Starting phenix.real_space_refine (version: dev) on Wed Feb 22 02:46:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/02_2023/5mke_3523_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C ARG 417": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 496": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 654": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 154 Unusual residues: {' CA': 2, 'CHS': 2, 'NAG': 2, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 10} Link IDs: {'TRANS': 1, None: 8} Not linked: pdbres="NAG A1001 " pdbres="NAG A1002 " Not linked: pdbres="NAG A1002 " pdbres="CHS A1005 " Not linked: pdbres="CHS A1006 " pdbres="PX6 A1007 " Not linked: pdbres="PX6 A1007 " pdbres="PLM A1008 " Not linked: pdbres="PLM A1008 " pdbres="PLM A1009 " ... (remaining 3 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 152 Unusual residues: {'CHS': 2, 'NAG': 2, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 8} Link IDs: {'TRANS': 1, None: 6} Not linked: pdbres="NAG B1001 " pdbres="NAG B1002 " Not linked: pdbres="NAG B1002 " pdbres="CHS B1005 " Not linked: pdbres="CHS B1006 " pdbres="PX6 B1007 " Not linked: pdbres="PX6 B1007 " pdbres="PLM B1008 " Not linked: pdbres="PLM B1008 " pdbres="PLM B1009 " Not linked: pdbres="PLM B1009 " pdbres="PLM B1010 " Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 152 Unusual residues: {'CHS': 2, 'NAG': 2, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 8} Link IDs: {'TRANS': 1, None: 6} Not linked: pdbres="NAG C1001 " pdbres="NAG C1002 " Not linked: pdbres="NAG C1002 " pdbres="CHS C1005 " Not linked: pdbres="CHS C1006 " pdbres="PX6 C1007 " Not linked: pdbres="PX6 C1007 " pdbres="PLM C1008 " Not linked: pdbres="PLM C1008 " pdbres="PLM C1009 " Not linked: pdbres="PLM C1009 " pdbres="PLM C1010 " Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 180 Unusual residues: {'CHS': 2, 'NAG': 4, 'PLM': 3, 'PX6': 1} Classifications: {'undetermined': 10} Link IDs: {'TRANS': 1, None: 8} Not linked: pdbres="NAG D1001 " pdbres="NAG D1002 " Not linked: pdbres="NAG D1002 " pdbres="NAG D1003 " Not linked: pdbres="NAG D1003 " pdbres="NAG D1004 " Not linked: pdbres="NAG D1004 " pdbres="CHS D1005 " Not linked: pdbres="CHS D1006 " pdbres="PX6 D1007 " ... (remaining 3 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.92, per 1000 atoms: 0.54 Number of scatterers: 16426 At special positions: 0 Unit cell: (115.14, 115.14, 101.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 76 16.00 P 4 15.00 O 2924 8.00 N 2508 7.00 C 10912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D1003 " - " NAG D1004 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1001 " - " ASN A 305 " " NAG A1002 " - " ASN A 362 " " NAG B1001 " - " ASN B 305 " " NAG B1002 " - " ASN B 362 " " NAG C1001 " - " ASN C 305 " " NAG C1002 " - " ASN C 362 " " NAG D1001 " - " ASN D 305 " " NAG D1002 " - " ASN D 362 " " NAG D1003 " - " ASN D 375 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 375 " " NAG G 1 " - " ASN C 375 " Time building additional restraints: 7.35 Conformation dependent library (CDL) restraints added in 2.1 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 8 sheets defined 52.4% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 216 through 241 removed outlier: 3.727A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.813A pdb=" N MET A 252 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.759A pdb=" N TRP A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 363 through 366 removed outlier: 3.755A pdb=" N TRP A 366 " --> pdb=" O GLY A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 399 through 411 removed outlier: 4.051A pdb=" N ALA A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 497 removed outlier: 4.138A pdb=" N CYS A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 482 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 541 removed outlier: 3.960A pdb=" N ILE A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 577 removed outlier: 3.760A pdb=" N PHE A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.740A pdb=" N SER A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 619 removed outlier: 4.192A pdb=" N PHE A 600 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 601 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 602 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 603 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 606 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 641 removed outlier: 3.515A pdb=" N PHE A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 removed outlier: 3.524A pdb=" N GLU A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 692 removed outlier: 3.731A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 679 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.726A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 254 removed outlier: 4.813A pdb=" N MET B 252 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.758A pdb=" N TRP B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 290 No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 363 through 366 removed outlier: 3.755A pdb=" N TRP B 366 " --> pdb=" O GLY B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 366' Processing helix chain 'B' and resid 399 through 411 removed outlier: 4.052A pdb=" N ALA B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 497 removed outlier: 4.139A pdb=" N CYS B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS B 481 " --> pdb=" O GLU B 477 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B 490 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU B 491 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 541 