Starting phenix.real_space_refine on Fri Feb 16 06:46:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/02_2024/7jth_22473.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/02_2024/7jth_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_22473/02_2024/7jth_22473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/02_2024/7jth_22473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/02_2024/7jth_22473.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jth_22473/02_2024/7jth_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-dev-5238/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: 11.37, per 1000 atoms: 0.78 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: 5.95 Conformation dependent library (CDL) restraints added in 4.9 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: 1.50 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: 4.76 Time building geometry restraints manager: 6.41 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: 2.920 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: 12.200 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 47.170 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.000 ------------------------------------------------------------------------------- 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 % Allowed : 6.01 % Favored : 93.54 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 630 HIS 0.015 0.001 HIS H 689 PHE 0.040 0.002 PHE G 516 TYR 0.013 0.001 TYR D 426 ARG 0.003 0.001 ARG D 693 *********************** 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 : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8316 (t80) cc_final: 0.7717 (t80) REVERT: A 451 VAL cc_start: 0.8474 (m) cc_final: 0.8148 (p) REVERT: A 472 LEU cc_start: 0.7656 (mt) cc_final: 0.7431 (mt) REVERT: A 499 VAL cc_start: 0.8653 (t) cc_final: 0.8441 (p) REVERT: A 565 LEU cc_start: 0.7873 (tt) cc_final: 0.7600 (tt) REVERT: A 567 SER cc_start: 0.8345 (p) cc_final: 0.8091 (p) REVERT: A 603 ILE cc_start: 0.7534 (mm) cc_final: 0.7279 (mm) REVERT: A 630 TRP cc_start: 0.7438 (m100) cc_final: 0.7182 (m100) REVERT: A 661 THR cc_start: 0.7236 (m) cc_final: 0.6862 (m) REVERT: B 500 ASN cc_start: 0.8352 (t0) cc_final: 0.7932 (t0) REVERT: B 507 ILE cc_start: 0.8070 (mt) cc_final: 0.7845 (mm) REVERT: B 560 GLN cc_start: 0.8446 (tt0) cc_final: 0.8005 (tt0) REVERT: B 564 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7006 (mm-40) REVERT: B 565 LEU cc_start: 0.7909 (tt) cc_final: 0.7634 (tp) REVERT: B 566 PHE cc_start: 0.8379 (m-80) cc_final: 0.8155 (m-80) REVERT: B 587 GLN cc_start: 0.8460 (pp30) cc_final: 0.7843 (pp30) REVERT: B 591 HIS cc_start: 0.5630 (m-70) cc_final: 0.5228 (m170) REVERT: B 630 TRP cc_start: 0.8177 (m100) cc_final: 0.7825 (m100) REVERT: B 645 MET cc_start: 0.7591 (mmm) cc_final: 0.7302 (mmm) REVERT: C 425 PRO cc_start: 0.9162 (Cg_exo) cc_final: 0.8929 (Cg_endo) REVERT: C 459 ILE cc_start: 0.8256 (tp) cc_final: 0.8044 (tp) REVERT: C 471 LEU cc_start: 0.8908 (mt) cc_final: 0.8636 (mt) REVERT: C 534 GLN cc_start: 0.6960 (tt0) cc_final: 0.6698 (tt0) REVERT: C 558 ILE cc_start: 0.8227 (tp) cc_final: 0.7856 (tp) REVERT: C 651 LEU cc_start: 0.8506 (mt) cc_final: 0.8249 (mm) REVERT: D 416 PHE cc_start: 0.7610 (t80) cc_final: 0.7182 (t80) REVERT: D 429 ILE cc_start: 0.8298 (mt) cc_final: 0.8042 (mm) REVERT: D 493 PHE cc_start: 0.8242 (m-80) cc_final: 0.7952 (m-10) REVERT: D 508 LYS cc_start: 0.8338 (tttp) cc_final: 0.7827 (ttmt) REVERT: D 565 LEU cc_start: 0.7874 (tt) cc_final: 0.7655 (tp) REVERT: D 630 TRP cc_start: 0.7099 (m100) cc_final: 0.6727 (m100) REVERT: E 422 LEU cc_start: 0.8290 (tp) cc_final: 0.8021 (tp) REVERT: E 425 PRO cc_start: 0.8814 (Cg_exo) cc_final: 0.8582 (Cg_endo) REVERT: E 441 PHE cc_start: 0.8378 (t80) cc_final: 0.7809 (t80) REVERT: E 472 LEU cc_start: 0.7639 (mt) cc_final: 0.7438 (mt) REVERT: E 495 SER cc_start: 0.8989 (p) cc_final: 0.8733 (p) REVERT: E 497 GLN cc_start: 0.7284 (tt0) cc_final: 0.7076 (tt0) REVERT: E 499 VAL cc_start: 0.8697 (t) cc_final: 0.8467 (p) REVERT: E 555 TYR cc_start: 0.8714 (m-10) cc_final: 0.8495 (m-80) REVERT: E 565 LEU cc_start: 0.7755 (tt) cc_final: 0.7469 (tt) REVERT: E 567 SER cc_start: 0.8181 (p) cc_final: 0.7942 (p) REVERT: E 630 TRP cc_start: 0.7302 (m100) cc_final: 0.6998 (m100) REVERT: F 500 ASN cc_start: 0.8334 (t0) cc_final: 0.7949 (t0) REVERT: F 554 TYR cc_start: 0.8399 (t80) cc_final: 0.8172 (t80) REVERT: F 560 GLN cc_start: 0.8354 (tt0) cc_final: 0.7962 (tt0) REVERT: F 564 GLN cc_start: 0.7381 (mm-40) cc_final: 0.6984 (mm-40) REVERT: F 565 LEU cc_start: 0.7835 (tt) cc_final: 0.7591 (tp) REVERT: F 566 PHE cc_start: 0.8374 (m-80) cc_final: 0.8173 (m-80) REVERT: F 587 GLN cc_start: 0.8405 (pp30) cc_final: 0.7814 (pp30) REVERT: F 591 HIS cc_start: 0.5679 (m-70) cc_final: 0.5206 (m170) REVERT: F 645 MET cc_start: 0.7641 (mmm) cc_final: 0.7387 (mmm) REVERT: G 471 LEU cc_start: 0.8816 (mt) cc_final: 0.8558 (mt) REVERT: G 534 GLN cc_start: 0.6928 (tt0) cc_final: 0.6675 (tt0) REVERT: G 558 ILE cc_start: 0.8238 (tp) cc_final: 0.7722 (tp) REVERT: G 565 LEU cc_start: 0.8031 (tp) cc_final: 0.7648 (tp) REVERT: G 603 ILE cc_start: 0.8269 (mm) cc_final: 0.8067 (mm) REVERT: G 651 LEU cc_start: 0.8520 (mt) cc_final: 0.8251 (mm) REVERT: H 429 ILE cc_start: 0.8327 (mt) cc_final: 0.8124 (mm) REVERT: H 493 PHE cc_start: 0.8266 (m-80) cc_final: 0.7940 (m-10) REVERT: H 508 LYS cc_start: 0.8386 (tttp) cc_final: 0.7831 (ttmt) REVERT: H 630 TRP cc_start: 0.7369 (m100) cc_final: 0.7067 (m100) outliers start: 4 outliers final: 2 residues processed: 604 average time/residue: 0.2103 time to fit residues: 197.3862 Evaluate side-chains 594 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 592 