Starting phenix.real_space_refine on Sun Mar 17 02:17:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/03_2024/5mke_3523_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/03_2024/5mke_3523.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/03_2024/5mke_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_3523/03_2024/5mke_3523_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/03_2024/5mke_3523_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/03_2024/5mke_3523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/03_2024/5mke_3523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/03_2024/5mke_3523_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mke_3523/03_2024/5mke_3523_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 76 5.16 5 C 10912 2.51 5 N 2508 2.21 5 O 2924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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-5265/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 10 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: 10 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: 10 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: 16 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.78, per 1000 atoms: 0.53 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: 6.94 Conformation dependent library (CDL) restraints added in 2.8 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: 2.70 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: 3.94 Time building geometry restraints manager: 7.55 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=" O3 PX6 D1007 " pdb=" P1 PX6 D1007 " ideal model delta sigma weight residual 1.510 1.452 0.058 2.00e-02 2.50e+03 8.35e+00 ... (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=" C ALA A 384 " pdb=" N THR A 385 " pdb=" CA THR A 385 " ideal model delta sigma weight residual 121.70 134.60 -12.90 1.80e+00 3.09e-01 5.14e+01 angle pdb=" C ALA C 384 " pdb=" N THR C 385 " pdb=" CA THR C 385 " ideal model delta sigma weight residual 121.70 134.55 -12.85 1.80e+00 3.09e-01 5.09e+01 angle pdb=" C ALA B 384 " pdb=" N THR B 385 " pdb=" CA THR B 385 " ideal model delta sigma weight residual 121.70 134.53 -12.83 1.80e+00 3.09e-01 5.08e+01 angle pdb=" C ALA D 384 " pdb=" N THR D 385 " pdb=" CA THR D 385 " ideal model delta sigma weight residual 121.70 134.50 -12.80 1.80e+00 3.09e-01 5.06e+01 angle pdb=" C2 PX6 B1007 " pdb=" C3 PX6 B1007 " pdb=" O5 PX6 B1007 " ideal model delta sigma weight residual 109.47 130.54 -21.07 3.00e+00 1.11e-01 4.93e+01 ... (remaining 22707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 9156 16.82 - 33.63: 607 33.63 - 50.45: 139 50.45 - 67.27: 78 67.27 - 84.08: 16 Dihedral angle restraints: 9996 sinusoidal: 4340 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 9993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2065 0.080 - 0.160: 404 0.160 - 0.240: 69 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 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.990 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 43.310 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.140 16828 Z= 0.612 Angle : 1.246 21.071 22712 Z= 0.636 Chirality : 0.068 0.401 2548 Planarity : 0.007 0.074 2764 Dihedral : 13.719 84.082 6332 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 % Allowed : 1.75 % Favored : 97.44 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 1.08 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP D 366 HIS 0.010 0.003 HIS B 379 PHE 0.032 0.004 PHE A 445 TYR 0.029 0.004 TYR A 248 ARG 0.008 0.001 ARG D 397 *********************** 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 : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5470 (mm) REVERT: A 313 ASN cc_start: 0.7196 (m-40) cc_final: 0.6806 (m110) REVERT: A 324 LEU cc_start: 0.8403 (mt) cc_final: 0.8140 (mp) REVERT: A 358 PHE cc_start: 0.7193 (t80) cc_final: 0.6980 (t80) REVERT: A 460 LEU cc_start: 0.8672 (tp) cc_final: 0.8435 (tp) REVERT: A 663 THR cc_start: 0.9005 (p) cc_final: 0.8584 (p) REVERT: A 676 PHE cc_start: 0.7792 (m-10) cc_final: 0.7231 (m-80) REVERT: B 283 THR cc_start: 0.8882 (p) cc_final: 0.8618 (p) REVERT: B 309 ILE cc_start: 0.5893 (OUTLIER) cc_final: 0.5551 (mm) REVERT: B 313 ASN cc_start: 0.7208 (m-40) cc_final: 0.6843 (m110) REVERT: B 324 LEU cc_start: 0.8129 (mt) cc_final: 0.7894 (mp) REVERT: B 460 LEU cc_start: 0.8710 (tp) cc_final: 0.8329 (tp) REVERT: B 504 ARG cc_start: 0.4800 (tpt90) cc_final: 0.2593 (ttp80) REVERT: B 663 