Starting phenix.real_space_refine on Fri Feb 16 21:45:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/02_2024/5mkf_3524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/02_2024/5mkf_3524.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/02_2024/5mkf_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_3524/02_2024/5mkf_3524_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/02_2024/5mkf_3524_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/02_2024/5mkf_3524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/02_2024/5mkf_3524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/02_2024/5mkf_3524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mkf_3524/02_2024/5mkf_3524_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 13 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: 13 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: 13 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: 13 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.26, per 1000 atoms: 0.56 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: 6.86 Conformation dependent library (CDL) restraints added in 2.6 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: 2.90 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: 4.11 Time building geometry restraints manager: 7.31 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: 9376 16.10 - 32.21: 580 32.21 - 48.31: 118 48.31 - 64.41: 93 64.41 - 80.52: 12 Dihedral angle restraints: 10179 sinusoidal: 4447 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 10176 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: 0.200 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: 1.900 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 43.200 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.650 ------------------------------------------------------------------------------- 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 : 13.054 80.517 6455 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 % 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP D 293 HIS 0.014 0.004 HIS B 379 PHE 0.020 0.003 PHE C 598 TYR 0.022 0.003 TYR A 391 ARG 0.007 0.001 ARG D 325 *********************** 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 : 1.765 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: 0.2567 time to fit residues: 200.2822 Evaluate side-chains 336 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 331 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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: 0.7063 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17023 Z= 0.286 Angle : 0.822 10.216 22987 Z= 0.427 Chirality : 0.054 0.470 2588 Planarity : 0.005 0.036 2804 Dihedral : 12.560 59.587 2848 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.67 % Favored : 92.12 % Rotamer: Outliers : 0.52 % Allowed : 3.36 % Favored : 96.12 % 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: -4.00 (0.16), residues: 1916 helix: -2.95 (0.13), residues: 920 sheet: -1.38 (0.33), residues: 200 loop : -2.42 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 293 HIS 0.003 0.001 HIS B 550 PHE 0.027 0.002 PHE C 608 TYR 0.023 0.003 TYR D 391 ARG 0.008 0.001 ARG D 654 *********************** 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 472 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 463 time to evaluate : 1.927 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. REVERT: A 230 PHE cc_start: 0.8268 (t80) cc_final: 0.7965 (t80) REVERT: A 241 MET cc_start: 0.7540 (mtt) cc_final: 0.6572 (ttp) REVERT: A 249 TYR cc_start: 0.8903 (t80) cc_final: 0.7869 (t80) REVERT: A 287 LEU cc_start: 0.8545 (mp) cc_final: 0.8337 (mp) REVERT: A 650 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7902 (mt-10) REVERT: B 241 MET cc_start: 0.7711 (mtt) cc_final: 0.6728 (ttp) REVERT: B 249 TYR cc_start: 0.8984 (t80) cc_final: 0.7943 (t80) REVERT: B 608 PHE cc_start: 0.8504 (t80) cc_final: 0.8298 (t80) REVERT: B 666 PHE cc_start: 0.8868 (t80) cc_final: 0.8645 (t80) REVERT: C 241 MET cc_start: 0.7244 (mtp) cc_final: 0.6130 (ttp) REVERT: C 249 TYR cc_start: 0.8859 (t80) cc_final: 0.7847 (t80) REVERT: C 287 LEU cc_start: 0.8548 (mp) cc_final: 0.8327 (mp) REVERT: C 650 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7922 (mt-10) REVERT: D 230 PHE cc_start: 0.8280 (t80) cc_final: 0.7979 (t80) REVERT: D 241 MET cc_start: 0.7592 (mtt) cc_final: 0.6594 (ttp) REVERT: D 249 TYR cc_start: 0.8898 (t80) cc_final: 0.7866 (t80) outliers start: 9 outliers final: 5 residues processed: 463 average time/residue: 0.2479 time to fit residues: 182.0408 Evaluate side-chains 359 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 354 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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: 4.9990 chunk 145 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 50.0000 chunk 174 optimal weight: 5.9990 chunk 188 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 chunk 173 optimal weight: 0.1980 chunk 59 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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: 0.7032 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17023 Z= 0.244 Angle : 0.705 7.194 22987 Z= 0.367 Chirality : 0.051 0.463 2588 Planarity : 0.004 0.027 2804 Dihedral : 11.514 59.961 2848 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.62 % Favored : 92.17 % Rotamer: Outliers : 0.52 % Allowed : 3.42 % Favored : 96.06 % 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: -3.17 (0.17), residues: 1916 helix: -2.15 (0.14), residues: 924 sheet: -1.32 (0.34), residues: 200 loop : -2.06 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 293 HIS 0.002 0.001 HIS A 550 PHE 0.017 0.002 PHE A 426 TYR 0.019 0.002 TYR B 391 ARG 0.005 0.000 ARG C 654 *********************** 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 455 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 446 time to evaluate : 1.934 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: 0.7098 (mtt) cc_final: 0.6178 (ttp) REVERT: A 249 TYR cc_start: 0.8844 (t80) cc_final: 0.7793 (t80) REVERT: B 241 MET cc_start: 0.7505 (mtt) cc_final: 0.6433 (ttp) REVERT: B 249 TYR cc_start: 0.8916 (t80) cc_final: 0.7971 (t80) REVERT: C 241 MET cc_start: 0.6900 (mtp) cc_final: 0.5966 (ttp) REVERT: C 249 TYR cc_start: 0.8853 (t80) cc_final: 0.7791 (t80) REVERT: C 551 LEU cc_start: 0.8349 (mt) cc_final: 0.8143 (mt) REVERT: C 608 PHE cc_start: 0.8295 (t80) cc_final: 0.8003 (t80) REVERT: D 241 MET cc_start: 0.6965 (mtt) cc_final: 0.6057 (ttp) REVERT: D 249 TYR cc_start: 0.8842 (t80) cc_final: 0.7770 (t80) REVERT: D 551 LEU cc_start: 0.8342 (mt) cc_final: 0.8131 (mt) outliers start: 9 outliers final: 4 residues processed: 446 average time/residue: 0.2439 time to fit residues: 172.3536 Evaluate side-chains 341 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 337 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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: 2.9990 chunk 131 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 83 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS B 501 HIS C 501 HIS D 501 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3690 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= 0.235 Angle : 0.687 9.433 22987 Z= 0.352 Chirality : 0.050 0.458 2588 Planarity : 0.004 0.031 2804 Dihedral : 11.000 58.723 2848 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.73 % Favored : 93.06 % Rotamer: Outliers : 0.46 % Allowed : 4.06 % Favored : 95.48 % 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: -2.98 (0.17), residues: 1916 helix: -1.87 (0.15), residues: 940 sheet: -1.42 (0.34), residues: 200 loop : -2.08 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 293 HIS 0.002 0.001 HIS C 550 PHE 0.028 0.002 PHE A 608 TYR 0.016 0.002 TYR C 247 ARG 0.010 0.000 ARG A 338 *********************** 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 442 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 434 time to evaluate : 1.913 