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain G residue 687 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN B 467 HIS ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN B 545 ASN B 547 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 HIS ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 527 ASN F 547 HIS F 636 HIS G 467 HIS G 500 ASN ** G 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 HIS 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14926 Z= 0.190 Angle : 0.617 8.575 20594 Z= 0.321 Chirality : 0.039 0.144 2546 Planarity : 0.004 0.044 2716 Dihedral : 4.720 44.836 2402 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.19 % Favored : 94.63 % Rotamer: Outliers : 3.67 % Allowed : 27.62 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.17), residues: 2296 helix: -1.01 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -3.10 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 542 HIS 0.010 0.002 HIS H 467 PHE 0.020 0.002 PHE C 516 TYR 0.019 0.002 TYR A 680 ARG 0.004 0.001 ARG B 464 *********************** 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 638 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 605 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8355 (t80) cc_final: 0.7750 (t80) REVERT: A 469 SER cc_start: 0.8541 (p) cc_final: 0.8317 (p) REVERT: A 506 ILE cc_start: 0.8265 (mt) cc_final: 0.8006 (tp) REVERT: A 541 PHE cc_start: 0.8028 (t80) cc_final: 0.7488 (t80) REVERT: A 565 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7488 (tt) REVERT: A 567 SER cc_start: 0.8380 (p) cc_final: 0.8116 (p) REVERT: B 500 ASN cc_start: 0.8335 (t0) cc_final: 0.8005 (t0) REVERT: B 508 LYS cc_start: 0.8192 (tttp) cc_final: 0.7760 (ttpp) REVERT: B 560 GLN cc_start: 0.8389 (tt0) cc_final: 0.7990 (tt0) REVERT: B 564 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7147 (mm-40) REVERT: B 587 GLN cc_start: 0.8585 (pp30) cc_final: 0.7974 (pp30) REVERT: B 645 MET cc_start: 0.7559 (mmm) cc_final: 0.7012 (mmm) REVERT: C 471 LEU cc_start: 0.9004 (mt) cc_final: 0.8767 (mt) REVERT: C 508 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8139 (ttpp) REVERT: C 534 GLN cc_start: 0.7241 (tt0) cc_final: 0.6887 (tt0) REVERT: C 651 LEU cc_start: 0.8622 (mt) cc_final: 0.8302 (mm) REVERT: D 416 PHE cc_start: 0.7713 (t80) cc_final: 0.7328 (t80) REVERT: D 493 PHE cc_start: 0.8365 (m-80) cc_final: 0.8098 (m-10) REVERT: D 508 LYS cc_start: 0.8424 (tttp) cc_final: 0.7912 (ttmt) REVERT: D 538 MET cc_start: 0.7967 (mmm) cc_final: 0.7754 (mmm) REVERT: D 630 TRP cc_start: 0.7256 (m100) cc_final: 0.6975 (m100) REVERT: E 425 PRO cc_start: 0.9000 (Cg_exo) cc_final: 0.8786 (Cg_endo) REVERT: E 441 PHE cc_start: 0.8403 (t80) cc_final: 0.7822 (t80) REVERT: E 497 GLN cc_start: 0.7411 (tt0) cc_final: 0.7080 (tt0) REVERT: E 506 ILE cc_start: 0.8243 (mt) cc_final: 0.7991 (tp) REVERT: E 541 PHE cc_start: 0.7916 (t80) cc_final: 0.7580 (t80) REVERT: E 555 TYR cc_start: 0.8819 (m-10) cc_final: 0.8400 (m-80) REVERT: E 565 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7279 (tt) REVERT: E 630 TRP cc_start: 0.7398 (m100) cc_final: 0.7160 (m100) REVERT: F 500 ASN cc_start: 0.8312 (t0) cc_final: 0.7998 (t0) REVERT: F 560 GLN cc_start: 0.8296 (tt0) cc_final: 0.7910 (tt0) REVERT: F 564 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7145 (mm-40) REVERT: F 587 GLN cc_start: 0.8521 (pp30) cc_final: 0.8111 (pp30) REVERT: F 591 HIS cc_start: 0.5993 (m-70) cc_final: 0.5612 (m170) REVERT: F 645 MET cc_start: 0.7536 (mmm) cc_final: 0.7275 (mmm) REVERT: G 471 LEU cc_start: 0.8938 (mt) cc_final: 0.8664 (mm) REVERT: G 498 THR cc_start: 0.8138 (p) cc_final: 0.7818 (t) REVERT: G 534 GLN cc_start: 0.7217 (tt0) cc_final: 0.6880 (tt0) REVERT: G 541 PHE cc_start: 0.8505 (t80) cc_final: 0.8185 (t80) REVERT: G 565 LEU cc_start: 0.8120 (tp) cc_final: 0.7737 (tp) REVERT: G 603 ILE cc_start: 0.8307 (mm) cc_final: 0.8090 (mm) REVERT: G 651 LEU cc_start: 0.8614 (mt) cc_final: 0.8377 (mm) REVERT: H 493 PHE cc_start: 0.8336 (m-80) cc_final: 0.8024 (m-10) REVERT: H 503 THR cc_start: 0.8540 (t) cc_final: 0.8103 (m) REVERT: H 508 LYS cc_start: 0.8474 (tttp) cc_final: 0.7945 (ttmt) REVERT: H 602 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8079 (tp-100) REVERT: H 630 TRP cc_start: 0.7476 (m100) cc_final: 0.7232 (m100) REVERT: H 671 ILE cc_start: 0.8732 (mm) cc_final: 0.8423 (tp) outliers start: 33 outliers final: 21 residues processed: 607 average time/residue: 0.2116 time to fit residues: 198.3961 Evaluate side-chains 626 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 603 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 624 ASP Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 500 ASN Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.5980 chunk 64 optimal weight: 0.0980 chunk 172 optimal weight: 0.3980 chunk 140 optimal weight: 0.8980 chunk 57 optimal weight: 0.0470 chunk 207 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 166 optimal weight: 0.3980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN B 636 HIS ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS D 689 HIS E 500 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 GLN F 497 GLN ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 ASN ** G 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14926 Z= 0.172 Angle : 0.567 8.218 20594 Z= 0.292 Chirality : 0.038 0.149 2546 Planarity : 0.004 0.060 2716 Dihedral : 4.135 19.706 2398 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 4.68 % Allowed : 33.52 % Favored : 61.80 % 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: -1.36 (0.18), residues: 2296 helix: -0.38 (0.12), residues: 1836 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 630 HIS 0.011 