THR cc_start: 0.9174 (p) cc_final: 0.8765 (p) REVERT: B 676 PHE cc_start: 0.7720 (m-10) cc_final: 0.7272 (m-80) REVERT: B 683 THR cc_start: 0.7541 (p) cc_final: 0.7279 (t) REVERT: C 313 ASN cc_start: 0.7197 (m-40) cc_final: 0.6855 (m110) REVERT: C 324 LEU cc_start: 0.8298 (mt) cc_final: 0.7973 (mp) REVERT: C 358 PHE cc_start: 0.7072 (t80) cc_final: 0.6833 (t80) REVERT: C 460 LEU cc_start: 0.8651 (tp) cc_final: 0.8398 (tp) REVERT: C 663 THR cc_start: 0.9048 (p) cc_final: 0.8677 (p) REVERT: C 676 PHE cc_start: 0.7806 (m-10) cc_final: 0.7242 (m-80) REVERT: D 313 ASN cc_start: 0.6894 (m-40) cc_final: 0.6673 (m110) REVERT: D 324 LEU cc_start: 0.8365 (mt) cc_final: 0.8053 (mp) REVERT: D 358 PHE cc_start: 0.7084 (t80) cc_final: 0.6859 (t80) REVERT: D 663 THR cc_start: 0.9078 (p) cc_final: 0.8682 (p) REVERT: D 676 PHE cc_start: 0.7782 (m-10) cc_final: 0.7067 (m-80) REVERT: D 683 THR cc_start: 0.7608 (p) cc_final: 0.7347 (t) outliers start: 14 outliers final: 7 residues processed: 577 average time/residue: 0.2592 time to fit residues: 227.3095 Evaluate side-chains 379 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 370 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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: 5.9990 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: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16828 Z= 0.364 Angle : 0.956 12.293 22712 Z= 0.506 Chirality : 0.056 0.256 2548 Planarity : 0.007 0.081 2764 Dihedral : 14.194 59.714 2736 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 35.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 1.11 % Allowed : 5.48 % Favored : 93.41 % Cbeta Deviations : 0.22 % 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: -4.93 (0.15), residues: 1884 helix: -3.54 (0.12), residues: 852 sheet: -3.24 (0.30), residues: 196 loop : -2.82 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 280 HIS 0.007 0.002 HIS D 379 PHE 0.030 0.003 PHE B 480 TYR 0.021 0.002 TYR D 502 ARG 0.006 0.001 ARG A 322 *********************** 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 493 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 474 time to evaluate : 1.774 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 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 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 REVERT: A 341 ILE cc_start: 0.1322 (pt) cc_final: 0.1066 (pt) REVERT: A 345 TYR cc_start: 0.7052 (m-80) cc_final: 0.6730 (m-10) REVERT: A 358 PHE cc_start: 0.7164 (t80) cc_final: 0.6870 (t80) REVERT: B 324 LEU cc_start: 0.8271 (mt) cc_final: 0.8058 (mt) REVERT: C 341 ILE cc_start: 0.1202 (pt) cc_final: 0.0981 (pt) REVERT: C 345 TYR cc_start: 0.7068 (m-80) cc_final: 0.6753 (m-10) REVERT: D 345 TYR cc_start: 0.7072 (m-80) cc_final: 0.6865 (m-10) REVERT: D 358 PHE cc_start: 0.7024 (t80) cc_final: 0.6741 (t80) REVERT: D 631 GLU cc_start: 0.7717 (tt0) cc_final: 0.7503 (tt0) REVERT: D 676 PHE cc_start: 0.7427 (m-10) cc_final: 0.7088 (m-80) outliers start: 19 outliers final: 9 residues processed: 492 average time/residue: 0.2379 time to fit residues: 184.2430 Evaluate side-chains 390 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 381 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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: 20.0000 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 456 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3592 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= 0.293 Angle : 0.857 13.513 22712 Z= 0.455 Chirality : 0.053 0.244 2548 Planarity : 0.006 0.070 2764 Dihedral : 13.583 59.887 2736 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 30.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.82 % Allowed : 3.21 % Favored : 95.98 % 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: -4.42 (0.17), residues: 1884 helix: -2.90 (0.14), residues: 868 sheet: -2.92 (0.35), residues: 184 loop : -2.84 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 280 HIS 0.006 0.001 HIS B 379 PHE 0.032 0.002 PHE A 670 TYR 0.019 0.002 TYR D 227 ARG 0.004 0.001 ARG C 322 *********************** 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 483 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 469 time to evaluate : 1.736 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 TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 341 ILE cc_start: 0.1587 (pt) cc_final: 0.1307 (pt) REVERT: A 345 TYR cc_start: 0.7217 (m-80) cc_final: 0.6530 (m-10) REVERT: B 553 