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: 0.6989 (mtt) cc_final: 0.6107 (ttp) REVERT: A 249 TYR cc_start: 0.8974 (t80) cc_final: 0.7884 (t80) REVERT: A 551 LEU cc_start: 0.8232 (mt) cc_final: 0.7988 (mt) REVERT: B 230 PHE cc_start: 0.8437 (t80) cc_final: 0.8160 (t80) REVERT: B 241 MET cc_start: 0.7214 (mtt) cc_final: 0.6316 (ttp) REVERT: B 249 TYR cc_start: 0.8983 (t80) cc_final: 0.7879 (t80) REVERT: C 241 MET cc_start: 0.6860 (mtp) cc_final: 0.6051 (ttp) REVERT: C 249 TYR cc_start: 0.8966 (t80) cc_final: 0.7858 (t80) REVERT: D 241 MET cc_start: 0.7000 (mtt) cc_final: 0.6111 (ttp) REVERT: D 249 TYR cc_start: 0.8966 (t80) cc_final: 0.7832 (t80) outliers start: 8 outliers final: 4 residues processed: 434 average time/residue: 0.2177 time to fit residues: 154.4084 Evaluate side-chains 340 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 336 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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: 9.9990 chunk 105 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 94 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS A 681 ASN B 537 GLN C 501 HIS C 681 ASN D 501 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17023 Z= 0.305 Angle : 0.717 6.695 22987 Z= 0.370 Chirality : 0.052 0.484 2588 Planarity : 0.004 0.033 2804 Dihedral : 10.579 59.897 2848 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.30 % Favored : 91.49 % Rotamer: Outliers : 0.41 % Allowed : 2.61 % Favored : 96.99 % 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: -2.86 (0.17), residues: 1916 helix: -1.86 (0.15), residues: 924 sheet: -1.32 (0.36), residues: 200 loop : -1.90 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP C 293 HIS 0.002 0.001 HIS A 550 PHE 0.037 0.002 PHE A 608 TYR 0.020 0.002 TYR B 391 ARG 0.005 0.000 ARG A 338 *********************** 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 422 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 415 time to evaluate : 1.855 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: 0.6997 (mtt) cc_final: 0.6146 (ttp) REVERT: A 249 TYR cc_start: 0.8932 (t80) cc_final: 0.7828 (t80) REVERT: A 551 LEU cc_start: 0.8324 (mt) cc_final: 0.7997 (mt) REVERT: B 241 MET cc_start: 0.7279 (mtt) cc_final: 0.6330 (ttp) REVERT: B 249 TYR cc_start: 0.8907 (t80) cc_final: 0.7741 (t80) REVERT: B 551 LEU cc_start: 0.8251 (mt) cc_final: 0.8000 (mt) REVERT: C 241 MET cc_start: 0.6889 (mtp) cc_final: 0.6085 (ttp) REVERT: C 249 TYR cc_start: 0.8941 (t80) cc_final: 0.7818 (t80) REVERT: C 551 LEU cc_start: 0.8442 (mt) cc_final: 0.8168 (mt) REVERT: D 241 MET cc_start: 0.6984 (mtt) cc_final: 0.6122 (ttp) REVERT: D 249 TYR cc_start: 0.8930 (t80) cc_final: 0.7779 (t80) REVERT: D 551 LEU cc_start: 0.8438 (mt) cc_final: 0.8159 (mt) REVERT: D 605 PHE cc_start: 0.7368 (m-80) cc_final: 0.7162 (m-80) outliers start: 7 outliers final: 4 residues processed: 415 average time/residue: 0.2127 time to fit residues: 146.3954 Evaluate side-chains 338 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 334 time to evaluate : 1.799 ------------------------------------------------------------------------------- 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: 7.9990 chunk 167 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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 537 GLN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN C 434 ASN D 434 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17023 Z= 0.190 Angle : 0.655 9.395 22987 Z= 0.334 Chirality : 0.049 0.442 2588 Planarity : 0.004 0.034 2804 Dihedral : 10.108 59.274 2848 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.69 % Favored : 94.10 % Rotamer: Outliers : 0.29 % Allowed : 2.32 % Favored : 97.39 % 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: -2.62 (0.17), residues: 1916 helix: -1.67 (0.15), residues: 912 sheet: -1.17 (0.36), residues: 200 loop : -1.80 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 293 HIS 0.002 0.001 HIS C 550 PHE 0.036 0.002 PHE D 608 TYR 0.017 0.002 TYR D 