 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 244 through 257 removed outlier: 4.194A pdb=" N TYR C 247 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG C 251 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C 252 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 254 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 256 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 335 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 399 through 412 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 470 through 497 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 506 through 511 Processing helix chain 'C' and resid 513 through 535 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) removed outlier: 4.806A pdb=" N ASN C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 532 " --> pdb=" O ARG C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 541 No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 549 through 575 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) Processing helix chain 'C' and resid 582 through 600 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 602 through 619 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 629 through 641 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 646 through 652 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 656 through 693 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 241 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 244 through 257 removed outlier: 4.193A pdb=" N TYR D 247 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG D 251 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET D 252 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 254 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 256 " --> pdb=" O MET D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 335 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 399 through 412 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 470 through 497 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 506 through 511 Processing helix chain 'D' and resid 513 through 535 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) removed outlier: 4.805A pdb=" N ASN D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL D 532 " --> pdb=" O ARG D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 541 No H-bonds generated for 'chain 'D' and resid 538 through 541' Processing helix chain 'D' and resid 549 through 575 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) Processing helix chain 'D' and resid 582 through 600 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 602 through 619 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 629 through 641 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 646 through 652 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 656 through 693 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= A, first strand: chain 'A' and resid 313 through 316 removed outlier: 3.704A pdb=" N LEU A 316 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 427 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id= B, 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) Processing sheet with id= C, first strand: chain 'B' and resid 313 through 316 removed outlier: 3.704A pdb=" N LEU B 316 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER B 427 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id= D, 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) Processing sheet with id= E, first strand: chain 'C' and resid 313 through 316 removed outlier: 3.705A pdb=" N LEU C 316 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER C 427 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id= F, 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) Processing sheet with id= G, first strand: chain 'D' and resid 313 through 316 removed outlier: 3.704A pdb=" N LEU D 316 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER D 427 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing sheet with id= H, 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) 644 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 8.11 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 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" O2 PX6 D1006 " pdb=" P1 PX6 D1006 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" O2 PX6 B1006 " pdb=" P1 PX6 B1006 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" O2 PX6 A1006 " pdb=" P1 PX6 A1006 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O3 PX6 D1006 " pdb=" P1 PX6 D1006 " ideal model delta sigma weight residual 1.510 1.456 0.054 2.00e-02 2.50e+03 7.37e+00 ... (remaining 17018 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.38: 267 106.38 - 113.29: 9485 113.29 - 120.21: 6436 120.21 - 127.13: 6655 127.13 - 134.05: 144 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 109.47 128.82 -19.35 3.00e+00 1.11e-01 4.16e+01 angle pdb=" C2 PX6 D1006 " pdb=" C3 PX6 D1006 " pdb=" O5 PX6 D1006 " ideal model delta sigma weight residual 109.47 128.78 -19.31 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C2 PX6 B1006 " pdb=" C3 PX6 B1006 " pdb=" O5 PX6 B1006 " ideal model delta sigma weight residual 109.47 128.73 -19.26 3.00e+00 1.11e-01 4.12e+01 angle pdb=" C2 PX6 C1006 " pdb=" C3 PX6 C1006 " pdb=" O5 PX6 C1006 " ideal model delta sigma weight residual 109.47 128.70 -19.23 3.00e+00 1.11e-01 