Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 18:44:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/08_2023/7jth_22473.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/08_2023/7jth_22473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/08_2023/7jth_22473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/08_2023/7jth_22473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/08_2023/7jth_22473.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/08_2023/7jth_22473.pdb" } resolution = 4.0 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= 0.020 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 9286 2.51 5 N 2620 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 624": "OD1" <-> "OD2" Residue "G ASP 624": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 14628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1823 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 311 Chain: "B" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 1839 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 599 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 18, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 255 Conformer: "B" Number of residues, atoms: 289, 1839 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 599 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 18, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 255 bond proxies already assigned to first conformer: 1873 Chain: "C" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1830 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 668 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 313 Chain: "D" Number of atoms: 1820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 1818 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 272 Conformer: "B" Number of residues, atoms: 289, 1818 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 272 bond proxies already assigned to first conformer: 1852 Chain: "E" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1823 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 311 Chain: "F" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 1839 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 599 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 18, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 255 Conformer: "B" Number of residues, atoms: 289, 1839 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 599 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 18, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 255 bond proxies already assigned to first conformer: 1873 Chain: "G" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1830 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 668 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 313 Chain: "H" Number of atoms: 1820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 1818 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 272 Conformer: "B" Number of residues, atoms: 289, 1818 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 272 bond proxies already assigned to first conformer: 1852 Time building chain proxies: 11.02, per 1000 atoms: 0.75 Number of scatterers: 14628 At special positions: 0 Unit cell: (138.182, 138.182, 130.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2678 8.00 N 2620 7.00 C 9286 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 Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 3.5 seconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 77.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.543A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.904A pdb=" N ASP A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.895A pdb=" N LYS A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.777A pdb=" N ILE A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.681A pdb=" N ILE A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 removed outlier: 3.710A pdb=" N ASN A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 546 removed outlier: 3.872A pdb=" N GLN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 562 through 574 removed outlier: 4.049A pdb=" N PHE A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 610 removed outlier: 4.512A pdb=" N SER A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N CYS A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 643 through 658 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 681 through 700 removed outlier: 3.838A pdb=" N ASP A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 718 removed outlier: 3.880A pdb=" N ARG A 718 " --> pdb=" O GLU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'B' and resid 415 through 423 removed outlier: 3.752A pdb=" N LEU B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 removed outlier: 3.935A pdb=" N SER B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.659A pdb=" N ILE B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 478 removed outlier: 4.374A pdb=" N LYS B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 495 through 514 removed outlier: 3.817A pdb=" N TYR B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 545 removed outlier: 3.595A pdb=" N VAL B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 4.034A pdb=" N ARG B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 removed outlier: 4.103A pdb=" N PHE B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 568 " --> pdb=" O GLN B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 611 Processing helix chain 'B' and resid 631 through 636 Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 662 through 676 removed outlier: 3.748A pdb=" N GLN B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 703 removed outlier: 3.817A pdb=" N ARG B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 690 " --> pdb=" O MET B 686 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.698A pdb=" N LEU B 714 " --> pdb=" O MET B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'C' and resid 415 through 422 removed outlier: 3.949A pdb=" N ALA C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 450 removed outlier: 3.930A pdb=" N ASP C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 478 removed outlier: 3.741A pdb=" N LYS C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 3.681A pdb=" N ILE C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 517 removed outlier: 3.510A pdb=" N ILE C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 516 " --> pdb=" O GLN C 512 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 546 removed outlier: 3.811A pdb=" N GLN C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 562 Processing helix chain 'C' and resid 562 through 575 removed outlier: 4.254A pdb=" N PHE C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 585 removed outlier: 3.720A pdb=" N LYS C 585 " --> pdb=" O PRO C 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 582 through 585' Processing helix chain 'C' and resid 586 through 610 removed outlier: 3.691A pdb=" N ASP C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 643 through 658 Processing helix chain 'C' and resid 663 through 675 Processing helix chain 'C' and resid 681 through 700 removed outlier: 3.840A pdb=" N ASP C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 718 removed outlier: 3.927A