TYR cc_start: 0.6680 (t80) cc_final: 0.5530 (t80) REVERT: C 252 MET cc_start: 0.8576 (ptt) cc_final: 0.8173 (ptt) REVERT: C 624 ASP cc_start: 0.4456 (m-30) cc_final: 0.3950 (m-30) REVERT: D 345 TYR cc_start: 0.7329 (m-80) cc_final: 0.6691 (m-10) REVERT: D 358 PHE cc_start: 0.7062 (t80) cc_final: 0.6802 (t80) REVERT: D 624 ASP cc_start: 0.4570 (m-30) cc_final: 0.4068 (m-30) REVERT: D 676 PHE cc_start: 0.6869 (m-10) cc_final: 0.6577 (m-80) outliers start: 14 outliers final: 5 residues processed: 478 average time/residue: 0.2334 time to fit residues: 176.6570 Evaluate side-chains 367 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 362 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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: 7.9990 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 432 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 630 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN ** B 560 ASN ** 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** C 613 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16828 Z= 0.264 Angle : 0.790 12.364 22712 Z= 0.418 Chirality : 0.051 0.344 2548 Planarity : 0.006 0.066 2764 Dihedral : 13.149 59.427 2736 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 30.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.18), residues: 1884 helix: -2.46 (0.15), residues: 868 sheet: -2.90 (0.37), residues: 184 loop : -2.70 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP C 280 HIS 0.005 0.001 HIS A 379 PHE 0.043 0.002 PHE D 676 TYR 0.021 0.002 TYR D 227 ARG 0.004 0.000 ARG D 320 *********************** 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 450 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 1.878 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 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 revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 341 ILE cc_start: 0.1762 (pt) cc_final: 0.1415 (pt) REVERT: A 345 TYR cc_start: 0.7109 (m-80) cc_final: 0.6509 (m-10) REVERT: B 230 PHE cc_start: 0.7470 (t80) cc_final: 0.7014 (t80) REVERT: B 252 MET cc_start: 0.8436 (ptt) cc_final: 0.8032 (ptt) REVERT: B 275 SER cc_start: 0.7049 (m) cc_final: 0.6683 (m) REVERT: C 230 PHE cc_start: 0.7228 (t80) cc_final: 0.6745 (t80) REVERT: C 341 ILE cc_start: 0.1804 (pt) cc_final: 0.1506 (pt) REVERT: C 345 TYR cc_start: 0.7164 (m-80) cc_final: 0.6548 (m-10) REVERT: D 252 MET cc_start: 0.8442 (ptt) cc_final: 0.8146 (ptt) REVERT: D 345 TYR cc_start: 0.7217 (m-80) cc_final: 0.6771 (m-10) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.2367 time to fit residues: 167.7308 Evaluate side-chains 351 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 1.865 ------------------------------------------------------------------------------- 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: 5.9990 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 613 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN C 613 GLN ** D 323 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16828 Z= 0.271 Angle : 0.789 12.440 22712 Z= 0.413 Chirality : 0.049 0.236 2548 Planarity : 0.006 0.061 2764 Dihedral : 12.802 59.935 2736 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 30.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.18), residues: 1884 helix: -2.24 (0.15), residues: 920 sheet: -2.88 (0.37), residues: 184 loop : -2.58 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP C 280 HIS 0.004 0.001 HIS A 379 PHE 0.043 0.002 PHE D 676 TYR 0.021 0.002 TYR D 227 ARG 0.003 0.000 ARG A 320 *********************** 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 435 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 1.756 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 252 MET cc_start: 0.8702 (ptt) cc_final: 0.8391 (ptt) REVERT: A 341 ILE cc_start: 0.1799 (pt) cc_final: 0.1423 (pt) REVERT: A 345 TYR cc_start: 0.7151 (m-80) cc_final: 0.6774 (m-10) REVERT: A 633 ILE cc_start: 0.8526 (tp) cc_final: 0.8309 (tp) REVERT: B 460 LEU cc_start: 0.7267 (tp) cc_final: 0.7009 (tp) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.2281 time to fit residues: 157.3084 Evaluate side-chains 356 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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: 6.9990 chunk 163 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 432 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16828 Z= 0.229 Angle : 0.776 12.048 22712 Z= 0.407 Chirality : 0.049 0.232 2548 Planarity : 