removed outlier: 3.961A pdb=" N ILE B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 516 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU B 535 " --> pdb=" O ASN B 531 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 577 removed outlier: 3.761A pdb=" N PHE B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.739A pdb=" N SER B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 619 removed outlier: 4.192A pdb=" N PHE B 600 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 601 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 602 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 603 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 606 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 641 removed outlier: 3.514A pdb=" N PHE B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 652 removed outlier: 3.524A pdb=" N GLU B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 692 removed outlier: 3.731A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 241 removed outlier: 3.726A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 254 removed outlier: 4.812A pdb=" N MET C 252 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.759A pdb=" N TRP C 280 " --> pdb=" O MET C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 290 No H-bonds generated for 'chain 'C' and resid 287 through 290' Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 363 through 366 removed outlier: 3.755A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 366' Processing helix chain 'C' and resid 399 through 411 removed outlier: 4.052A pdb=" N ALA C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 497 removed outlier: 4.139A pdb=" N CYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE C 479 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C 482 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 487 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 490 " --> pdb=" O TYR C 486 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU C 491 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 541 removed outlier: 3.960A pdb=" N ILE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 516 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 538 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 577 removed outlier: 3.760A pdb=" N PHE C 568 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C 574 " --> pdb=" O TRP C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 592 removed outlier: 3.739A pdb=" N SER C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR C 588 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 591 " --> pdb=" O SER C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 619 removed outlier: 4.191A pdb=" N PHE C 600 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 601 " --> pdb=" O PHE C 598 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE C 602 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C 603 " --> pdb=" O PHE C 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE C 606 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 641 removed outlier: 3.514A pdb=" N PHE C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 640 " --> pdb=" O GLN C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 652 removed outlier: 3.523A pdb=" N GLU C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 692 removed outlier: 3.731A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 673 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE C 679 " --> pdb=" O MET C 675 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 683 " --> pdb=" O ILE C 679 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 241 removed outlier: 3.726A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 254 removed outlier: 4.813A pdb=" N MET D 252 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 removed outlier: 3.759A pdb=" N TRP D 280 " --> pdb=" O MET D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 290 No H-bonds generated for 'chain 'D' and resid 287 through 290' Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 363 through 366 removed outlier: 3.755A pdb=" N TRP D 366 " --> pdb=" O GLY D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 366' Processing helix chain 'D' and resid 399 through 411 removed outlier: 4.052A pdb=" N ALA D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL D 406 " --> pdb=" O THR D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 497 removed outlier: 4.139A pdb=" N CYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS D 481 " --> pdb=" O GLU D 477 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE D 482 " --> pdb=" O ILE D 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 487 " --> pdb=" O PHE D 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 490 " --> pdb=" O TYR D 486 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU D 491 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 541 removed outlier: 3.961A pdb=" N ILE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 516 " --> pdb=" O VAL D 512 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE D 526 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU D 535 " --> pdb=" O ASN D 531 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 538 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 577 removed outlier: 3.761A pdb=" N PHE D 568 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE D 574 " --> pdb=" O TRP D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.739A pdb=" N SER D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 619 removed outlier: 4.192A pdb=" N PHE D 600 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 601 " --> pdb=" O PHE D 598 