pdb=" N ARG C 718 " --> pdb=" O GLU C 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 715 through 718' Processing helix chain 'D' and resid 415 through 423 removed outlier: 3.720A pdb=" N LEU D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 431 removed outlier: 3.920A pdb=" N SER D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 450 removed outlier: 3.690A pdb=" N ILE D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TRP D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 478 removed outlier: 4.278A pdb=" N LYS D 458 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 495 through 514 removed outlier: 3.872A pdb=" N TYR D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 545 removed outlier: 3.631A pdb=" N VAL D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 4.027A pdb=" N ARG D 556 " --> pdb=" O GLU D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 removed outlier: 4.070A pdb=" N PHE D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE D 568 " --> pdb=" O GLN D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 4.171A pdb=" N SER D 588 " --> pdb=" O THR D 584 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS D 589 " --> pdb=" O LYS D 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 584 through 589' Processing helix chain 'D' and resid 590 through 611 Processing helix chain 'D' and resid 631 through 636 Processing helix chain 'D' and resid 643 through 649 Processing helix chain 'D' and resid 662 through 676 removed outlier: 3.750A pdb=" N GLN D 666 " --> pdb=" O LEU D 662 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 669 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 703 removed outlier: 3.712A pdb=" N ARG D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL D 690 " --> pdb=" O MET D 686 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.803A pdb=" N LEU D 714 " --> pdb=" O MET D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 717 No H-bonds generated for 'chain 'D' and resid 715 through 717' Processing helix chain 'E' and resid 415 through 422 removed outlier: 3.923A pdb=" N ALA E 420 " --> pdb=" O PHE E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 429 Processing helix chain 'E' and resid 437 through 450 removed outlier: 3.904A pdb=" N ASP E 447 " --> pdb=" O ASP E 443 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 478 removed outlier: 3.895A pdb=" N LYS E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL E 465 " --> pdb=" O ASP E 461 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN E 477 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 494 removed outlier: 3.777A pdb=" N ILE E 492 " --> pdb=" O SER E 488 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 493 " --> pdb=" O THR E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 515 removed outlier: 3.681A pdb=" N ILE E 507 " --> pdb=" O THR E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 527 removed outlier: 3.710A pdb=" N ASN E 527 " --> pdb=" O GLN E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 546 removed outlier: 3.872A pdb=" N GLN E 536 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E 544 " --> pdb=" O LEU E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 562 Processing helix chain 'E' and resid 562 through 574 removed outlier: 4.049A pdb=" N PHE E 566 " --> pdb=" O THR E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 610 removed outlier: 4.512A pdb=" N SER E 588 " --> pdb=" O THR E 584 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N CYS E 589 " --> pdb=" O LYS E 585 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP E 605 " --> pdb=" O PHE E 601 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP E 606 " --> pdb=" O GLN E 602 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN E 608 " --> pdb=" O ARG E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 638 Processing helix chain 'E' and resid 643 through 658 Processing helix chain 'E' and resid 663 through 675 Processing helix chain 'E' and resid 681 through 700 removed outlier: 3.838A pdb=" N ASP E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 690 " --> pdb=" O MET E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 714 Processing helix chain 'E' and resid 715 through 718 removed outlier: 3.880A pdb=" N ARG E 718 " --> pdb=" O GLU E 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 715 through 718' Processing helix chain 'F' and resid 415 through 423 removed outlier: 3.752A pdb=" N LEU F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU F 423 " --> pdb=" O LYS F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 431 removed outlier: 3.935A pdb=" N SER F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 450 removed outlier: 3.659A pdb=" N ILE F 442 " --> pdb=" O ARG F 438 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP F 443 " --> pdb=" O ASP F 439 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP F 447 " --> pdb=" O ASP F 443 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP F 448 " --> pdb=" O ALA F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 478 removed outlier: 4.374A pdb=" N LYS F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE F 476 " --> pdb=" O LEU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 495 through 514 removed outlier: 3.817A pdb=" N TYR F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 545 removed outlier: 3.595A pdb=" N VAL F 525 " --> pdb=" O SER F 521 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 532 " --> pdb=" O SER F 528 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP F 539 " --> pdb=" O GLY F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 562 removed outlier: 4.034A pdb=" N ARG F 556 " --> pdb=" O GLU F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 572 removed outlier: 4.103A pdb=" N PHE F 566 " --> pdb=" O THR F 562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 589 Processing helix chain 'F' and resid 590 through 611 Processing helix chain 'F' and resid 631 through 636 Processing helix chain 'F' and resid 643 through 649 Processing helix chain 'F' and resid 662 through 676 removed outlier: 3.748A pdb=" N GLN F 666 " --> pdb=" O LEU F 662 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU F 669 " --> pdb=" O LYS F 665 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 673 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU F 674 " --> pdb=" O ASP F 670 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU F 675 " --> pdb=" O ILE F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 703 removed outlier: 3.817A pdb=" N ARG F 682 " --> pdb=" O LEU F 678 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 690 " --> pdb=" O MET F 686 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA F 694 " --> pdb=" O VAL F 690 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 697 " --> pdb=" O ARG F 693 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG F 698 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 699 " --> pdb=" O GLU F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 714 removed outlier: 3.698A pdb=" N LEU F 714 " --> pdb=" O MET F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 717 No H-bonds generated for 'chain 'F' and resid 715 through 717' Processing helix chain 'G' and resid 415 through 422 removed