0.005 0.066 2764 Dihedral : 12.566 59.785 2736 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.12 % Allowed : 2.27 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.16 % 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: -3.58 (0.18), residues: 1884 helix: -2.05 (0.15), residues: 900 sheet: -2.79 (0.38), residues: 184 loop : -2.52 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 280 HIS 0.004 0.001 HIS C 379 PHE 0.029 0.002 PHE C 669 TYR 0.025 0.002 TYR D 227 ARG 0.003 0.000 ARG B 440 *********************** 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 441 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 439 time to evaluate : 1.816 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 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 TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 275 SER cc_start: 0.7083 (m) cc_final: 0.5163 (m) outliers start: 2 outliers final: 0 residues processed: 439 average time/residue: 0.2284 time to fit residues: 159.3245 Evaluate side-chains 363 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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: 7.9990 chunk 20 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 0.0010 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- 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 432 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16828 Z= 0.225 Angle : 0.777 11.697 22712 Z= 0.405 Chirality : 0.051 0.398 2548 Planarity : 0.005 0.056 2764 Dihedral : 12.269 59.886 2736 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 26.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -3.57 (0.18), residues: 1884 helix: -1.94 (0.15), residues: 940 sheet: -2.71 (0.39), residues: 184 loop : -2.69 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 280 HIS 0.005 0.001 HIS A 379 PHE 0.034 0.002 PHE A 669 TYR 0.025 0.002 TYR D 227 ARG 0.003 0.000 ARG B 361 *********************** 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 435 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 242 MET cc_start: 0.8331 (mpp) cc_final: 0.8048 (mmt) REVERT: D 313 ASN cc_start: 0.8244 (t0) cc_final: 0.8031 (t0) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.2235 time to fit residues: 155.2479 Evaluate side-chains 346 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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: 4.9990 chunk 72 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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 432 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 681 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16828 Z= 0.250 Angle : 0.767 11.945 22712 Z= 0.400 Chirality : 0.050 0.292 2548 Planarity : 0.005 0.048 2764 Dihedral : 12.028 59.694 2736 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -3.59 (0.18), residues: 1884 helix: -1.86 (0.15), residues: 980 sheet: -2.70 (0.40), residues: 184 loop : -2.86 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 280 HIS 0.005 0.001 HIS C 379 PHE 0.037 0.002 PHE C 669 TYR 0.017 0.001 TYR D 227 ARG 0.003 0.000 ARG D 320 *********************** 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 419 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 623 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL D 623 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 269 ASN cc_start: 0.7276 (p0) cc_final: 0.7029 (p0) REVERT: B 426 PHE cc_start: 0.6493 (p90) cc_final: 0.6165 (p90) REVERT: C 313 ASN cc_start: 0.8005 (t0) cc_final: 0.7703 (t0) REVERT: D 345 TYR cc_start: 0.7301 (m-80) cc_final: 0.7092 (m-10) REVERT: D 426 PHE cc_start: 0.6524 (p90) cc_final: 0.6127 (p90) REVERT: D 621 THR cc_start: 0.7665 (p) cc_final: 0.7431 (t) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.2296 time to fit residues: 152.7104 Evaluate side-chains 349 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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: 0.8980 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 51 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 110 optimal weight: 0.3980 chunk 178 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 432 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** 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 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16828 Z= 0.197 Angle : 0.758 11.409 22712 Z= 0.393 Chirality : 0.048 0.233 2548 Planarity : 0.005 0.060 2764 Dihedral : 11.636 59.966 2736 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.06 % Allowed : 0.93 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.19), residues: 1884 helix: -1.72 (0.15), residues: 972 sheet: -2.65 (0.40), residues: 184 loop : -2.70 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 280 HIS 0.004 0.001 HIS D 379 PHE 0.037 0.002 PHE B 669 TYR 0.032 0.002 TYR C 227 ARG 0.002 0.000 ARG C 528 *********************** 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 415 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 1.844 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. 