4.11e+01 angle pdb=" C TYR B 311 " pdb=" CA TYR B 311 " pdb=" CB TYR B 311 " ideal model delta sigma weight residual 117.23 111.55 5.68 1.36e+00 5.41e-01 1.74e+01 ... (remaining 22982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 9012 16.10 - 32.21: 548 32.21 - 48.31: 114 48.31 - 64.41: 65 64.41 - 80.52: 12 Dihedral angle restraints: 9751 sinusoidal: 4019 harmonic: 5732 Sorted by residual: dihedral pdb=" C CHS C1011 " pdb=" N CHS C1011 " pdb=" CA CHS C1011 " pdb=" CB CHS C1011 " ideal model delta harmonic sigma weight residual -122.60 -97.08 -25.52 0 2.50e+00 1.60e-01 1.04e+02 dihedral pdb=" C CHS A1011 " pdb=" N CHS A1011 " pdb=" CA CHS A1011 " pdb=" CB CHS A1011 " ideal model delta harmonic sigma weight residual -122.60 -97.14 -25.46 0 2.50e+00 1.60e-01 1.04e+02 dihedral pdb=" C CHS D1011 " pdb=" N CHS D1011 " pdb=" CA CHS D1011 " pdb=" CB CHS D1011 " ideal model delta harmonic sigma weight residual -122.60 -97.24 -25.36 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 9748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 2577 0.218 - 0.437: 3 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: 378 2.57 - 3.15: 16865 3.15 - 3.74: 25475 3.74 - 4.32: 35899 4.32 - 4.90: 53640 Nonbonded interactions: 132257 Sorted by model distance: nonbonded pdb=" O3 NAG A1002 " pdb=" O7 NAG A1002 " model vdw 1.989 2.440 nonbonded pdb=" O3 NAG D1002 " pdb=" O7 NAG D1002 " model vdw 1.989 2.440 nonbonded pdb=" O3 NAG B1002 " pdb=" O7 NAG B1002 " model vdw 1.989 2.440 nonbonded pdb=" O3 NAG C1002 " pdb=" O7 NAG C1002 " model vdw 1.990 2.440 nonbonded pdb=" OD1 ASN B 328 " pdb=" O5 NAG B1001 " model vdw 2.037 3.040 ... (remaining 132252 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 695 or resid 1001 through 1011 \ )) selection = (chain 'B' and (resid 215 through 695 or resid 1001 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.750 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 41.730 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.139 17023 Z= 0.634 Angle : 1.124 19.346 22987 Z= 0.575 Chirality : 0.073 1.092 2588 Planarity : 0.005 0.046 2804 Dihedral : 12.753 80.517 6027 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 33.58 Ramachandran Plot: Outliers : 0.84 % Allowed : 11.69 % Favored : 87.47 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 9 poor density : 501 time to evaluate : 1.983 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. outliers start: 9 outliers final: 5 residues processed: 505 average time/residue: 0.2672 time to fit residues: 207.0625 Evaluate side-chains 336 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 331 time to evaluate : 1.858 Switching outliers to nearest non-outliers 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. outliers start: 5 outliers final: 4 residues processed: 5 average time/residue: 0.1485 time to fit residues: 3.9356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN B 498 HIS ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 17023 Z= 0.289 Angle : 0.835 10.614 22987 Z= 0.430 Chirality : 0.052 0.425 2588 Planarity : 0.005 0.036 2804 Dihedral : 12.104 59.528 2420 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.57 % Favored : 92.22 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.16), residues: 1916 helix: -2.97 (0.13), residues: 892 sheet: -1.37 (0.33), residues: 200 loop : -2.38 (0.19), residues: 824 *********************** 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 470 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 461 time to evaluate : 2.112 Fit side-chains 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. 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. outliers start: 9 outliers final: 5 residues processed: 461 average time/residue: 0.2480 time to fit residues: 179.6575 Evaluate side-chains 357 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 352 time to evaluate : 1.843 Switching outliers to nearest non-outliers 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. outliers start: 5 outliers final: 4 residues processed: 5 average time/residue: 0.1441 time to fit residues: 3.9148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 48 optimal weight: 50.0000 chunk 174 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 501 HIS B 430 ASN B 498 HIS B 501 HIS C 430 ASN C 501 HIS D 430 ASN D 501 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 17023 Z= 0.269 Angle : 0.729 8.809 22987 Z= 0.377 Chirality : 0.052 0.454 2588 Planarity : 0.004 0.027 2804 Dihedral : 11.093 59.221 2420 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.09 % Favored : 91.70 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.16), residues: 1916 helix: -2.30 (0.14), residues: 952 sheet: -1.34 (0.34), residues: 200 loop : -2.18 (0.20), residues: 764 *********************** 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 449 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 438 time to evaluate : 1.920 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. outliers start: 11 outliers final: 4 residues processed: 438 average time/residue: 0.2416 time to fit residues: 167.4286 Evaluate side-chains 334 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 330 time to evaluate : 1.780 Switching outliers to nearest non-outliers 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. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1446 time to fit residues: 3.7195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 0.0000 chunk 166 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN A 501 HIS B 498 HIS B 501 HIS C 501 HIS D 501 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 17023 Z= 0.203 Angle : 0.689 9.026 22987 Z= 0.350 Chirality : 0.050 0.439 2588 Planarity : 0.004 0.031 2804 Dihedral : 10.630 59.112 2420 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.42 % Favored : 93.37 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.17), residues: 1916 helix: -1.97 (0.14), residues: 948 sheet: -1.40 (0.33), residues: 200 loop : -2.05 (0.21), residues: 768 *********************** 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 441 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 433 time to evaluate : 1.776 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. outliers start: 8 outliers final: 4 residues processed: 433 average time/residue: 0.2410 time to fit residues: 167.6441 Evaluate side-chains 349 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 345 time to evaluate : 1.800 Switching outliers to nearest non-outliers 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. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1422 time to fit residues: 3.5520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 128 optimal weight: 0.0980 chunk 0 optimal weight: 50.0000 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS D 501 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 17023 Z= 0.198 Angle : 0.677 7.763 22987 Z= 0.342 Chirality : 0.049 0.435 2588 Planarity : 0.004 0.031 2804 Dihedral : 10.310 59.165 2420 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.84 % Favored : 92.95 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.17), residues: 1916 helix: -1.77 (0.15), residues: 940 sheet: -1.41 (0.35), residues: 196 loop : -1.85 (0.21), residues: 780 *********************** 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 442 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 435 time to evaluate : 1.961 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. revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. outliers start: 7 outliers final: 4 residues processed: 435 average time/residue: 0.2486 time to fit residues: 170.4922 Evaluate side-chains 361 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 357 time to evaluate : 1.908 Switching outliers to nearest non-outliers 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. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1478 time to fit residues: 3.8097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 185 optimal weight: 0.1980 chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 501 HIS A 681 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17023 Z= 0.228 Angle : 0.676 9.967 22987 Z= 0.344 Chirality : 0.049 0.430 2588 Planarity : 0.004 0.034 2804 Dihedral : 10.121 59.518 2420 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.84 % Favored : 92.95 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.17), residues: 1916 helix: -1.84 (0.14), residues: 944 sheet: -1.14 (0.36), residues: 200 loop : -1.77 (0.21), residues: 772 *********************** 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 428 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 421 time to evaluate : 2.012 Fit side-chains 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. 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. outliers start: 7 outliers final: 4 residues processed: 421 average time/residue: 0.2324 time to fit residues: 158.0279 Evaluate side-chains 349 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 345 time to evaluate : 1.926 Switching outliers to nearest non-outliers 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. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1530 time to fit residues: 3.7983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 105 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 185 optimal weight: 0.0170 chunk 115 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 overall best weight: 3.8824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN B 456 GLN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN C 622 GLN ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 17023 Z= 0.292 Angle : 0.705 8.007 22987 Z= 0.362 Chirality : 0.050 0.477 2588 Planarity : 0.004 0.034 2804 Dihedral : 10.101 59.705 2420 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.36 % Favored : 92.43 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.17), residues: 1916 helix: -1.77 (0.15), residues: 944 sheet: -1.10 (0.37), residues: 200 loop : -1.83 (0.21), residues: 772 *********************** 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 419 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 414 time to evaluate : 2.145 Fit side-chains 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. 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. outliers start: 5 outliers final: 4 residues processed: 415 average time/residue: 0.2268 time to fit residues: 154.5856 Evaluate side-chains 334 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 330 time to evaluate : 1.791 Switching outliers to nearest non-outliers 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. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1427 time to fit residues: 3.4811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 0.0770 chunk 17 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 overall best weight: 3.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 17023 Z= 0.260 Angle : 0.698 12.335 22987 Z= 0.355 Chirality : 0.050 0.469 2588 Planarity : 0.004 0.035 2804 Dihedral : 9.957 59.763 2420 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.89 % Favored : 92.90 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.17), residues: 1916 helix: -1.67 (0.15), residues: 940 sheet: -1.04 (0.37), residues: 200 loop : -1.85 (0.21), residues: 776 *********************** 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 427 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 423 time to evaluate : 1.981 Fit side-chains 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. 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. outliers start: 4 outliers final: 4 residues processed: 423 average time/residue: 0.2262 time to fit residues: 157.6716 Evaluate side-chains 330 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 326 time to evaluate : 1.981 Switching outliers to nearest non-outliers 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. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1524 time to fit residues: 4.0137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 498 HIS ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 ASN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN B 501 HIS B 681 ASN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS D 313 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 HIS ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 17023 Z= 0.238 Angle : 0.684 9.378 22987 Z= 0.350 Chirality : 0.048 0.441 2588 Planarity : 0.004 0.034 2804 Dihedral : 9.826 59.991 2420 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.84 % Favored : 92.95 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.18), residues: 1916 helix: -1.57 (0.15), residues: 936 sheet: -0.99 (0.37), residues: 200 loop : -1.95 (0.21), residues: 780 *********************** 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 415 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 410 time to evaluate : 2.017 Fit side-chains 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. 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. outliers start: 5 outliers final: 4 residues processed: 410 average time/residue: 0.2255 time to fit residues: 152.4531 Evaluate side-chains 335 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 331 time to evaluate : 1.888 Switching outliers to nearest non-outliers 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. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1411 time to fit residues: 3.5922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 191 optimal weight: 0.4980 chunk 176 optimal weight: 0.2980 chunk 152 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 498 HIS ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS D 313 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 HIS ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17023 Z= 0.221 Angle : 0.678 9.462 22987 Z= 0.344 Chirality : 0.047 0.419 2588 Planarity : 0.004 0.035 2804 Dihedral : 9.671 59.921 2420 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.47 % Favored : 93.32 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.18), residues: 1916 helix: -1.51 (0.15), residues: 928 sheet: -0.94 (0.37), residues: 200 loop : -1.66 (0.22), residues: 788 ********************** 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 424 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 420 time to evaluate : 1.899 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 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. outliers start: 4 outliers final: 4 residues processed: 420 average time/residue: 0.2249 time to fit residues: 155.2295 Evaluate side-chains 340 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 336 time to evaluate : 1.964 Switching outliers to nearest non-outliers 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. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1538 time to fit residues: 3.8645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 133 optimal weight: 0.0270 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 HIS ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 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 = 0.3891 r_free = 0.3891 target = 0.143938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110022 restraints weight = 33977.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113295 restraints weight = 20359.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115517 restraints weight = 14768.431| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17023 Z= 0.183 Angle : 0.662 10.089 22987 Z= 0.333 Chirality : 0.046 0.369 2588 Planarity : 0.004 0.035 2804 Dihedral : 9.464 59.808 2420 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.37 % Favored : 93.42 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.18), residues: 1916 helix: -1.37 (0.15), residues: 932 sheet: -0.81 (0.38), residues: 200 loop : -1.80 (0.21), residues: 784 =============================================================================== Job complete usr+sys time: 3406.82 seconds wall clock time: 62 minutes 52.68 seconds (3772.68 seconds total)