outlier: 3.949A pdb=" N ALA G 420 " --> pdb=" O PHE G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 429 Processing helix chain 'G' and resid 437 through 450 removed outlier: 3.930A pdb=" N ASP G 447 " --> pdb=" O ASP G 443 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP G 448 " --> pdb=" O ALA G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 478 removed outlier: 3.741A pdb=" N LYS G 460 " --> pdb=" O VAL G 456 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL G 465 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE G 476 " --> pdb=" O LEU G 472 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN G 477 " --> pdb=" O LEU G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 494 removed outlier: 3.681A pdb=" N ILE G 492 " --> pdb=" O SER G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 517 removed outlier: 3.510A pdb=" N ILE G 507 " --> pdb=" O THR G 503 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE G 516 " --> pdb=" O GLN G 512 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER G 517 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 546 removed outlier: 3.811A pdb=" N GLN G 536 " --> pdb=" O LEU G 532 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR G 544 " --> pdb=" O LEU G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 562 Processing helix chain 'G' and resid 562 through 575 removed outlier: 4.254A pdb=" N PHE G 566 " --> pdb=" O THR G 562 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 585 removed outlier: 3.720A pdb=" N LYS G 585 " --> pdb=" O PRO G 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 582 through 585' Processing helix chain 'G' and resid 586 through 610 removed outlier: 3.691A pdb=" N ASP G 605 " --> pdb=" O PHE G 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 638 Processing helix chain 'G' and resid 643 through 658 Processing helix chain 'G' and resid 663 through 675 Processing helix chain 'G' and resid 681 through 700 removed outlier: 3.840A pdb=" N ASP G 687 " --> pdb=" O SER G 683 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 714 Processing helix chain 'G' and resid 715 through 718 removed outlier: 3.927A pdb=" N ARG G 718 " --> pdb=" O GLU G 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 715 through 718' Processing helix chain 'H' and resid 415 through 423 removed outlier: 3.720A pdb=" N LEU H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU H 423 " --> pdb=" O LYS H 419 " (cutoff:3.500A) Processing helix chain 'H' and resid 423 through 431 removed outlier: 3.920A pdb=" N SER H 431 " --> pdb=" O ASP H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 450 removed outlier: 3.690A pdb=" N ILE H 442 " --> pdb=" O ARG H 438 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP H 443 " --> pdb=" O ASP H 439 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP H 447 " --> pdb=" O ASP H 443 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TRP H 448 " --> pdb=" O ALA H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 478 removed outlier: 4.278A pdb=" N LYS H 458 " --> pdb=" O VAL H 454 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE H 476 " --> pdb=" O LEU H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 495 through 514 removed outlier: 3.872A pdb=" N TYR H 504 " --> pdb=" O ASN H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 545 removed outlier: 3.631A pdb=" N VAL H 525 " --> pdb=" O SER H 521 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU H 532 " --> pdb=" O SER H 528 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN H 536 " --> pdb=" O LEU H 532 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP H 539 " --> pdb=" O GLY H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 550 through 562 removed outlier: 4.027A pdb=" N ARG H 556 " --> pdb=" O GLU H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 572 removed outlier: 4.070A pdb=" N PHE H 566 " --> pdb=" O THR H 562 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE H 568 " --> pdb=" O GLN H 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 584 through 589 removed outlier: 4.171A pdb=" N SER H 588 " --> pdb=" O THR H 584 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS H 589 " --> pdb=" O LYS H 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 584 through 589' Processing helix chain 'H' and resid 590 through 611 Processing helix chain 'H' and resid 631 through 636 Processing helix chain 'H' and resid 643 through 649 Processing helix chain 'H' and resid 662 through 676 removed outlier: 3.750A pdb=" N GLN H 666 " --> pdb=" O LEU H 662 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU H 669 " --> pdb=" O LYS H 665 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU H 673 " --> pdb=" O LEU H 669 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU H 675 " --> pdb=" O ILE H 671 " (cutoff:3.500A) Processing helix chain 'H' and resid 676 through 703 removed outlier: 3.712A pdb=" N ARG H 682 " --> pdb=" O LEU H 678 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL H 690 " --> pdb=" O MET H 686 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 694 " --> pdb=" O VAL H 690 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY H 697 " --> pdb=" O ARG H 693 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG H 698 " --> pdb=" O ALA H 694 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE H 699 " --> pdb=" O GLU H 695 " (cutoff:3.500A) Processing helix chain 'H' and resid 709 through 714 removed outlier: 3.803A pdb=" N LEU H 714 " --> pdb=" O MET H 710 " (cutoff:3.500A) Processing helix chain 'H' and resid 715 through 717 No H-bonds generated for 'chain 'H' and resid 715 through 717' 1082 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4998 1.34 - 1.46: 3472 1.46 - 1.58: 6384 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 14926 Sorted by residual: bond pdb=" CB PRO C 481 " pdb=" CG PRO C 481 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.22e+00 bond pdb=" CB PRO G 481 " pdb=" CG PRO G 481 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.22e+00 bond pdb=" C SER C 705 " pdb=" N PRO C 706 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" C SER G 705 " pdb=" N PRO G 706 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" C SER A 705 " pdb=" N PRO A 706 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.07e+00 ... (remaining 14921 not shown) Histogram of bond angle deviations from ideal: 100.65 - 107.32: 508 107.32 - 113.99: 8512 113.99 - 120.66: 6400 120.66 - 127.32: 5010 127.32 - 133.99: 164 Bond angle restraints: 20594 Sorted by residual: angle pdb=" N GLU C 580 " pdb=" CA GLU C 580 " pdb=" C GLU C 580 " ideal model delta sigma weight residual 110.80 102.06 8.74 2.13e+00 2.20e-01 1.68e+01 angle pdb=" N GLU G 580 " pdb=" CA GLU G 580 " pdb=" C GLU G 580 " ideal model delta sigma weight residual 110.80 102.06 8.74 2.13e+00 2.20e-01 1.68e+01 angle pdb=" N ASN C 579 " pdb=" CA ASN C 579 " pdb=" C ASN C 579 " ideal model delta sigma weight residual 113.29 107.89 5.40 2.00e+00 2.50e-01 7.30e+00 angle pdb=" N ASN G 579 " pdb=" CA ASN G 579 " pdb=" C ASN G 579 " ideal model delta sigma weight residual 113.29 107.89 5.40 2.00e+00 2.50e-01 7.30e+00 angle pdb=" N VAL G 525 " pdb=" CA VAL G 525 " pdb=" C VAL G 525 " ideal model delta sigma weight residual 113.39 