348 ARG 0.003 0.000 ARG C 399 *********************** 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 437 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 432 time to evaluate : 1.740 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: 0.6933 (mtt) cc_final: 0.6107 (ttp) REVERT: A 249 TYR cc_start: 0.8836 (t80) cc_final: 0.7914 (t80) REVERT: A 551 LEU cc_start: 0.8407 (mt) cc_final: 0.8136 (mt) REVERT: B 241 MET cc_start: 0.7165 (mtt) cc_final: 0.6319 (ttp) REVERT: B 249 TYR cc_start: 0.8784 (t80) cc_final: 0.7820 (t80) REVERT: B 255 GLN cc_start: 0.9170 (mt0) cc_final: 0.8939 (mm-40) REVERT: B 551 LEU cc_start: 0.8262 (mt) cc_final: 0.8051 (mt) REVERT: C 241 MET cc_start: 0.6723 (mtp) cc_final: 0.5976 (ttp) REVERT: C 249 TYR cc_start: 0.8827 (t80) cc_final: 0.7904 (t80) REVERT: C 255 GLN cc_start: 0.9198 (mt0) cc_final: 0.8955 (mm-40) REVERT: C 551 LEU cc_start: 0.8482 (mt) cc_final: 0.8220 (mt) REVERT: D 241 MET cc_start: 0.6906 (mtt) cc_final: 0.6102 (ttp) REVERT: D 249 TYR cc_start: 0.8821 (t80) cc_final: 0.7884 (t80) REVERT: D 255 GLN cc_start: 0.9199 (mt0) cc_final: 0.8947 (mm-40) REVERT: D 551 LEU cc_start: 0.8479 (mt) cc_final: 0.8207 (mt) outliers start: 5 outliers final: 4 residues processed: 432 average time/residue: 0.2568 time to fit residues: 175.8680 Evaluate side-chains 350 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 156 optimal weight: 0.0020 chunk 103 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 537 GLN D 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17023 Z= 0.207 Angle : 0.655 7.815 22987 Z= 0.334 Chirality : 0.048 0.427 2588 Planarity : 0.004 0.036 2804 Dihedral : 9.858 59.961 2848 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.58 % Favored : 93.22 % Rotamer: Outliers : 0.29 % Allowed : 2.61 % Favored : 97.10 % 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: -2.61 (0.17), residues: 1916 helix: -1.62 (0.15), residues: 936 sheet: -0.99 (0.37), residues: 200 loop : -1.89 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 293 HIS 0.002 0.000 HIS B 550 PHE 0.042 0.002 PHE A 608 TYR 0.018 0.002 TYR A 684 ARG 0.007 0.000 ARG D 251 *********************** 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 424 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 419 time to evaluate : 2.042 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 239 TYR cc_start: 0.8848 (t80) cc_final: 0.8605 (t80) REVERT: A 241 MET cc_start: 0.6925 (mtt) cc_final: 0.6077 (ttp) REVERT: A 249 TYR cc_start: 0.8882 (t80) cc_final: 0.8011 (t80) REVERT: A 551 LEU cc_start: 0.8441 (mt) cc_final: 0.8142 (mt) REVERT: B 241 MET cc_start: 0.7118 (mtt) cc_final: 0.6151 (ttp) REVERT: B 249 TYR cc_start: 0.8942 (t80) cc_final: 0.7954 (t80) REVERT: B 255 GLN cc_start: 0.9143 (mt0) cc_final: 0.8929 (mm-40) REVERT: B 551 LEU cc_start: 0.8305 (mt) cc_final: 0.8022 (mt) REVERT: C 239 TYR cc_start: 0.8875 (t80) cc_final: 0.8576 (t80) REVERT: C 241 MET cc_start: 0.6784 (mtp) cc_final: 0.6007 (ttp) REVERT: C 249 TYR cc_start: 0.8866 (t80) cc_final: 0.7895 (t80) REVERT: C 255 GLN cc_start: 0.9165 (mt0) cc_final: 0.8936 (mm-40) REVERT: D 239 TYR cc_start: 0.8856 (t80) cc_final: 0.8643 (t80) REVERT: D 241 MET cc_start: 0.6917 (mtt) cc_final: 0.6064 (ttp) REVERT: D 249 TYR cc_start: 0.8850 (t80) cc_final: 0.7875 (t80) REVERT: D 255 GLN cc_start: 0.9204 (mt0) cc_final: 0.8974 (mm-40) outliers start: 5 outliers final: 4 residues processed: 419 average time/residue: 0.2227 time to fit residues: 152.8023 Evaluate side-chains 339 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 335 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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: 5.9990 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 0.0570 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- 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** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17023 Z= 0.175 Angle : 0.656 9.714 22987 Z= 0.329 Chirality : 0.047 0.385 2588 Planarity : 0.004 