0.001 HIS D 636 PHE 0.017 0.002 PHE B 493 TYR 0.012 0.001 TYR A 426 ARG 0.007 0.001 ARG B 464 *********************** 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 641 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 599 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8079 (tp) REVERT: A 441 PHE cc_start: 0.8350 (t80) cc_final: 0.7750 (t80) REVERT: A 469 SER cc_start: 0.8555 (p) cc_final: 0.8313 (p) REVERT: A 506 ILE cc_start: 0.8343 (mt) cc_final: 0.8047 (tp) REVERT: A 567 SER cc_start: 0.8361 (p) cc_final: 0.8019 (p) REVERT: B 441 PHE cc_start: 0.8214 (t80) cc_final: 0.7971 (t80) REVERT: B 500 ASN cc_start: 0.8283 (t0) cc_final: 0.7953 (t0) REVERT: B 508 LYS cc_start: 0.8154 (tttp) cc_final: 0.7668 (ttpp) REVERT: B 530 MET cc_start: 0.7424 (mmt) cc_final: 0.7145 (mmt) REVERT: B 560 GLN cc_start: 0.8306 (tt0) cc_final: 0.7846 (tt0) REVERT: B 564 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7240 (mm-40) REVERT: B 587 GLN cc_start: 0.8616 (pp30) cc_final: 0.8103 (pp30) REVERT: B 645 MET cc_start: 0.7606 (mmm) cc_final: 0.7007 (mmm) REVERT: C 471 LEU cc_start: 0.8998 (mt) cc_final: 0.8735 (mt) REVERT: C 534 GLN cc_start: 0.7324 (tt0) cc_final: 0.6951 (tt0) REVERT: C 651 LEU cc_start: 0.8638 (mt) cc_final: 0.8311 (mm) REVERT: C 667 PHE cc_start: 0.8722 (t80) cc_final: 0.8385 (t80) REVERT: D 416 PHE cc_start: 0.7742 (t80) cc_final: 0.7336 (t80) REVERT: D 493 PHE cc_start: 0.8367 (m-80) cc_final: 0.8141 (m-10) REVERT: D 508 LYS cc_start: 0.8402 (tttp) cc_final: 0.7988 (ttmt) REVERT: D 538 MET cc_start: 0.7876 (mmm) cc_final: 0.7498 (tpp) REVERT: D 630 TRP cc_start: 0.7270 (m100) cc_final: 0.6973 (m100) REVERT: E 425 PRO cc_start: 0.8946 (Cg_exo) cc_final: 0.8716 (Cg_endo) REVERT: E 441 PHE cc_start: 0.8382 (t80) cc_final: 0.7786 (t80) REVERT: E 497 GLN cc_start: 0.7365 (tt0) cc_final: 0.7096 (tt0) REVERT: E 541 PHE cc_start: 0.7897 (t80) cc_final: 0.7650 (t80) REVERT: E 555 TYR cc_start: 0.8774 (m-10) cc_final: 0.8404 (m-80) REVERT: E 565 LEU cc_start: 0.7458 (tt) cc_final: 0.7209 (tt) REVERT: E 667 PHE cc_start: 0.8731 (t80) cc_final: 0.8466 (t80) REVERT: F 464 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.7156 (ttm-80) REVERT: F 493 PHE cc_start: 0.8320 (m-80) cc_final: 0.8051 (m-10) REVERT: F 508 LYS cc_start: 0.8073 (tttp) cc_final: 0.7553 (ttmt) REVERT: F 560 GLN cc_start: 0.8196 (tt0) cc_final: 0.7901 (tt0) REVERT: F 564 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7195 (mm-40) REVERT: F 587 GLN cc_start: 0.8547 (pp30) cc_final: 0.8102 (pp30) REVERT: F 602 GLN cc_start: 0.7871 (tp40) cc_final: 0.7533 (tp40) REVERT: F 645 MET cc_start: 0.7581 (mmm) cc_final: 0.7257 (mmm) REVERT: G 471 LEU cc_start: 0.8941 (mt) cc_final: 0.8657 (mt) REVERT: G 498 THR cc_start: 0.8036 (p) cc_final: 0.7807 (t) REVERT: G 534 GLN cc_start: 0.7280 (tt0) cc_final: 0.6957 (tt0) REVERT: G 565 LEU cc_start: 0.8064 (tp) cc_final: 0.7766 (tp) REVERT: G 651 LEU cc_start: 0.8554 (mt) cc_final: 0.8266 (mm) REVERT: G 667 PHE cc_start: 0.8651 (t80) cc_final: 0.8333 (t80) REVERT: G 668 VAL cc_start: 0.8870 (m) cc_final: 0.8631 (t) REVERT: H 493 PHE cc_start: 0.8360 (m-80) cc_final: 0.8073 (m-10) REVERT: H 503 THR cc_start: 0.8555 (t) cc_final: 0.8138 (m) REVERT: H 508 LYS cc_start: 0.8431 (tttp) cc_final: 0.8002 (ttmt) REVERT: H 630 TRP cc_start: 0.7469 (m100) cc_final: 0.7195 (m100) REVERT: H 671 ILE cc_start: 0.8689 (mm) cc_final: 0.8440 (tp) outliers start: 42 outliers final: 31 residues processed: 605 average time/residue: 0.2167 time to fit residues: 204.6212 Evaluate side-chains 626 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 594 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 540 LEU 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: 1.9990 chunk 107 optimal weight: 0.0060 chunk 22 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 139 optimal weight: 0.3980 chunk 208 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 197 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN B 467 HIS ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 ASN F 467 HIS F 497 GLN F 575 ASN H 414 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14926 Z= 0.176 Angle : 0.561 8.662 20594 Z= 0.290 Chirality : 0.038 0.146 2546 Planarity : 0.004 0.062 2716 Dihedral : 3.956 18.546 2398 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.06 % Favored : 94.76 % Rotamer: Outliers : 6.24 % Allowed : 34.97 % Favored : 58.80 % 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: -0.68 (0.18), residues: 2296 helix: 0.05 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -2.06 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 630 HIS 0.012 0.001 HIS H 636 PHE 0.019 0.002 PHE B 493 TYR 0.018 0.001 TYR H 504 ARG 0.009 0.001 ARG F 556 *********************** 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 661 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 605 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8369 (t80) cc_final: 0.7768 (t80) REVERT: A 472 LEU cc_start: 0.7673 (mt) cc_final: 0.7397 (mt) REVERT: A 503 THR cc_start: 0.8358 (m) cc_final: 0.7984 (t) REVERT: A 567 SER cc_start: 0.8353 (p) cc_final: 0.8011 (p) REVERT: B 441 PHE cc_start: 0.8250 (t80) cc_final: 0.8013 (t80) REVERT: B 500 ASN cc_start: 0.8328 (t0) cc_final: 0.8013 (t0) REVERT: B 508 LYS cc_start: 0.8098 (tttp) cc_final: 0.7634 (ttmt) REVERT: B 530 MET cc_start: 0.7430 (mmt) cc_final: 0.7224 (mmt) REVERT: B 560 GLN cc_start: 0.8268 (tt0) cc_final: 0.7803 (tt0) REVERT: B 564 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7339 (mm-40) REVERT: B 587 GLN cc_start: 0.8671 (pp30) cc_final: 0.8193 (pp30) REVERT: B 645 MET cc_start: 0.7583 (mmm) cc_final: 0.7233 (mmm) REVERT: C 471 LEU cc_start: 