109.68 3.71 1.47e+00 4.63e-01 6.35e+00 ... (remaining 20589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 8126 16.94 - 33.88: 352 33.88 - 50.82: 90 50.82 - 67.77: 8 67.77 - 84.71: 4 Dihedral angle restraints: 8580 sinusoidal: 1768 harmonic: 6812 Sorted by residual: dihedral pdb=" CA THR C 661 " pdb=" C THR C 661 " pdb=" N LEU C 662 " pdb=" CA LEU C 662 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA THR G 661 " pdb=" C THR G 661 " pdb=" N LEU G 662 " pdb=" CA LEU G 662 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA THR E 661 " pdb=" C THR E 661 " pdb=" N LEU E 662 " pdb=" CA LEU E 662 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1700 0.038 - 0.076: 726 0.076 - 0.113: 102 0.113 - 0.151: 16 0.151 - 0.189: 2 Chirality restraints: 2546 Sorted by residual: chirality pdb=" CA PHE G 516 " pdb=" N PHE G 516 " pdb=" C PHE G 516 " pdb=" CB PHE G 516 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA PHE C 516 " pdb=" N PHE C 516 " pdb=" C PHE C 516 " pdb=" CB PHE C 516 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA VAL C 548 " pdb=" N VAL C 548 " pdb=" C VAL C 548 " pdb=" CB VAL C 548 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2543 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 516 " 0.020 2.00e-02 2.50e+03 1.76e-02 5.44e+00 pdb=" CG PHE C 516 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 516 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 516 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 516 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 516 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 516 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 516 " -0.020 2.00e-02 2.50e+03 1.76e-02 5.44e+00 pdb=" CG PHE G 516 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE G 516 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 516 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 516 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 516 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE G 516 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 480 " -0.033 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO C 481 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 481 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 481 " -0.027 5.00e-02 4.00e+02 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3814 2.78 - 3.31: 15082 3.31 - 3.84: 23410 3.84 - 4.37: 25721 4.37 - 4.90: 41741 Nonbonded interactions: 109768 Sorted by model distance: nonbonded pdb=" O MET G 660 " pdb=" OG1 THR G 661 " model vdw 2.250 2.440 nonbonded pdb=" O MET C 660 " pdb=" OG1 THR C 661 " model vdw 2.250 2.440 nonbonded pdb=" O MET A 660 " pdb=" OG1 THR A 661 " model vdw 2.263 2.440 nonbonded pdb=" O MET E 660 " pdb=" OG1 THR E 661 " model vdw 2.263 2.440 nonbonded pdb=" O HIS D 467 " pdb=" OG SER D 470 " model vdw 2.273 2.440 ... (remaining 109763 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 414 through 421 or (resid 422 through 424 and (name N or n \ ame CA or name C or name O or name CB )) or resid 425 through 437 or resid 439 t \ hrough 453 or (resid 454 through 456 and (name N or name CA or name C or name O \ or name CB )) or (resid 457 through 462 and (name N or name CA or name C or name \ O or name CB )) or resid 463 through 470 or (resid 471 through 472 and (name N \ or name CA or name C or name O or name CB )) or resid 473 through 504 or (resid \ 505 and (name N or name CA or name C or name O or name CB )) or resid 506 throug \ h 515 or (resid 516 through 518 and (name N or name CA or name C or name O or na \ me CB )) or (resid 519 through 527 and (name N or name CA or name C or name O or \ name CB )) or resid 528 through 533 or (resid 534 and (name N or name CA or nam \ e C or name O or name CB )) or resid 535 or (resid 536 through 537 and (name N o \ r name CA or name C or name O or name CB )) or resid 538 or (resid 539 through 5 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 541 through \ 556 or (resid 557 through 559 and (name N or name CA or name C or name O or nam \ e CB )) or resid 560 through 566 or (resid 567 through 570 and (name N or name C \ A or name C or name O or name CB )) or resid 571 through 577 or resid 581 throug \ h 588 or (resid 589 through 597 and (name N or name CA or name C or name O or na \ me CB )) or resid 598 through 602 or (resid 603 through 611 and (name N or name \ CA or name C or name O or name CB )) or (resid 624 through 627 and (name N or na \ me CA or name C or name O or name CB )) or resid 628 through 646 or (resid 647 t \ hrough 649 and (name N or name CA or name C or name O or name CB )) or resid 650 \ or (resid 651 and (name N or name CA or name C or name O or name CB )) or resid \ 652 through 655 or (resid 656 through 657 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 658 through 666 and (name N or name CA or name C o \ r name O or name CB )) or resid 667 or (resid 668 through 670 and (name N or nam \ e CA or name C or name O or name CB )) or resid 671 through 676 or (resid 677 th \ rough 679 and (name N or name CA or name C or name O or name CB )) or resid 680 \ or (resid 681 through 683 and (name N or name CA or name C or name O or name CB \ )) or resid 684 through 686 or (resid 687 through 696 and (name N or name CA or \ name C or name O or name CB )) or resid 697 through 717)) selection = (chain 'B' and (resid 414 or (resid 415 through 416 and (name N or name CA or na \ me C or name O or name CB )) or resid 417 through 430 or (resid 431 through 432 \ and (name N or name CA or name C or name O or name CB )) or resid 433 through 43 \ 7 or resid 439 through 441 or (resid 442 through 447 and (name N or name CA or n \ ame C or name O or name CB )) or resid 448 through 457 or (resid 458 through 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 or (resid \ 464 and (name N or name CA or name C or name O or name CB )) or resid 465 throu \ gh 467 or (resid 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 479 or (resid 480 and (name N or name CA or name C or name O \ or name CB )) or resid 481 through 500 or (resid 501 through 502 and (name N or \ name CA or name C or name O or name CB )) or resid 503 through 507 or (resid 508 \ through 509 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 10 through 520 or (resid 521 through 527 and (name N or name CA or name C or nam \ e O or name CB )) or resid 528 through 529 or (resid 530 and (name N or name CA \ or name C or name O or name CB )) or resid 531 or (resid 532 and (name N or name \ CA or name C or name O or name CB )) or resid 533 through 539 or (resid 540 and \ (name N or name CA or name C or name O or name CB )) or resid 541 through 544 o \ r (resid 545 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 46 through 555 or (resid 556 through 559 and (name N or name CA or name C or nam \ e O or name CB )) or resid 560 through 563 or (resid 564 and (name N or name CA \ or name C or name O or name CB )) or resid 565 through 572 or (resid 573 through \ 581 and (name N or name CA or name C or name O or name CB )) or resid 582 throu \ gh 583 or (resid 584 through 597 and (name N or name CA or name C or name O or n \ ame CB )) or resid 598 through 600 or (resid 601 through 627 and (name N or name \ CA or name C or name O or name CB )) or resid 628 through 633 or (resid 634 thr \ ough 635 and (name N or name CA or name C or name O or name CB )) or resid 636 t \ hrough 642 or (resid 643 and (name N or name CA or name C or name O or name CB ) \ ) or resid 644 through 663 or (resid 664 through 666 and (name N or name CA or n \ ame C or name O or name CB )) or resid 667 through 681 or (resid 682 through 683 \ and (name N or name CA or name C or name O or name CB )) or resid 684 through 7 \ 01 or (resid 702 through 704 and (name N or name CA or name C or name O or name \ CB )) or resid 705 through 706 or (resid 707 and (name N or name CA or name C or \ name O or name CB )) or resid 708 through 717)) selection = (chain 'C' and (resid 414 or (resid 415 through 416 and (name N or name CA or na \ me C or name O or name CB )) or resid 417 through 421 or (resid 422 through 424 \ and (name N or name CA or name C or name O or name CB )) or resid 425 through 42 \ 6 or (resid 427 and (name N or name CA or name C or name O or name CB )) or resi \ d 428 through 430 or (resid 431 through 432 and (name N or name CA or name C or \ name O or name CB )) or resid 433 through 437 or resid 439 through 453 or (resid \ 454 through 456 and (name N or name CA or name C or name O or name CB )) or (re \ sid 457 through 462 and (name N or name CA or name C or name O or name CB )) or \ resid 463 through 470 or (resid 471 through 472 and (name N or name CA or name C \ or name O or name CB )) or resid 473 through 478 or (resid 479 through 480 and \ (name N or name CA or name C or name O or name CB )) or resid 481 through 504 or \ (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 6 through 507 or (resid 508 through 509 and (name N or name CA or name C or name \ O or name CB )) or resid 510 through 515 or (resid 516 through 518 and (name N \ or name CA or name C or name O or name CB )) or (resid 519 through 527 and (name \ N or name CA or name C or name O or name CB )) or resid 528 through 533 or (res \ id 534 and (name N or name CA or name C or name O or name CB )) or resid 535 or \ (resid 536 through 537 and (name N or name CA or name C or name O or name CB )) \ or resid 538 or (resid 539 through 540 and (name N or name CA or name C or name \ O or name CB )) or resid 541 through 556 or (resid 557 through 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 566 or (resid 5 \ 67 through 570 and (name N or name CA or name C or name O or name CB )) or resid \ 571 through 577 or resid 581 through 588 or (resid 589 through 597 and (name N \ or name CA or name C or name O or name CB )) or resid 598 through 602 or (resid \ 603 through 611 and (name N or name CA or name C or name O or name CB )) or (res \ id 624 through 627 and (name N or name CA or name C or name O or name CB )) or r \ esid 628 through 634 or (resid 635 and (name N or name CA or name C or name O or \ name CB )) or resid 636 through 646 or (resid 647 through 649 and (name N or na \ me CA or name C or name O or name CB )) or resid 650 or (resid 651 and (name N o \ r name CA or name C or name O or name CB )) or resid 652 through 656 or (resid 6 \ 57 and (name N or name CA or name C or name O or name CB )) or (resid 658 throug \ h 666 and (name N or name CA or name C or name O or name CB )) or resid 667 or ( \ resid 668 through 670 and (name N or name CA or name C or name O or name CB )) o \ r resid 671 through 676 or (resid 677 through 679 and (name N or name CA or name \ C or name O or name CB )) or resid 680 or (resid 681 through 683 and (name N or \ name CA or name C or name O or name CB )) or resid 684 through 686 or (resid 68 \ 7 through 696 and (name N or name CA or name C or name O or name CB )) or resid \ 697 through 717)) selection = (chain 'D' and (resid 414 or (resid 415 through 416 and (name N or name CA or na \ me C or name O or name CB )) or resid 417 through 430 or (resid 431 through 432 \ and (name N or name CA or name C or name O or name CB )) or resid 433 through 43 \ 7 or resid 439 through 441 or (resid 442 through 447 and (name N or name CA or n \ ame C or name O or name CB )) or resid 448 through 463 or (resid 464 and (name N \ or name CA or name C or name O or name CB )) or resid 465 through 467 or (resid \ 468 and (name N or name CA or name C or name O or name CB )) or resid 469 throu \ gh 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) or \ resid 481 through 500 or (resid 501 through 502 and (name N or name CA or name \ C or name O or name CB )) or resid 503 through 507 or (resid 508 through 509 and \ (name N or name CA or name C or name O or name CB )) or resid 510 through 520 o \ r (resid 521 through 527 and (name N or name CA or name C or name O or name CB ) \ ) or resid 528 through 529 or (resid 530 and (name N or name CA or name C or nam \ e O or name CB )) or resid 531 through 535 or (resid 536 through 537 and (name N \ or name CA or name C or name O or name CB )) or resid 538 through 539 or (resid \ 540 and (name N or name CA or name C or name O or name CB )) or resid 541 throu \ gh 544 or (resid 545 and (name N or name CA or name C or name O or name CB )) or \ resid 546 through 556 or (resid 557 through 559 and (name N or name CA or name \ C or name O or name CB )) or resid 560 through 572 or (resid 573 through 581 and \ (name N or name CA or name C or name O or name CB )) or resid 582 through 583 o \ r (resid 584 through 597 and (name N or name CA or name C or name O or name CB ) \ ) or resid 598 through 601 or (resid 602 through 627 and (name N or name CA or n \ ame C or name O or name CB )) or resid 628 through 633 or (resid 634 through 635 \ and (name N or name CA or name C or name O or name CB )) or resid 636 through 6 \ 42 or (resid 643 and (name N or name CA or name C or name O or name CB )) or res \ id 644 through 659 or (resid 660 through 666 and (name N or name CA or name C or \ name O or name CB )) or resid 667 through 676 or (resid 677 through 679 and (na \ me N or name CA or name C or name O or name CB )) or resid 680 through 688 or (r \ esid 689 through 696 and (name N or name CA or name C or name O or name CB )) or \ (resid 697 through 704 and (name N or name CA or name C or name O or name CB )) \ or resid 705 through 706 or (resid 707 and (name N or name CA or name C or name \ O or name CB )) or resid 708 through 717)) selection = (chain 'E' and (resid 414 through 421 or (resid 422 through 424 and (name N or n \ ame CA or name C or name O or name CB )) or resid 425 through 437 or resid 439 t \ hrough 453 or (resid 454 through 456 and (name N or name CA or name C or name O \ or name CB )) or (resid 457 through 462 and (name N or name CA or name C or name \ O or name CB )) or resid 463 through 470 or (resid 471 through 472 and (name N \ or name CA or name C or name O or name CB )) or resid 473 through 504 or (resid \ 505 and (name N or name CA or name C or name O or name CB )) or resid 506 throug \ h 515 or (resid 516 through 518 and (name N or name CA or name C or name O or na \ me CB )) or (resid 519 through 527 and (name N or name CA or name C or name O or \ name CB )) or resid 528 through 533 or (resid 534 and (name N or name CA or nam \ e C or name O or name CB )) or resid 535 or (resid 536 through 537 and (name N o \ r name CA or name C or name O or name CB )) or resid 538 