0.036 2804 Dihedral : 9.613 59.279 2848 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.63 % Favored : 93.16 % Rotamer: Outliers : 0.29 % Allowed : 1.39 % Favored : 98.32 % 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: -2.38 (0.18), residues: 1916 helix: -1.46 (0.15), residues: 936 sheet: -0.83 (0.37), residues: 200 loop : -1.76 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 293 HIS 0.002 0.001 HIS C 550 PHE 0.030 0.002 PHE B 608 TYR 0.017 0.001 TYR B 348 ARG 0.006 0.000 ARG D 251 *********************** 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 fitting. rotamer outliers: 5 poor density : 446 time to evaluate : 1.745 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. REVERT: A 239 TYR cc_start: 0.8861 (t80) cc_final: 0.8551 (t80) REVERT: A 241 MET cc_start: 0.6953 (mtt) cc_final: 0.6038 (ttp) REVERT: A 249 TYR cc_start: 0.9041 (t80) cc_final: 0.8274 (t80) REVERT: A 551 LEU cc_start: 0.8394 (mt) cc_final: 0.8120 (mt) REVERT: B 241 MET cc_start: 0.7053 (mtt) cc_final: 0.6197 (ttp) REVERT: B 249 TYR cc_start: 0.8867 (t80) cc_final: 0.7916 (t80) REVERT: B 498 HIS cc_start: 0.4537 (m170) cc_final: 0.3954 (m170) REVERT: B 501 HIS cc_start: 0.4304 (OUTLIER) cc_final: 0.3275 (m170) REVERT: B 551 LEU cc_start: 0.8330 (mt) cc_final: 0.8050 (mt) REVERT: C 239 TYR cc_start: 0.8860 (t80) cc_final: 0.8589 (t80) REVERT: C 241 MET cc_start: 0.6741 (mtp) cc_final: 0.5912 (ttp) REVERT: C 249 TYR cc_start: 0.8959 (t80) cc_final: 0.7935 (t80) REVERT: C 255 GLN cc_start: 0.9153 (mt0) cc_final: 0.8950 (mm-40) REVERT: C 288 LEU cc_start: 0.9147 (tp) cc_final: 0.8937 (tt) REVERT: C 395 LEU cc_start: 0.8491 (mp) cc_final: 0.7897 (tp) REVERT: C 460 LEU cc_start: 0.9031 (pp) cc_final: 0.8724 (pt) REVERT: D 239 TYR cc_start: 0.8921 (t80) cc_final: 0.8578 (t80) REVERT: D 241 MET cc_start: 0.6971 (mtt) cc_final: 0.6019 (ttp) REVERT: D 249 TYR cc_start: 0.8961 (t80) cc_final: 0.7912 (t80) REVERT: D 255 GLN cc_start: 0.9172 (mt0) cc_final: 0.8971 (mm-40) outliers start: 5 outliers final: 4 residues processed: 446 average time/residue: 0.2260 time to fit residues: 163.7092 Evaluate side-chains 368 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 363 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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: 0.0770 chunk 161 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17023 Z= 0.210 Angle : 0.660 9.142 22987 Z= 0.334 Chirality : 0.047 0.565 2588 Planarity : 0.004 0.037 2804 Dihedral : 9.550 59.433 2848 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.32 % Favored : 93.48 % Rotamer: Outliers : 0.23 % Allowed : 0.64 % Favored : 99.13 % 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: -2.25 (0.18), residues: 1916 helix: -1.36 (0.15), residues: 932 sheet: -0.75 (0.37), residues: 200 loop : -1.69 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 293 HIS 0.005 0.001 HIS B 498 PHE 0.032 0.002 PHE A 608 TYR 0.017 0.002 TYR A 247 ARG 0.007 0.001 ARG C 251 *********************** 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 425 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 2.030 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 239 TYR cc_start: 0.8884 (t80) cc_final: 0.8586 (t80) REVERT: A 241 MET cc_start: 0.6928 (mtt) cc_final: 0.6040 (ttp) REVERT: A 249 TYR cc_start: 0.8962 (t80) cc_final: 0.8241 (t80) REVERT: A 395 LEU cc_start: 0.8567 (mp) cc_final: 0.7985 (tp) REVERT: B 241 MET cc_start: 0.7084 (mtt) cc_final: 0.6182 (ttp) REVERT: B 249 TYR cc_start: 0.8880 (t80) cc_final: 0.7952 (t80) REVERT: B 279 PHE cc_start: 0.8989 (t80) cc_final: 0.8773 (t80) REVERT: B 551 LEU cc_start: 0.8349 (mt) cc_final: 0.8134 (mt) REVERT: C 239 TYR cc_start: 0.8897 (t80) cc_final: 0.8614 (t80) REVERT: C 241 MET cc_start: 0.6708 (mtp) cc_final: 0.5940 (ttp) REVERT: C 249 TYR cc_start: 0.8895 (t80) cc_final: 0.7905 (t80) REVERT: C 395 LEU cc_start: 0.8537 (mp) cc_final: 0.7941 (tp) REVERT: D 239 TYR cc_start: 0.8898 (t80) cc_final: 0.8601 (t80) REVERT: D 241 MET