0.8990 (mt) cc_final: 0.8689 (mt) REVERT: C 534 GLN cc_start: 0.7412 (tt0) cc_final: 0.7057 (tt0) REVERT: C 651 LEU cc_start: 0.8632 (mt) cc_final: 0.8279 (mm) REVERT: C 667 PHE cc_start: 0.8717 (t80) cc_final: 0.8419 (t80) REVERT: D 416 PHE cc_start: 0.7792 (t80) cc_final: 0.7396 (t80) REVERT: D 493 PHE cc_start: 0.8381 (m-80) cc_final: 0.8172 (m-10) REVERT: D 504 TYR cc_start: 0.7201 (t80) cc_final: 0.6977 (t80) REVERT: D 508 LYS cc_start: 0.8373 (tttp) cc_final: 0.8027 (ttmt) REVERT: D 536 GLN cc_start: 0.7510 (tt0) cc_final: 0.7196 (tt0) REVERT: D 538 MET cc_start: 0.7909 (mmm) cc_final: 0.7577 (mmm) REVERT: D 630 TRP cc_start: 0.7351 (m100) cc_final: 0.7056 (m100) REVERT: E 441 PHE cc_start: 0.8415 (t80) cc_final: 0.7803 (t80) REVERT: E 497 GLN cc_start: 0.7402 (tt0) cc_final: 0.7183 (tt0) REVERT: E 503 THR cc_start: 0.8397 (m) cc_final: 0.8031 (t) REVERT: E 541 PHE cc_start: 0.7936 (t80) cc_final: 0.7626 (t80) REVERT: E 555 TYR cc_start: 0.8782 (m-10) cc_final: 0.8371 (m-80) REVERT: E 565 LEU cc_start: 0.7510 (tt) cc_final: 0.7277 (tt) REVERT: E 630 TRP cc_start: 0.7294 (m100) cc_final: 0.7038 (m100) REVERT: E 667 PHE cc_start: 0.8764 (t80) cc_final: 0.8465 (t80) REVERT: F 415 ILE cc_start: 0.8680 (mm) cc_final: 0.8262 (tp) REVERT: F 464 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.7204 (ttm-80) REVERT: F 493 PHE cc_start: 0.8366 (m-80) cc_final: 0.8134 (m-10) REVERT: F 508 LYS cc_start: 0.8070 (tttp) cc_final: 0.7565 (ttmt) REVERT: F 560 GLN cc_start: 0.8147 (tt0) cc_final: 0.7932 (tt0) REVERT: F 564 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7238 (mm-40) REVERT: F 587 GLN cc_start: 0.8610 (pp30) cc_final: 0.8248 (pp30) REVERT: F 591 HIS cc_start: 0.6176 (m-70) cc_final: 0.5792 (m170) REVERT: F 645 MET cc_start: 0.7526 (mmm) cc_final: 0.7254 (mmm) REVERT: G 471 LEU cc_start: 0.8905 (mt) cc_final: 0.8591 (mm) REVERT: G 498 THR cc_start: 0.7974 (p) cc_final: 0.7706 (t) REVERT: G 534 GLN cc_start: 0.7362 (tt0) cc_final: 0.6994 (tt0) REVERT: G 565 LEU cc_start: 0.8060 (tp) cc_final: 0.7851 (tp) REVERT: G 651 LEU cc_start: 0.8546 (mt) cc_final: 0.8242 (mm) REVERT: G 667 PHE cc_start: 0.8681 (t80) cc_final: 0.8397 (t80) REVERT: G 668 VAL cc_start: 0.8931 (m) cc_final: 0.8654 (t) REVERT: H 493 PHE cc_start: 0.8365 (m-80) cc_final: 0.8141 (m-10) REVERT: H 503 THR cc_start: 0.8560 (t) cc_final: 0.8151 (m) REVERT: H 508 LYS cc_start: 0.8453 (tttp) cc_final: 0.8128 (ttmt) REVERT: H 630 TRP cc_start: 0.7512 (m100) cc_final: 0.7282 (m100) outliers start: 56 outliers final: 44 residues processed: 612 average time/residue: 0.2105 time to fit residues: 198.6144 Evaluate side-chains 646 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 602 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU 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: 2.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 0.0370 chunk 152 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 55 optimal weight: 0.0370 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS D 644 HIS E 500 ASN E 664 GLN F 414 HIS F 467 HIS F 497 GLN G 664 GLN H 414 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14926 Z= 0.188 Angle : 0.570 9.786 20594 Z= 0.293 Chirality : 0.038 0.135 2546 Planarity : 0.004 0.051 2716 Dihedral : 3.875 17.001 2398 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.81 % Rotamer: Outliers : 7.02 % Allowed : 38.31 % Favored : 54.68 % 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: -0.19 (0.18), residues: 2296 helix: 0.37 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 630 HIS 0.012 0.001 HIS A 547 PHE 0.027 0.002 PHE A 667 TYR 0.016 0.001 TYR H 504 ARG 0.009 0.001 ARG D 693 *********************** 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 663 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 600 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8361 (t80) cc_final: 0.7769 (t80) REVERT: A 471 LEU cc_start: 0.8740 (tp) cc_final: 0.8420 (tt) REVERT: A 472 LEU cc_start: 0.7711 (mt) cc_final: 0.7458 (mt) REVERT: A 503 THR cc_start: 0.8365 (m) cc_final: 0.8056 (t) REVERT: A 567 SER cc_start: 0.8363 (p) cc_final: 0.7967 (p) REVERT: B 508 LYS cc_start: 0.8075 (tttp) cc_final: 0.7626 (ttmt) REVERT: B 530 MET cc_start: 0.7449 (mmt) cc_final: 0.7243 (mmt) REVERT: B 560 GLN cc_start: 0.8282 (tt0) cc_final: 0.7890 (tt0) REVERT: B 564 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7364 (mm-40) REVERT: B 587 GLN cc_start: 0.8683 (pp30) cc_final: 0.8189 (pp30) REVERT: B 591 HIS cc_start: 0.6203 (m-70) cc_final: 0.5754 (m170) REVERT: B 645 MET cc_start: 0.7558 (mmm) cc_final: 0.7158 (mmm) REVERT: C 471 LEU cc_start: 0.8980 (mt) cc_final: 0.8734 (mm) REVERT: C 534 GLN cc_start: 0.7483 (tt0) cc_final: 0.7127 (tt0) REVERT: C 651 LEU cc_start: 0.8639 (mt) cc_final: 0.8271 (mm) REVERT: C 667 PHE cc_start: 0.8699 (t80) cc_final: 0.8426 (t80) REVERT: D 416 PHE cc_start: 0.7812 (t80) cc_final: 0.7390 (t80) REVERT: D 489 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8009 (m) REVERT: D 493 PHE cc_start: 0.8401 (m-80) cc_final: 0.8198 (m-10) REVERT: D 504 TYR cc_start: 0.7227 (t80) cc_final: 0.7013 (t80) REVERT: D 508 LYS cc_start: 0.8405 (tttp) cc_final: 0.8052 (ttmt) REVERT: D 536 GLN cc_start: 0.7478 (tt0) cc_final: 0.7204 (tt0) REVERT: D 538 MET cc_start: 0.7915 (mmm) cc_final: 0.7546 (mmm) REVERT: D 630 TRP cc_start: 0.7353 (m100) cc_final: 0.7057 (m100) REVERT: D 680 TYR cc_start: 0.8028 (t80) cc_final: 0.7715 (t80) REVERT: D 689 HIS cc_start: 0.5337 (m90) cc_final: 0.4800 (m170) REVERT: E 441 PHE cc_start: 0.8419 (t80) cc_final: 0.7839 (t80) REVERT: E 471 LEU cc_start: 0.8838 (tp) cc_final: 0.8465 (tt) REVERT: E 503 THR cc_start: 0.8321 (m) cc_final: 0.7984 (t) REVERT: E 541 PHE cc_start: 0.8030 (t80) cc_final: 0.7744 (t80) REVERT: E 555 TYR cc_start: 0.8778 (m-10) cc_final: 0.8352 (m-80) REVERT: E 565 LEU cc_start: 0.7515 (tt) cc_final: 0.7301 (tt) REVERT: E 667 PHE cc_start: 0.8773 (t80) cc_final: 0.8472 (t80) REVERT: F 415 ILE cc_start: 0.8583 (mm) cc_final: 0.8084 (tp) REVERT: F 464 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.7240 (ttm-80) REVERT: F 493 PHE cc_start: 0.8365 (m-80) cc_final: 0.8132 (m-10) REVERT: F 508 LYS cc_start: 0.8009 (tttp) cc_final: 0.7567 (ttmt) REVERT: F 560 GLN cc_start: 0.8156 (tt0) cc_final: 0.7951 (tt0) REVERT: F 564 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7307 (mm-40) REVERT: F 587 GLN cc_start: 0.8658 (pp30) cc_final: 0.8276 (pp30) REVERT: F 591 HIS cc_start: 0.6243 (m-70) cc_final: 0.5831 (m170) REVERT: F 645 MET cc_start: 0.7522 (mmm) cc_final: 0.7218 (mmm) REVERT: G 471 LEU cc_start: 0.8949 (mt) cc_final: 0.8725 (mm) REVERT: G 534 GLN cc_start: 0.7405 (tt0) cc_final: 0.7054 (tt0) REVERT: G 565 LEU cc_start: 0.8077 (tp) cc_final: 0.7871 (tp) REVERT: G 667 PHE cc_start: 0.8656 (t80) cc_final: 0.8400 (t80) REVERT: G 668 VAL cc_start: 0.8950 (m) cc_final: 0.8668 (t) REVERT: H 493 PHE cc_start: 0.8389 (m-80) cc_final: 0.8180 (m-10) REVERT: H 503 THR cc_start: 0.8562 (t) cc_final: 0.8202 (m) REVERT: H 508 LYS cc_start: 0.8463 (tttp) cc_final: 0.8135 (ttmt) REVERT: H 630 TRP cc_start: 0.7546 (m100) cc_final: 0.7311 (m100) outliers start: 63 outliers final: 47 residues processed: 612 average time/residue: 0.2122 time to fit residues: 200.8069 Evaluate side-chains 643 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 595 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 575 ASN Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 129 optimal weight: 0.6980 chunk 54 optimal weight: 0.0470 chunk 220 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 0.0570 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN E 500 ASN E 534 GLN F 467 HIS F 497 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14926 Z= 0.167 Angle : 0.567 9.874 20594 Z= 0.286 Chirality : 0.038 0.137 2546 Planarity : 0.004 0.056 2716 Dihedral : 3.796 16.417 2398 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.20 % Rotamer: Outliers : 6.68 % Allowed : 39.42 % Favored : 53.90 % 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: 0.30 (0.18), residues: 2296 helix: 0.75 (0.13), residues: 1816 sheet: None (None), residues: 0 loop : -1.72 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 630 HIS 0.012 0.001 HIS H 636 PHE 0.022 0.002 PHE A 667 TYR 0.015 0.001 TYR H 504 ARG 0.016 0.001 ARG D 693 *********************** 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 651 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 591 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8304 (t80) cc_final: 0.7732 (t80) REVERT: A 471 LEU cc_start: 0.8703 (tp) cc_final: 0.8337 (tt) REVERT: A 472 LEU cc_start: 0.7711 (mt) cc_final: 0.7460 (mt) REVERT: A 503 THR cc_start: 0.8350 (m) cc_final: 0.8019 (t) REVERT: A 567 SER cc_start: 0.8305 (p) cc_final: 0.7947 (p) REVERT: B 508 LYS cc_start: 0.8038 (tttp) cc_final: 0.7593 (ttmt) REVERT: B 530 MET cc_start: 0.7494 (mmt) cc_final: 0.7283 (mmt) REVERT: B 560 GLN cc_start: 0.8272 (tt0) cc_final: 0.7869 (tt0) REVERT: B 564 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7384 (mm-40) REVERT: B 587 GLN cc_start: 0.8692 (pp30) cc_final: 0.8243 (pp30) REVERT: B 645 MET cc_start: 0.7498 (mmm) cc_final: 0.6945 (mmm) REVERT: C 471 LEU cc_start: 0.8975 (mt) cc_final: 0.8710 (mm) REVERT: C 534 GLN cc_start: 0.7466 (tt0) cc_final: 0.7139 (tt0) REVERT: C 651 LEU cc_start: 0.8614 (mt) cc_final: 0.8266 (mm) REVERT: C 667 PHE cc_start: 0.8694 (t80) cc_final: 0.8444 (t80) REVERT: D 489 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8001 (m) REVERT: D 504 TYR cc_start: 0.7229 (t80) cc_final: 0.7017 (t80) REVERT: D 508 LYS cc_start: 0.8419 (tttp) cc_final: 0.8051 (ttmt) REVERT: D 536 GLN cc_start: 0.7419 (tt0) cc_final: 0.7179 (tt0) REVERT: D 538 MET cc_start: 0.7885 (mmm) cc_final: 0.7512 (mmm) REVERT: D 630 TRP cc_start: 0.7349 (m100) cc_final: 0.7014 (m100) REVERT: D 680 TYR cc_start: 0.8043 (t80) cc_final: 0.7747 (t80) REVERT: E 441 PHE cc_start: 0.8357 (t80) cc_final: 0.7759 (t80) REVERT: E 471 LEU cc_start: 0.8810 (tp) cc_final: 0.8428 (tt) REVERT: E 503 THR cc_start: 0.8338 (m) cc_final: 0.7881 (t) REVERT: E 541 PHE cc_start: 0.8069 (t80) cc_final: 0.7763 (t80) REVERT: E 555 TYR cc_start: 0.8750 (m-10) cc_final: 0.8324 (m-80) REVERT: E 565 LEU cc_start: 0.7615 (tt) cc_final: 0.7401 (tt) REVERT: E 667 PHE cc_start: 0.8764 (t80) cc_final: 0.8485 (t80) REVERT: F 415 ILE cc_start: 0.8522 (mm) cc_final: 0.8058 (tp) REVERT: F 464 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.7234 (ttm-80) REVERT: F 493 PHE cc_start: 0.8382 (m-80) cc_final: 0.8165 (m-10) REVERT: F 508 LYS cc_start: 0.7942 (tttp) cc_final: 0.7465 (ttmt) REVERT: F 530 MET cc_start: 0.7033 (tpp) cc_final: 0.6822 (mmm) REVERT: F 560 GLN cc_start: 0.8178 (tt0) cc_final: 0.7912 (tt0) REVERT: F 564 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7286 (mm-40) REVERT: F 587 GLN cc_start: 0.8662 (pp30) cc_final: 0.8251 (pp30) REVERT: F 591 HIS cc_start: 0.6269 (m-70) cc_final: 0.5847 (m170) REVERT: F 645 MET cc_start: 0.7447 (mmm) cc_final: 0.7147 (mmm) REVERT: F 682 ARG cc_start: 0.6244 (mtt-85) cc_final: 0.5855 (mtt-85) REVERT: G 471 LEU cc_start: 0.8951 (mt) cc_final: 0.8712 (mm) REVERT: G 534 GLN cc_start: 0.7387 (tt0) cc_final: 0.7028 (tt0) REVERT: G 667 PHE cc_start: 0.8639 (t80) cc_final: 0.8379 (t80) REVERT: H 489 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8050 (m) REVERT: H 503 THR cc_start: 0.8559 (t) cc_final: 0.8228 (m) REVERT: H 508 LYS cc_start: 0.8427 (tttp) cc_final: 0.8096 (ttmt) REVERT: H 630 TRP cc_start: 0.7509 (m100) cc_final: 0.7241 (m100) outliers start: 60 outliers final: 48 residues processed: 603 average time/residue: 0.2156 time to fit residues: 200.9928 Evaluate side-chains 640 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 590 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 575 ASN Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 470 SER Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 219 optimal weight: 0.0020 chunk 137 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN B 414 HIS D 644 HIS E 500 ASN E 534 GLN E 664 GLN F 497 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14926 Z= 0.221 Angle : 0.597 9.791 20594 Z= 0.308 Chirality : 0.039 0.144 2546 Planarity : 0.005 0.104 2716 Dihedral : 3.868 18.159 2398 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.33 % Rotamer: Outliers : 7.80 % Allowed : 38.42 % Favored : 53.79 % 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: 0.61 (0.19), residues: 2296 helix: 0.94 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.50 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 630 HIS 0.012 0.001 HIS H 636 PHE 0.034 0.002 PHE D 493 TYR 0.014 0.001 TYR E 426 ARG 0.011 0.001 ARG D 693 *********************** 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 673 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 603 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8316 (t80) cc_final: 0.7720 (t80) REVERT: A 471 LEU cc_start: 0.8669 (tp) cc_final: 0.8324 (tt) REVERT: A 472 LEU cc_start: 0.7798 (mt) cc_final: 0.7538 (mt) REVERT: A 503 THR cc_start: 0.8345 (m) cc_final: 0.7990 (t) REVERT: A 567 SER cc_start: 0.8248 (p) cc_final: 0.7910 (p) REVERT: B 508 LYS cc_start: 0.8089 (tttp) cc_final: 0.7685 (ttmt) REVERT: B 560 GLN cc_start: 0.8327 (tt0) cc_final: 0.7958 (tt0) REVERT: B 564 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7404 (mm-40) REVERT: B 587 GLN cc_start: 0.8719 (pp30) cc_final: 0.8221 (pp30) REVERT: B 591 HIS cc_start: 0.6357 (m-70) cc_final: 0.5854 (m170) REVERT: B 645 MET cc_start: 0.7405 (mmm) cc_final: 0.6912 (mmm) REVERT: C 471 LEU cc_start: 0.9051 (mt) cc_final: 0.8753 (mm) REVERT: C 534 GLN cc_start: 0.7530 (tt0) cc_final: 0.7299 (tt0) REVERT: C 651 LEU cc_start: 0.8586 (mt) cc_final: 0.8322 (mt) REVERT: D 489 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8001 (m) REVERT: D 504 TYR cc_start: 0.7252 (t80) cc_final: 0.7019 (t80) REVERT: D 508 LYS cc_start: 0.8351 (tttp) cc_final: 0.8015 (ttmt) REVERT: D 536 GLN cc_start: 0.7523 (tt0) cc_final: 0.7166 (tt0) REVERT: D 538 MET cc_start: 0.7905 (mmm) cc_final: 0.7455 (mmm) REVERT: D 630 TRP cc_start: 0.7387 (m100) cc_final: 0.7059 (m100) REVERT: D 680 TYR cc_start: 0.8089 (t80) cc_final: 0.7817 (t80) REVERT: E 441 PHE cc_start: 0.8385 (t80) cc_final: 0.7772 (t80) REVERT: E 471 LEU cc_start: 0.8843 (tp) cc_final: 0.8465 (tt) REVERT: E 503 THR cc_start: 0.8370 (m) cc_final: 0.7959 (t) REVERT: E 541 PHE cc_start: 0.8130 (t80) cc_final: 0.7812 (t80) REVERT: E 565 LEU cc_start: 0.7682 (tt) cc_final: 0.7473 (tt) REVERT: E 656 LYS cc_start: 0.7840 (tttt) cc_final: 0.7638 (tttt) REVERT: E 667 PHE cc_start: 0.8782 (t80) cc_final: 0.8477 (t80) REVERT: F 415 ILE cc_start: 0.8550 (mm) cc_final: 0.8222 (tp) REVERT: F 493 PHE cc_start: 0.8337 (m-80) cc_final: 0.8130 (m-10) REVERT: F 508 LYS cc_start: 0.8014 (tttp) cc_final: 0.7571 (ttmt) REVERT: F 564 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7383 (mm-40) REVERT: F 587 GLN cc_start: 0.8696 (pp30) cc_final: 0.8288 (pp30) REVERT: F 591 HIS cc_start: 0.6378 (m-70) cc_final: 0.5872 (m170) REVERT: F 645 MET cc_start: 0.7328 (mmm) cc_final: 0.6973 (mmm) REVERT: F 682 ARG cc_start: 0.6306 (mtt-85) cc_final: 0.5939 (mtt-85) REVERT: G 471 LEU cc_start: 0.9005 (mt) cc_final: 0.8723 (mm) REVERT: G 534 GLN cc_start: 0.7414 (tt0) cc_final: 0.7099 (tt0) REVERT: G 542 TRP cc_start: 0.7780 (m-10) cc_final: 0.7521 (m-10) REVERT: H 489 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8049 (m) REVERT: H 503 THR cc_start: 0.8525 (t) cc_final: 0.8228 (m) REVERT: H 508 LYS cc_start: 0.8426 (tttp) cc_final: 0.8113 (ttmt) REVERT: H 630 TRP cc_start: 0.7524 (m100) cc_final: 0.7250 (m100) outliers start: 70 outliers final: 55 residues processed: 614 average time/residue: 0.2145 time to fit residues: 203.7454 Evaluate side-chains 658 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 601 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 624 ASP Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 414 HIS Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 575 ASN Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 470 SER Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.0030 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS E 500 ASN E 664 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 664 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14926 Z= 0.201 Angle : 0.601 11.065 20594 Z= 0.304 Chirality : 0.039 0.145 2546 Planarity : 0.004 0.086 2716 Dihedral : 3.856 16.994 2398 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.28 % Favored : 94.55 % Rotamer: Outliers : 6.57 % Allowed : 40.31 % Favored : 53.