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 602 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET D 603 " --> pdb=" O PHE D 600 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 606 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 641 removed outlier: 3.514A pdb=" N PHE D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE D 640 " --> pdb=" O GLN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.523A pdb=" N GLU D 650 " --> pdb=" O PHE D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 692 removed outlier: 3.731A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU D 673 " --> pdb=" O PHE D 669 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE D 679 " --> pdb=" O MET D 675 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 683 " --> pdb=" O ILE D 679 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 421 through 423 removed outlier: 3.566A pdb=" N GLN A 458 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 442 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 426 through 429 Processing sheet with id= C, first strand: chain 'B' and resid 421 through 423 removed outlier: 3.566A pdb=" N GLN B 458 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 442 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 426 through 429 Processing sheet with id= E, first strand: chain 'C' and resid 421 through 423 removed outlier: 3.566A pdb=" N GLN C 458 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 442 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 426 through 429 Processing sheet with id= G, first strand: chain 'D' and resid 421 through 423 removed outlier: 3.566A pdb=" N GLN D 458 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU D 442 " --> pdb=" O SER D 454 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 426 through 429 612 hydrogen bonds defined for protein. 1500 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: 4.13 Time building geometry restraints manager: 7.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2492 1.31 - 1.43: 5007 1.43 - 1.56: 9192 1.56 - 1.68: 21 1.68 - 1.81: 116 Bond restraints: 16828 Sorted by residual: bond pdb=" O2 PX6 B1007 " pdb=" P1 PX6 B1007 " ideal model delta sigma weight residual 1.510 1.650 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" O2 PX6 D1007 " pdb=" P1 PX6 D1007 " ideal model delta sigma weight residual 1.510 1.650 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" O2 PX6 A1007 " pdb=" P1 PX6 A1007 " ideal model delta sigma weight residual 1.510 1.650 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" O2 PX6 C1007 " pdb=" P1 PX6 C1007 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C5 NAG F 1 " pdb=" C6 NAG F 1 " ideal model delta sigma weight residual 1.511 1.555 -0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 16823 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.33: 177 104.33 - 111.90: 7907 111.90 - 119.47: 5773 119.47 - 127.03: 8708 127.03 - 134.60: 147 Bond angle restraints: 22712 Sorted by residual: angle pdb=" C2 PX6 B1007 " pdb=" C3 PX6 B1007 " pdb=" O5 PX6 B1007 " ideal model delta sigma weight residual 109.47 130.54 -21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C2 PX6 D1007 " pdb=" C3 PX6 D1007 " pdb=" O5 PX6 D1007 " ideal model delta sigma weight residual 109.47 130.42 -20.95 3.00e+00 1.11e-01 4.88e+01 angle pdb=" C2 PX6 A1007 " pdb=" C3 PX6 A1007 " pdb=" O5 PX6 A1007 " ideal model delta sigma weight residual 109.47 130.40 -20.93 3.00e+00 1.11e-01 4.87e+01 angle pdb=" C2 PX6 C1007 " pdb=" C3 PX6 C1007 " pdb=" O5 PX6 C1007 " ideal model delta sigma weight residual 109.47 130.30 -20.83 3.00e+00 1.11e-01 4.82e+01 angle pdb=" CA ALA D 384 " pdb=" C ALA D 384 " pdb=" N THR D 385 " ideal model delta sigma weight residual 116.48 123.38 -6.90 1.39e+00 5.18e-01 2.46e+01 ... (remaining 22707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 8952 16.82 - 33.63: 581 33.63 - 50.45: 128 50.45 - 67.27: 71 67.27 - 84.08: 16 Dihedral angle restraints: 9748 sinusoidal: 4092 harmonic: 5656 Sorted by residual: dihedral pdb=" CA SER D 627 " pdb=" C SER D 627 " pdb=" N THR D 628 " pdb=" CA THR D 628 " ideal model delta harmonic sigma weight residual 180.00 137.07 42.93 0 5.00e+00 4.00e-02 7.37e+01 dihedral pdb=" CA SER C 627 " pdb=" C SER C 627 " pdb=" N THR C 628 " pdb=" CA THR C 628 " ideal model delta harmonic sigma weight residual 180.00 137.07 42.93 0 5.00e+00 4.00e-02 7.37e+01 dihedral pdb=" CA SER A 627 " pdb=" C SER A 627 " pdb=" N THR A 628 " pdb=" CA THR A 628 " ideal model delta harmonic sigma weight residual 180.00 137.09 42.91 0 5.00e+00 4.00e-02 7.37e+01 ... (remaining 9745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2073 0.080 - 0.160: 407 0.160 - 0.240: 58 0.240 - 0.321: 2 0.321 - 0.401: 8 Chirality restraints: 2548 Sorted by residual: chirality pdb=" C1 NAG D1004 " pdb=" O4 NAG D1003 " pdb=" C2 NAG D1004 " pdb=" O5 NAG D1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 4.01e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-02 2.50e+03 3.52e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-02 2.50e+03 3.24e+02 ... (remaining 2545 not shown) Planarity restraints: 2776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 362 " 0.088 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN C 362 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 362 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 362 " -0.140 2.00e-02 2.50e+03 pdb=" C1 NAG C1002 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 362 " -0.088 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN A 362 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 362 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 