or (resid 539 through 5 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 541 through \ 556 or (resid 557 through 559 and (name N or name CA or name C or name O or nam \ e CB )) or resid 560 through 566 or (resid 567 through 570 and (name N or name C \ A or name C or name O or name CB )) or resid 571 through 577 or resid 581 throug \ h 588 or (resid 589 through 597 and (name N or name CA or name C or name O or na \ me CB )) or resid 598 through 602 or (resid 603 through 611 and (name N or name \ CA or name C or name O or name CB )) or (resid 624 through 627 and (name N or na \ me CA or name C or name O or name CB )) or resid 628 through 646 or (resid 647 t \ hrough 649 and (name N or name CA or name C or name O or name CB )) or resid 650 \ or (resid 651 and (name N or name CA or name C or name O or name CB )) or resid \ 652 through 655 or (resid 656 through 657 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 658 through 666 and (name N or name CA or name C o \ r name O or name CB )) or resid 667 or (resid 668 through 670 and (name N or nam \ e CA or name C or name O or name CB )) or resid 671 through 676 or (resid 677 th \ rough 679 and (name N or name CA or name C or name O or name CB )) or resid 680 \ or (resid 681 through 683 and (name N or name CA or name C or name O or name CB \ )) or resid 684 through 686 or (resid 687 through 696 and (name N or name CA or \ name C or name O or name CB )) or resid 697 through 717)) selection = (chain 'F' and (resid 414 or (resid 415 through 416 and (name N or name CA or na \ me C or name O or name CB )) or resid 417 through 430 or (resid 431 through 432 \ and (name N or name CA or name C or name O or name CB )) or resid 433 through 43 \ 7 or resid 439 through 441 or (resid 442 through 447 and (name N or name CA or n \ ame C or name O or name CB )) or resid 448 through 457 or (resid 458 through 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 or (resid \ 464 and (name N or name CA or name C or name O or name CB )) or resid 465 throu \ gh 467 or (resid 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 479 or (resid 480 and (name N or name CA or name C or name O \ or name CB )) or resid 481 through 500 or (resid 501 through 502 and (name N or \ name CA or name C or name O or name CB )) or resid 503 through 507 or (resid 508 \ through 509 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 10 through 520 or (resid 521 through 527 and (name N or name CA or name C or nam \ e O or name CB )) or resid 528 through 529 or (resid 530 and (name N or name CA \ or name C or name O or name CB )) or resid 531 or (resid 532 and (name N or name \ CA or name C or name O or name CB )) or resid 533 through 539 or (resid 540 and \ (name N or name CA or name C or name O or name CB )) or resid 541 through 544 o \ r (resid 545 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 46 through 555 or (resid 556 through 559 and (name N or name CA or name C or nam \ e O or name CB )) or resid 560 through 563 or (resid 564 and (name N or name CA \ or name C or name O or name CB )) or resid 565 through 572 or (resid 573 through \ 581 and (name N or name CA or name C or name O or name CB )) or resid 582 throu \ gh 583 or (resid 584 through 597 and (name N or name CA or name C or name O or n \ ame CB )) or resid 598 through 600 or (resid 601 through 627 and (name N or name \ CA or name C or name O or name CB )) or resid 628 through 633 or (resid 634 thr \ ough 635 and (name N or name CA or name C or name O or name CB )) or resid 636 t \ hrough 642 or (resid 643 and (name N or name CA or name C or name O or name CB ) \ ) or resid 644 through 663 or (resid 664 through 666 and (name N or name CA or n \ ame C or name O or name CB )) or resid 667 through 681 or (resid 682 through 683 \ and (name N or name CA or name C or name O or name CB )) or resid 684 through 7 \ 01 or (resid 702 through 704 and (name N or name CA or name C or name O or name \ CB )) or resid 705 through 706 or (resid 707 and (name N or name CA or name C or \ name O or name CB )) or resid 708 through 717)) selection = (chain 'G' and (resid 414 or (resid 415 through 416 and (name N or name CA or na \ me C or name O or name CB )) or resid 417 through 421 or (resid 422 through 424 \ and (name N or name CA or name C or name O or name CB )) or resid 425 through 42 \ 6 or (resid 427 and (name N or name CA or name C or name O or name CB )) or resi \ d 428 through 430 or (resid 431 through 432 and (name N or name CA or name C or \ name O or name CB )) or resid 433 through 437 or resid 439 through 453 or (resid \ 454 through 456 and (name N or name CA or name C or name O or name CB )) or (re \ sid 457 through 462 and (name N or name CA or name C or name O or name CB )) or \ resid 463 through 470 or (resid 471 through 472 and (name N or name CA or name C \ or name O or name CB )) or resid 473 through 478 or (resid 479 through 480 and \ (name N or name CA or name C or name O or name CB )) or resid 481 through 504 or \ (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 6 through 507 or (resid 508 through 509 and (name N or name CA or name C or name \ O or name CB )) or resid 510 through 515 or (resid 516 through 518 and (name N \ or name CA or name C or name O or name CB )) or (resid 519 through 527 and (name \ N or name CA or name C or name O or name CB )) or resid 528 through 533 or (res \ id 534 and (name N or name CA or name C or name O or name CB )) or resid 535 or \ (resid 536 through 537 and (name N or name CA or name C or name O or name CB )) \ or resid 538 or (resid 539 through 540 and (name N or name CA or name C or name \ O or name CB )) or resid 541 through 556 or (resid 557 through 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 566 or (resid 5 \ 67 through 570 and (name N or name CA or name C or name O or name CB )) or resid \ 571 through 577 or resid 581 through 588 or (resid 589 through 597 and (name N \ or name CA or name C or name O or name CB )) or resid 598 through 602 or (resid \ 603 through 611 and (name N or name CA or name C or name O or name CB )) or (res \ id 624 through 627 and (name N or name CA or name C or name O or name CB )) or r \ esid 628 through 634 or (resid 635 and (name N or name CA or name C or name O or \ name CB )) or resid 636 through 646 or (resid 647 through 649 and (name N or na \ me CA or name C or name O or name CB )) or resid 650 or (resid 651 and (name N o \ r name CA or name C or name O or name CB )) or resid 652 through 656 or (resid 6 \ 57 and (name N or name CA or name C or name O or name CB )) or (resid 658 throug \ h 666 and (name N or name CA or name C or name O or name CB )) or resid 667 or ( \ resid 668 through 670 and (name N or name CA or name C or name O or name CB )) o \ r resid 671 through 676 or (resid 677 through 679 and (name N or name CA or name \ C or name O or name CB )) or resid 680 or (resid 681 through 683 and (name N or \ name CA or name C or name O or name CB )) or resid 684 through 686 or (resid 68 \ 7 through 696 and (name N or name CA or name C or name O or name CB )) or resid \ 697 through 717)) selection = (chain 'H' and (resid 414 or (resid 415 through 416 and (name N or name CA or na \ me C or name O or name CB )) or resid 417 through 430 or (resid 431 through 432 \ and (name N or name CA or name C or name O or name CB )) or resid 433 through 43 \ 7 or resid 439 through 441 or (resid 442 through 447 and (name N or name CA or n \ ame C or name O or name CB )) or resid 448 through 463 or (resid 464 and (name N \ or name CA or name C or name O or name CB )) or resid 465 through 467 or (resid \ 468 and (name N or name CA or name C or name O or name CB )) or resid 469 throu \ gh 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) or \ resid 481 through 500 or (resid 501 through 502 and (name N or name CA or name \ C or name O or name CB )) or resid 503 through 507 or (resid 508 through 509 and \ (name N or name CA or name C or name O or name CB )) or resid 510 through 520 o \ r (resid 521 through 527 and (name N or name CA or name C or name O or name CB ) \ ) or resid 528 through 529 or (resid 530 and (name N or name CA or name C or nam \ e O or name CB )) or resid 531 through 535 or (resid 536 through 537 and (name N \ or name CA or name C or name O or name CB )) or resid 538 through 539 or (resid \ 540 and (name N or name CA or name C or name O or name CB )) or resid 541 throu \ gh 544 or (resid 545 and (name N or name CA or name C or name O or name CB )) or \ resid 546 through 556 or (resid 557 through 559 and (name N or name CA or name \ C or name O or name CB )) or resid 560 through 572 or (resid 573 through 581 and \ (name N or name CA or name C or name O or name CB )) or resid 582 through 583 o \ r (resid 584 through 597 and (name N or name CA or name C or name O or name CB ) \ ) or resid 598 through 601 or (resid 602 through 627 and (name N or name CA or n \ ame C or name O or name CB )) or resid 628 through 633 or (resid 634 through 635 \ and (name N or name CA or name C or name O or name CB )) or resid 636 through 6 \ 42 or (resid 643 and (name N or name CA or name C or name O or name CB )) or res \ id 644 through 659 or (resid 660 through 666 and (name N or name CA or name C or \ name O or name CB )) or resid 667 through 676 or (resid 677 through 679 and (na \ me N or name CA or name C or name O or name CB )) or resid 680 through 688 or (r \ esid 689 through 696 and (name N or name CA or name C or name O or name CB )) or \ (resid 697 through 704 and (name N or name CA or name C or name O or name CB )) \ or resid 705 through 706 or (resid 707 and (name N or name CA or name C or name \ O or name CB )) or resid 708 through 717)) } 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=0.50 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: 2.860 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: 12.530 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.700 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.080 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.003 0.074 14926 Z= 0.177 Angle : 0.626 8.741 20594 Z= 0.357 Chirality : 0.039 0.189 2546 Planarity : 0.005 0.049 2716 Dihedral : 11.388 84.707 4148 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.03 % Favored : 89.35 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.14), residues: 2296 helix: -2.55 (0.10), residues: 1736 sheet: None (None), residues: 0 loop : -3.54 (0.24), residues: 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 602 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 604 average time/residue: 0.2100 time to fit residues: 197.7218 Evaluate side-chains 592 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 590 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1211 time to fit residues: 2.6474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 467 HIS B 500 ASN B 527 ASN B 545 ASN B 547 HIS B 591 HIS C 467 HIS ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 HIS D 500 ASN D 575 ASN D 591 HIS D 636 HIS D 644 HIS D 689 HIS E 536 GLN F 467 HIS F 527 ASN F 547 HIS F 591 HIS F 636 HIS G 467 HIS G 500 ASN ** G 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 HIS H 497 GLN H 500 ASN H 575 ASN H 591 HIS H 636 HIS H 644 HIS H 689 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 14926 Z= 0.225 Angle : 0.651 8.646 20594 Z= 0.339 Chirality : 0.040 0.160 2546 Planarity : 0.004 0.044 2716 Dihedral : 4.587 20.287 2398 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.45 % Favored : 94.46 % Rotamer Outliers : 4.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.17), residues: 2296 helix: -0.98 (0.12), residues: 1808 sheet: None (None), residues: 0 loop : -2.72 (0.27), residues: 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 611 time to evaluate : 1.632 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 28 residues processed: 613 average time/residue: 0.2139 time to fit residues: 202.7714 Evaluate side-chains 636 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 608 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1327 time to fit residues: 9.1994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.2980 chunk 64 optimal weight: 0.0970 chunk 172 optimal weight: 0.0170 chunk 140 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 207 optimal weight: 0.0970 chunk 224 optimal weight: 0.9980 chunk 184 optimal weight: 0.0570 chunk 205 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 166 optimal weight: 0.1980 overall best weight: 0.0932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN B 500 ASN B 575 ASN B 636 HIS ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS D 689 HIS ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN F 545 ASN F 575 ASN H 547 HIS H 602 GLN ** H 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 14926 Z= 0.161 Angle : 0.575 9.133 20594 Z= 0.293 Chirality : 0.037 0.148 2546 Planarity : 0.004 0.053 2716 Dihedral : 4.094 18.842 2398 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.84 % Favored : 94.98 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 2296 helix: -0.32 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -2.57 (0.28), residues: 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 596 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 603 average time/residue: 0.2314 time to fit residues: 217.9534 Evaluate side-chains 607 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 593 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1336 time to fit residues: 5.7836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 139 optimal weight: 0.0970 chunk 208 optimal weight: 0.6980 chunk 220 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 467 HIS B 500 ASN B 591 HIS ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 GLN F 467 HIS F 560 GLN F 591 HIS G 664 GLN H 547 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 14926 Z= 0.187 Angle : 0.577 9.144 20594 Z= 0.297 Chirality : 0.038 0.146 2546 Planarity : 0.004 0.060 2716 Dihedral : 3.932 18.864 2398 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.80 % Favored : 95.03 % Rotamer Outliers : 4.