cc_start: 0.6941 (mtt) cc_final: 0.6102 (ttp) REVERT: D 249 TYR cc_start: 0.8896 (t80) cc_final: 0.7887 (t80) REVERT: D 255 GLN cc_start: 0.9205 (mt0) cc_final: 0.8999 (mm-40) REVERT: D 279 PHE cc_start: 0.9017 (t80) cc_final: 0.8807 (t80) outliers start: 4 outliers final: 4 residues processed: 421 average time/residue: 0.2108 time to fit residues: 146.8976 Evaluate side-chains 356 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 352 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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: 9.9990 chunk 126 optimal weight: 0.3980 chunk 191 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 152 optimal weight: 50.0000 chunk 15 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 498 HIS D 498 HIS ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17023 Z= 0.219 Angle : 0.672 8.923 22987 Z= 0.341 Chirality : 0.048 0.541 2588 Planarity : 0.004 0.037 2804 Dihedral : 9.483 59.747 2848 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.52 % Favored : 93.27 % Rotamer: Outliers : 0.23 % Allowed : 0.35 % Favored : 99.42 % 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: -2.23 (0.18), residues: 1916 helix: -1.35 (0.15), residues: 920 sheet: -0.69 (0.38), residues: 200 loop : -1.69 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 293 HIS 0.006 0.001 HIS A 550 PHE 0.038 0.002 PHE B 608 TYR 0.017 0.002 TYR A 247 ARG 0.007 0.001 ARG B 251 ********************** 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 430 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 426 time to evaluate : 2.058 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. 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 239 TYR cc_start: 0.8878 (t80) cc_final: 0.8589 (t80) REVERT: A 241 MET cc_start: 0.6986 (mtt) cc_final: 0.6003 (ttp) REVERT: A 249 TYR cc_start: 0.8976 (t80) cc_final: 0.8235 (t80) REVERT: B 241 MET cc_start: 0.7138 (mtt) cc_final: 0.6365 (ttp) REVERT: B 249 TYR cc_start: 0.8899 (t80) cc_final: 0.7975 (t80) REVERT: B 551 LEU cc_start: 0.8411 (mt) cc_final: 0.8183 (mt) REVERT: C 239 TYR cc_start: 0.8920 (t80) cc_final: 0.8623 (t80) REVERT: C 241 MET cc_start: 0.6752 (mtp) cc_final: 0.5951 (ttp) REVERT: C 249 TYR cc_start: 0.8914 (t80) cc_final: 0.8025 (t80) REVERT: C 395 LEU cc_start: 0.8545 (mp) cc_final: 0.7963 (tp) REVERT: C 593 CYS cc_start: 0.7372 (p) cc_final: 0.7117 (p) REVERT: D 239 TYR cc_start: 0.8926 (t80) cc_final: 0.8668 (t80) REVERT: D 241 MET cc_start: 0.7015 (mtt) cc_final: 0.6052 (ttp) REVERT: D 249 TYR cc_start: 0.8904 (t80) cc_final: 0.7879 (t80) outliers start: 4 outliers final: 4 residues processed: 426 average time/residue: 0.2112 time to fit residues: 149.1017 Evaluate side-chains 350 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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: 20.0000 chunk 46 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 498 HIS ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.144176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110094 restraints weight = 33918.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113319 restraints weight = 20602.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115501 restraints weight = 15087.667| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17023 Z= 0.194 Angle : 0.648 7.225 22987 Z= 0.331 Chirality : 0.046 0.430 2588 Planarity : 0.004 0.037 2804 Dihedral : 9.382 59.863 2848 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.37 % Favored : 93.42 % Rotamer: Outliers : 0.23 % Allowed : 0.41 % Favored : 99.36 % 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: -2.15 (0.18), residues: 1916 helix: -1.27 (0.15), residues: 916 sheet: -0.79 (0.38), residues: 196 loop : -1.62 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 293 HIS 0.001 0.000 HIS B 550 PHE 0.038 0.002 PHE C 608 TYR 0.027 0.002 TYR C 227 ARG 0.006 0.001 ARG C 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3512.51 seconds wall clock time: 64 minutes 55.88 seconds (3895.88 seconds total)