362 " 0.140 2.00e-02 2.50e+03 pdb=" C1 NAG A1002 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 362 " -0.088 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN D 362 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN D 362 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN D 362 " 0.140 2.00e-02 2.50e+03 pdb=" C1 NAG D1002 " -0.116 2.00e-02 2.50e+03 ... (remaining 2773 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 294 2.43 - 3.04: 13635 3.04 - 3.66: 26291 3.66 - 4.28: 39398 4.28 - 4.90: 57530 Nonbonded interactions: 137148 Sorted by model distance: nonbonded pdb=" CD1 LEU B 573 " pdb=" CD1 ILE C 606 " model vdw 1.806 3.880 nonbonded pdb=" CD1 LEU A 573 " pdb=" CD1 ILE B 606 " model vdw 1.829 3.880 nonbonded pdb=" O PHE D 310 " pdb=" OE1 GLU D 312 " model vdw 1.847 3.040 nonbonded pdb=" CD1 LEU C 573 " pdb=" CD1 ILE D 606 " model vdw 1.871 3.880 nonbonded pdb=" CD1 ILE A 606 " pdb=" CD1 LEU D 573 " model vdw 1.909 3.880 ... (remaining 137143 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 695 or resid 1001 through 1002 or resid 1010)) \ selection = (chain 'B' and (resid 215 through 695 or resid 1001 through 1002 or resid 1010)) \ selection = (chain 'C' and (resid 215 through 695 or resid 1001 through 1002 or resid 1010)) \ selection = (chain 'D' and (resid 215 through 695 or resid 1001 through 1002 or resid 1008)) \ } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 76 5.16 5 C 10912 2.51 5 N 2508 2.21 5 O 2924 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.570 Check model and map are aligned: 0.240 Process input model: 42.440 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.140 16828 Z= 0.611 Angle : 1.233 21.071 22712 Z= 0.647 Chirality : 0.066 0.401 2548 Planarity : 0.007 0.074 2764 Dihedral : 13.624 84.082 6084 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 56.89 Ramachandran Plot: Outliers : 0.48 % Allowed : 18.47 % Favored : 81.05 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 1.08 % 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: -5.74 (0.14), residues: 1884 helix: -4.86 (0.07), residues: 852 sheet: -3.20 (0.28), residues: 196 loop : -2.57 (0.19), residues: 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 563 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 577 average time/residue: 0.2642 time to fit residues: 230.7667 Evaluate side-chains 367 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 360 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1587 time to fit residues: 4.3906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 432 ASN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 HIS A 550 HIS A 555 GLN A 613 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN B 432 ASN B 434 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS B 550 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 622 GLN B 630 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN C 432 ASN C 456 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS C 550 HIS C 555 GLN C 613 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN D 432 ASN D 456 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 HIS D 550 HIS D 555 GLN D 613 GLN D 622 GLN D 653 ASN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 16828 Z= 0.355 Angle : 0.963 22.324 22712 Z= 0.500 Chirality : 0.055 0.250 2548 Planarity : 0.007 0.081 2764 Dihedral : 14.204 59.560 2488 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 35.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.76 % 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: -4.90 (0.15), residues: 1884 helix: -3.51 (0.12), residues: 852 sheet: -3.20 (0.31), residues: 192 loop : -2.81 (0.20), residues: 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 474 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 488 average time/residue: 0.2449 time to fit residues: 187.2770 Evaluate side-chains 387 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 377 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1588 time to fit residues: 5.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN A 456 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN B 613 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN C 613 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 16828 Z= 0.337 Angle : 0.899 23.610 22712 Z= 0.463 Chirality : 0.053 0.221 2548 Planarity : 0.006 0.071 2764 Dihedral : 13.843 59.959 2488 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 34.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -4.46 (0.17), residues: 1884 helix: -2.95 (0.14), residues: 864 sheet: -2.76 (0.37), residues: 184 loop : -2.90 (0.21), residues: 836 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 463 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 472 average time/residue: 0.2386 time to fit residues: 178.1538 Evaluate side-chains 370 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 363 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1571 time to fit residues: 4.3513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 181 optimal weight: 0.0870 chunk 89 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN A 613 GLN A 630 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 16828 Z= 0.210 Angle : 0.815 22.710 22712 Z= 0.414 Chirality : 0.050 0.283 2548 Planarity : 0.006 0.068 2764 Dihedral : 13.268 59.985 2488 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.93 (0.18), residues: 1884 helix: -2.40 (0.15), residues: 888 sheet: -2.65 (0.38), residues: 184 loop : -2.70 (0.22), residues: 812 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 467 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.2351 