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 REVERT: B 426 PHE cc_start: 0.6279 (p90) cc_final: 0.5911 (p90) REVERT: B 608 PHE cc_start: 0.7268 (t80) cc_final: 0.5807 (t80) REVERT: C 380 TRP cc_start: 0.7660 (t60) cc_final: 0.7407 (t60) REVERT: C 426 PHE cc_start: 0.5655 (p90) cc_final: 0.5238 (p90) REVERT: C 622 GLN cc_start: 0.7870 (tt0) cc_final: 0.7662 (tt0) REVERT: D 414 TRP cc_start: 0.6894 (m-90) cc_final: 0.6416 (m-90) REVERT: D 426 PHE cc_start: 0.6124 (p90) cc_final: 0.5789 (p90) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.2340 time to fit residues: 153.1981 Evaluate side-chains 351 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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: 8.9990 chunk 124 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 0.0770 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 overall best weight: 4.2146 ------------------------------------------------------------------------------- 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 432 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** 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 432 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16828 Z= 0.305 Angle : 0.812 11.679 22712 Z= 0.421 Chirality : 0.051 0.265 2548 Planarity : 0.005 0.046 2764 Dihedral : 11.800 59.980 2736 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 29.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.18), residues: 1884 helix: -1.78 (0.15), residues: 956 sheet: -2.63 (0.39), residues: 184 loop : -2.61 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 280 HIS 0.007 0.001 HIS D 379 PHE 0.034 0.002 PHE D 608 TYR 0.014 0.002 TYR D 227 ARG 0.017 0.001 ARG C 251 ********************** 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 412 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 1.657 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 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: A 275 SER cc_start: 0.6789 (m) cc_final: 0.6124 (m) REVERT: B 426 PHE cc_start: 0.6713 (p90) cc_final: 0.6332 (p90) REVERT: C 426 PHE cc_start: 0.6106 (p90) cc_final: 0.5728 (p90) REVERT: D 414 TRP cc_start: 0.6945 (m-90) cc_final: 0.6686 (m-90) REVERT: D 426 PHE cc_start: 0.6595 (p90) cc_final: 0.6204 (p90) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.2317 time to fit residues: 151.4303 Evaluate side-chains 338 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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: 10.0000 chunk 137 optimal weight: 0.0870 chunk 22 optimal weight: 0.0570 chunk 41 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 0.0470 chunk 153 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- 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 432 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN C 432 ASN C 434 ASN C 613 GLN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.173939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.143320 restraints weight = 38824.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.147427 restraints weight = 25092.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.149533 restraints weight = 18107.397| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.6378 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= 0.195 Angle : 0.763 10.995 22712 Z= 0.391 Chirality : 0.049 0.254 2548 Planarity : 0.005 0.043 2764 Dihedral : 11.338 59.568 2736 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.38 % 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: -3.09 (0.19), residues: 1884 helix: -1.58 (0.16), residues: 940 sheet: -2.47 (0.40), residues: 184 loop : -2.39 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 380 HIS 0.006 0.001 HIS D 379 PHE 0.051 0.002 PHE D 608 TYR 0.023 0.002 TYR C 227 ARG 0.008 0.000 ARG C 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3554.89 seconds wall clock time: 65 minutes 22.62 seconds (3922.62 seconds total)