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2296 helix: 0.10 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -2.29 (0.29), residues: 468 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 601 time to evaluate : 1.566 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 606 average time/residue: 0.2097 time to fit residues: 197.0222 Evaluate side-chains 623 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 597 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1469 time to fit residues: 8.6655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 152 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 HIS B 500 ASN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS D 644 HIS ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN F 591 HIS H 414 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 14926 Z= 0.282 Angle : 0.624 9.123 20594 Z= 0.330 Chirality : 0.040 0.141 2546 Planarity : 0.004 0.058 2716 Dihedral : 4.083 18.575 2398 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.41 % Favored : 94.42 % Rotamer Outliers : 4.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2296 helix: 0.36 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.77 (0.30), residues: 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 616 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 621 average time/residue: 0.2215 time to fit residues: 213.1878 Evaluate side-chains 640 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 614 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1314 time to fit residues: 8.5929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 0.0170 chunk 183 optimal weight: 0.5980 chunk 102 optimal weight: 0.0040 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 115 optimal weight: 0.0970 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 414 HIS B 467 HIS ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN E 500 ASN E 534 GLN E 664 GLN F 414 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14926 Z= 0.186 Angle : 0.592 10.003 20594 Z= 0.301 Chirality : 0.038 0.141 2546 Planarity : 0.004 0.058 2716 Dihedral : 3.877 16.540 2398 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.80 % Favored : 95.03 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2296 helix: 0.87 (0.13), residues: 1820 sheet: None (None), residues: 0 loop : -1.59 (0.30), residues: 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 608 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 26 residues processed: 613 average time/residue: 0.2136 time to fit residues: 202.5463 Evaluate side-chains 632 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 606 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1579 time to fit residues: 9.3861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 219 optimal weight: 0.0020 chunk 137 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN D 644 HIS E 500 ASN ** F 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 664 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14926 Z= 0.202 Angle : 0.607 10.030 20594 Z= 0.307 Chirality : 0.039 0.150 2546 Planarity : 0.004 0.044 2716 Dihedral : 3.814 16.388 2398 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.76 % Favored : 95.07 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 2296 helix: 1.10 (0.13), residues: 1820 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 607 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 611 average time/residue: 0.2110 time to fit residues: 199.9415 Evaluate side-chains 620 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 606 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1298 time to fit residues: 5.5659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.0170 chunk 87 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 149 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN A 664 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN E 500 ASN E 664 GLN ** F 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 664 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 14926 Z= 0.210 Angle : 0.628 10.777 20594 Z= 0.313 Chirality : 0.039 0.160 2546 Planarity : 0.004 0.052 2716 Dihedral : 3.787 16.090 2398 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.20 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2296 helix: 1.24 (0.13), residues: 1836 sheet: None (None), residues: 0 loop : -1.49 (0.31), residues: 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 601 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 602 average time/residue: 0.2103 time to fit residues: 196.7021 Evaluate side-chains 613 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 600 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1371 time to fit residues: 5.4145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 0.0970 chunk 185 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN D 414 HIS ** F 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 664 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 14926 Z= 0.261 Angle : 0.669 15.565 20594 Z= 0.338 Chirality : 0.041 0.160 2546 Planarity : 0.004 0.042 2716 Dihedral : 3.934 18.457 2398 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 2296 helix: 1.21 (0.13), residues: 1832 sheet: None (None), residues: 0 loop : -1.18 (0.31), residues: 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 617 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 618 average time/residue: 0.2167 time to fit residues: 209.4122 Evaluate side-chains 625 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 615 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1582 time to fit residues: 5.3699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 0.0770 chunk 150 optimal weight: 0.2980 chunk 227 optimal weight: 0.6980 chunk 209 optimal weight: 0.6980 chunk 180 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN A 560 GLN A 664 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS E 500 ASN E 664 GLN ** F 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 664 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 14926 Z= 0.214 Angle : 0.663 12.512 20594 Z= 0.327 Chirality : 0.039 0.164 2546 Planarity : 0.004 0.045 2716 Dihedral : 3.831 16.626 2398 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.76 % Favored : 95.07 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 2296 helix: 1.45 (0.13), residues: 1804 sheet: None (None), residues: 0 loop : -1.12 (0.30), residues: 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 606 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 606 average time/residue: 0.2127 time to fit residues: 199.7751 Evaluate side-chains 607 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 605 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1345 time to fit residues: 2.6076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 159 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS E 500 ASN E 636 HIS ** F 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.078617 restraints weight = 69620.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.082666 restraints weight = 32445.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085421 restraints weight = 18707.659| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 14926 Z= 0.230 Angle : 0.668 13.784 20594 Z= 0.331 Chirality : 0.040 0.164 2546 Planarity : 0.004 0.041 2716 Dihedral : 3.825 16.158 2398 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.81 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 2296 helix: 1.48 (0.13), residues: 1820 sheet: None (None), residues: 0 loop : -1.15 (0.30), residues: 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3887.16 seconds wall clock time: 69 minutes 57.18 seconds (4197.18 seconds total)