time to fit residues: 173.7849 Evaluate side-chains 384 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 74 optimal weight: 0.0470 chunk 155 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 16828 Z= 0.210 Angle : 0.782 21.822 22712 Z= 0.393 Chirality : 0.047 0.228 2548 Planarity : 0.005 0.076 2764 Dihedral : 12.717 59.887 2488 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % 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: -3.75 (0.18), residues: 1884 helix: -2.21 (0.14), residues: 928 sheet: -2.59 (0.38), residues: 184 loop : -2.65 (0.22), residues: 772 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.2307 time to fit residues: 159.6805 Evaluate side-chains 351 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 613 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 16828 Z= 0.360 Angle : 0.874 23.283 22712 Z= 0.447 Chirality : 0.052 0.253 2548 Planarity : 0.006 0.069 2764 Dihedral : 12.983 59.811 2488 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 32.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.22 % 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: -3.69 (0.18), residues: 1884 helix: -2.21 (0.15), residues: 884 sheet: -2.58 (0.39), residues: 184 loop : -2.55 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 434 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 434 average time/residue: 0.2429 time to fit residues: 167.8605 Evaluate side-chains 359 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 102 optimal weight: 0.0770 chunk 153 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 16828 Z= 0.230 Angle : 0.815 23.165 22712 Z= 0.410 Chirality : 0.049 0.236 2548 Planarity : 0.005 0.063 2764 Dihedral : 12.601 59.870 2488 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 26.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.11 % 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: -3.44 (0.18), residues: 1884 helix: -1.98 (0.15), residues: 908 sheet: -2.57 (0.38), residues: 192 loop : -2.41 (0.23), residues: 784 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 1.858 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.2343 time to fit residues: 162.7892 Evaluate side-chains 373 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 16828 Z= 0.291 Angle : 0.845 23.933 22712 Z= 0.424 Chirality : 0.050 0.229 2548 Planarity : 0.005 0.052 2764 Dihedral : 12.604 59.833 2488 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % 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: -3.51 (0.18), residues: 1884 helix: -1.96 (0.15), residues: 920 sheet: -2.60 (0.37), residues: 192 loop : -2.56 (0.22), residues: 772 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 1.757 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2381 time to fit residues: 157.2742 Evaluate side-chains 353 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.0670 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 110 optimal weight: 0.1980 chunk 178 optimal weight: 0.9980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN C 434 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 ASN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 16828 Z= 0.206 Angle : 0.814 23.310 22712 Z= 0.404 Chirality : 0.048 0.239 2548 Planarity : 0.005 0.049 2764 Dihedral : 12.037 59.765 2488 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.20 (0.19), residues: 1884 helix: -1.78 (0.15), residues: 932 sheet: -2.44 (0.38), residues: 192 loop : -2.30 (0.24), residues: 760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 428 time to evaluate : 2.009 Fit side-chains TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 428 average time/residue: 0.2432 time to fit residues: 165.7604 Evaluate side-chains 359 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 622 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 622 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 16828 Z= 0.308 Angle : 0.840 23.763 22712 Z= 0.422 Chirality : 0.050 0.248 2548 Planarity : 0.005 0.049 2764 Dihedral : 12.187 59.986 2488 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 29.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % 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: -3.26 (0.19), residues: 1884 helix: -1.82 (0.15), residues: 936 sheet: -2.44 (0.38), residues: 192 loop : -2.36 (0.23), residues: 756 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2564 time to fit residues: 170.7331 Evaluate side-chains 343 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.0000 chunk 137 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 153 optimal weight: 0.3980 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 432 ASN B 434 ASN B 555 GLN B 613 GLN B 622 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.171563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.142185 restraints weight = 39830.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.146403 restraints weight = 25900.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.148590 restraints weight = 18519.336| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 16828 Z= 0.192 Angle : 0.794 22.785 22712 Z= 0.394 Chirality : 0.048 0.226 2548 Planarity : 0.005 0.047 2764 Dihedral : 11.704 59.968 2488 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % 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: -3.06 (0.19), residues: 1884 helix: -1.63 (0.15), residues: 940 sheet: -2.29 (0.38), residues: 192 loop : -2.31 (0.24), residues: 752 =============================================================================== Job complete usr+sys time: 3528.52 seconds wall clock time: 64 minutes 55.21 seconds (3895.21 seconds total)