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 2296 helix: 1.11 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.38 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 448 HIS 0.015 0.001 HIS D 644 PHE 0.036 0.002 PHE D 493 TYR 0.014 0.001 TYR E 426 ARG 0.013 0.001 ARG D 693 *********************** 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 663 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 604 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8308 (t80) cc_final: 0.7655 (t80) REVERT: A 471 LEU cc_start: 0.8665 (tp) cc_final: 0.8310 (tt) REVERT: A 472 LEU cc_start: 0.7792 (mt) cc_final: 0.7542 (mt) REVERT: A 503 THR cc_start: 0.8316 (m) cc_final: 0.7980 (t) REVERT: A 567 SER cc_start: 0.8268 (p) cc_final: 0.7935 (p) REVERT: B 508 LYS cc_start: 0.8038 (tttp) cc_final: 0.7651 (ttmt) REVERT: B 560 GLN cc_start: 0.8331 (tt0) cc_final: 0.7982 (tt0) REVERT: B 561 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7858 (ttpp) REVERT: B 564 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7446 (mm-40) REVERT: B 587 GLN cc_start: 0.8718 (pp30) cc_final: 0.8031 (pp30) REVERT: B 591 HIS cc_start: 0.6361 (m-70) cc_final: 0.5734 (m170) REVERT: B 645 MET cc_start: 0.7354 (mmm) cc_final: 0.6894 (mmm) REVERT: B 702 LEU cc_start: 0.8365 (tp) cc_final: 0.8127 (tt) REVERT: C 471 LEU cc_start: 0.9033 (mt) cc_final: 0.8728 (mm) REVERT: C 534 GLN cc_start: 0.7532 (tt0) cc_final: 0.7277 (tt0) REVERT: C 651 LEU cc_start: 0.8566 (mt) cc_final: 0.8342 (mt) REVERT: D 489 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7988 (m) REVERT: D 504 TYR cc_start: 0.7244 (t80) cc_final: 0.7027 (t80) REVERT: D 508 LYS cc_start: 0.8401 (tttp) cc_final: 0.8042 (ttmt) REVERT: D 536 GLN cc_start: 0.7512 (tt0) cc_final: 0.7261 (tt0) REVERT: D 538 MET cc_start: 0.7859 (mmm) cc_final: 0.7427 (mmm) REVERT: D 630 TRP cc_start: 0.7372 (m100) cc_final: 0.7055 (m100) REVERT: D 680 TYR cc_start: 0.8079 (t80) cc_final: 0.7816 (t80) REVERT: E 441 PHE cc_start: 0.8370 (t80) cc_final: 0.7786 (t80) REVERT: E 471 LEU cc_start: 0.8833 (tp) cc_final: 0.8446 (tt) REVERT: E 503 THR cc_start: 0.8354 (m) cc_final: 0.7971 (t) REVERT: E 534 GLN cc_start: 0.7817 (tm130) cc_final: 0.7334 (tm-30) REVERT: E 541 PHE cc_start: 0.8131 (t80) cc_final: 0.7819 (t80) REVERT: E 565 LEU cc_start: 0.7655 (tt) cc_final: 0.7446 (tt) REVERT: E 656 LYS cc_start: 0.7828 (tttt) cc_final: 0.7601 (tttt) REVERT: E 667 PHE cc_start: 0.8798 (t80) cc_final: 0.8392 (t80) REVERT: F 415 ILE cc_start: 0.8521 (mm) cc_final: 0.8250 (tp) REVERT: F 508 LYS cc_start: 0.7992 (tttp) cc_final: 0.7528 (ttmt) REVERT: F 564 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7375 (mm-40) REVERT: F 587 GLN cc_start: 0.8694 (pp30) cc_final: 0.8254 (pp30) REVERT: F 591 HIS cc_start: 0.6377 (m-70) cc_final: 0.5916 (m170) REVERT: F 645 MET cc_start: 0.7292 (mmm) cc_final: 0.6995 (mmm) REVERT: F 682 ARG cc_start: 0.6291 (mtt-85) cc_final: 0.5988 (mtt-85) REVERT: G 471 LEU cc_start: 0.8986 (mt) cc_final: 0.8723 (mm) REVERT: G 534 GLN cc_start: 0.7422 (tt0) cc_final: 0.7108 (tt0) REVERT: G 541 PHE cc_start: 0.8566 (t80) cc_final: 0.8240 (t80) REVERT: G 542 TRP cc_start: 0.7785 (m-10) cc_final: 0.7474 (m-10) REVERT: H 489 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8030 (m) REVERT: H 503 THR cc_start: 0.8529 (t) cc_final: 0.8233 (m) REVERT: H 508 LYS cc_start: 0.8413 (tttp) cc_final: 0.8124 (ttmt) REVERT: H 630 TRP cc_start: 0.7482 (m100) cc_final: 0.7229 (m100) outliers start: 59 outliers final: 51 residues processed: 612 average time/residue: 0.2118 time to fit residues: 200.5479 Evaluate side-chains 654 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 601 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 575 ASN Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 470 SER Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 160 optimal weight: 0.0030 chunk 62 optimal weight: 1.9990 chunk 185 optimal weight: 0.0570 chunk 193 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 0.5708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN D 644 HIS E 500 ASN E 664 GLN ** 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: 0.7663 moved from start: 0.4001 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 : 0.630 11.387 20594 Z= 0.317 Chirality : 0.039 0.151 2546 Planarity : 0.005 0.120 2716 Dihedral : 3.857 16.457 2398 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 6.68 % Allowed : 40.98 % Favored : 52.34 % 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: 1.03 (0.19), residues: 2296 helix: 1.21 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.30 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 448 HIS 0.024 0.001 HIS D 644 PHE 0.036 0.002 PHE D 493 TYR 0.014 0.001 TYR E 426 ARG 0.017 0.001 ARG D 693 *********************** 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 665 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 605 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8291 (t80) cc_final: 0.7707 (t80) REVERT: A 471 LEU cc_start: 0.8665 (tp) cc_final: 0.8322 (tt) REVERT: A 472 LEU cc_start: 0.7839 (mt) cc_final: 0.7617 (mt) REVERT: A 503 THR cc_start: 0.8338 (m) cc_final: 0.7977 (t) REVERT: A 567 SER cc_start: 0.8273 (p) cc_final: 0.7929 (p) REVERT: B 508 LYS cc_start: 0.8046 (tttp) cc_final: 0.7644 (ttmt) REVERT: B 560 GLN cc_start: 0.8340 (tt0) cc_final: 0.7966 (tt0) REVERT: B 561 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7877 (ttpp) REVERT: B 564 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7502 (mm-40) REVERT: B 587 GLN cc_start: 0.8721 (pp30) cc_final: 0.8002 (pp30) REVERT: B 591 HIS cc_start: 0.6400 (m-70) cc_final: 0.5767 (m170) REVERT: B 645 MET cc_start: 0.7248 (mmm) cc_final: 0.6829 (mmm) REVERT: C 471 LEU cc_start: 0.9026 (mt) cc_final: 0.8724 (mt) REVERT: C 534 GLN cc_start: 0.7525 (tt0) cc_final: 0.7316 (tt0) REVERT: C 541 PHE cc_start: 0.8505 (t80) cc_final: 0.8107 (t80) REVERT: C 566 PHE cc_start: 0.7958 (m-10) cc_final: 0.7624 (m-80) REVERT: C 651 LEU cc_start: 0.8561 (mt) cc_final: 0.8347 (mt) REVERT: D 489 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7971 (m) REVERT: D 504 TYR cc_start: 0.7243 (t80) cc_final: 0.7026 (t80) REVERT: D 508 LYS cc_start: 0.8338 (tttp) cc_final: 0.8011 (ttmt) REVERT: D 536 GLN cc_start: 0.7527 (tt0) cc_final: 0.7283 (tt0) REVERT: D 538 MET cc_start: 0.7849 (mmm) cc_final: 0.7425 (mmm) REVERT: D 630 TRP cc_start: 0.7347 (m100) cc_final: 0.6998 (m100) REVERT: D 680 TYR cc_start: 0.8093 (t80) cc_final: 0.7864 (t80) REVERT: E 441 PHE cc_start: 0.8372 (t80) cc_final: 0.7788 (t80) REVERT: E 471 LEU cc_start: 0.8839 (tp) cc_final: 0.8450 (tt) REVERT: E 503 THR cc_start: 0.8399 (m) cc_final: 0.7958 (t) REVERT: E 534 GLN cc_start: 0.7817 (tm130) cc_final: 0.7324 (tm-30) REVERT: E 541 PHE cc_start: 0.8117 (t80) cc_final: 0.7825 (t80) REVERT: E 656 LYS cc_start: 0.7824 (tttt) cc_final: 0.7615 (tttt) REVERT: E 667 PHE cc_start: 0.8798 (t80) cc_final: 0.8408 (t80) REVERT: F 415 ILE cc_start: 0.8510 (mm) cc_final: 0.8256 (tp) REVERT: F 508 LYS cc_start: 0.7948 (tttp) cc_final: 0.7537 (ttmt) REVERT: F 564 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7380 (mm-40) REVERT: F 587 GLN cc_start: 0.8687 (pp30) cc_final: 0.8232 (pp30) REVERT: F 591 HIS cc_start: 0.6400 (m-70) cc_final: 0.5918 (m170) REVERT: F 645 MET cc_start: 0.7256 (mmm) cc_final: 0.6961 (mmm) REVERT: F 680 TYR cc_start: 0.8689 (t80) cc_final: 0.8116 (t80) REVERT: F 682 ARG cc_start: 0.6274 (mtt-85) cc_final: 0.5997 (mtt-85) REVERT: G 471 LEU cc_start: 0.8970 (mt) cc_final: 0.8715 (mm) REVERT: G 534 GLN cc_start: 0.7443 (tt0) cc_final: 0.7118 (tt0) REVERT: G 541 PHE cc_start: 0.8568 (t80) cc_final: 0.8245 (t80) REVERT: H 503 THR cc_start: 0.8514 (t) cc_final: 0.8207 (m) REVERT: H 508 LYS cc_start: 0.8413 (tttp) cc_final: 0.8129 (ttmt) REVERT: H 630 TRP cc_start: 0.7508 (m100) cc_final: 0.7254 (m100) outliers start: 60 outliers final: 54 residues processed: 614 average time/residue: 0.2154 time to fit residues: 204.3335 Evaluate side-chains 660 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 605 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 414 HIS Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 575 ASN Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 470 SER Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.0670 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 0.0570 chunk 150 optimal weight: 0.0010 chunk 227 optimal weight: 0.0270 chunk 209 optimal weight: 0.9990 chunk 180 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 0.0060 chunk 110 optimal weight: 0.5980 chunk 143 optimal weight: 0.3980 overall best weight: 0.0316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 ASN E 664 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14926 Z= 0.161 Angle : 0.633 11.402 20594 Z= 0.306 Chirality : 0.038 0.203 2546 Planarity : 0.004 0.118 2716 Dihedral : 3.706 17.553 2398 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.49 % Favored : 95.33 % Rotamer: Outliers : 4.79 % Allowed : 43.43 % Favored : 51.78 % 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: 1.31 (0.19), residues: 2296 helix: 1.46 (0.13), residues: 1836 sheet: None (None), residues: 0 loop : -1.49 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 448 HIS 0.013 0.001 HIS H 636 PHE 0.035 0.002 PHE H 493 TYR 0.028 0.001 TYR B 680 ARG 0.017 0.001 ARG D 693 ********************** 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 638 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 595 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8214 (t80) cc_final: 0.7648 (t80) REVERT: A 472 LEU cc_start: 0.7771 (mt) cc_final: 0.7568 (mt) REVERT: A 503 THR cc_start: 0.8220 (m) cc_final: 0.7949 (t) REVERT: B 441 PHE cc_start: 0.8518 (t80) cc_final: 0.8258 (t80) REVERT: B 508 LYS cc_start: 0.7899 (tttp) cc_final: 0.7474 (ttmt) REVERT: B 530 MET cc_start: 0.7368 (mmt) cc_final: 0.7005 (mmm) REVERT: B 560 GLN cc_start: 0.8266 (tt0) cc_final: 0.7929 (tt0) REVERT: B 561 LYS cc_start: 0.8105 (ttpp) cc_final: 0.7874 (ttpp) REVERT: B 564 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7376 (mm-40) REVERT: B 587 GLN cc_start: 0.8694 (pp30) cc_final: 0.7986 (pp30) REVERT: B 591 HIS cc_start: 0.6312 (m-70) cc_final: 0.5665 (m170) REVERT: B 608 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7994 (mm-40) REVERT: B 645 MET cc_start: 0.7244 (mmm) cc_final: 0.6840 (mmm) REVERT: C 471 LEU cc_start: 0.8990 (mt) cc_final: 0.8708 (mt) REVERT: C 534 GLN cc_start: 0.7409 (tt0) cc_final: 0.7111 (tt0) REVERT: C 541 PHE cc_start: 0.8470 (t80) cc_final: 0.8106 (t80) REVERT: C 566 PHE cc_start: 0.7850 (m-10) cc_final: 0.7552 (m-80) REVERT: C 651 LEU cc_start: 0.8540 (mt) cc_final: 0.8324 (mt) REVERT: C 667 PHE cc_start: 0.8737 (t80) cc_final: 0.8511 (t80) REVERT: D 489 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7882 (m) REVERT: D 508 LYS cc_start: 0.8276 (tttp) cc_final: 0.7941 (ttmt) REVERT: D 536 GLN cc_start: 0.7486 (tt0) cc_final: 0.7209 (tt0) REVERT: D 538 MET cc_start: 0.7789 (mmm) cc_final: 0.7381 (mmm) REVERT: D 599 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7178 (ttm-80) REVERT: D 630 TRP cc_start: 0.7312 (m100) cc_final: 0.6935 (m100) REVERT: D 680 TYR cc_start: 0.8093 (t80) cc_final: 0.7803 (t80) REVERT: E 441 PHE cc_start: 0.8298 (t80) cc_final: 0.7736 (t80) REVERT: E 471 LEU cc_start: 0.8791 (tp) cc_final: 0.8375 (tt) REVERT: E 503 THR cc_start: 0.8294 (m) cc_final: 0.7907 (t) REVERT: E 541 PHE cc_start: 0.8027 (t80) cc_final: 0.7733 (t80) REVERT: E 667 PHE cc_start: 0.8777 (t80) cc_final: 0.8448 (t80) REVERT: F 415 ILE cc_start: 0.8481 (mm) cc_final: 0.8176 (tp) REVERT: F 508 LYS cc_start: 0.7777 (tttp) cc_final: 0.7404 (ttmt) REVERT: F 564 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7241 (mm-40) REVERT: F 587 GLN cc_start: 0.8652 (pp30) cc_final: 0.8207 (pp30) REVERT: F 591 HIS cc_start: 0.6292 (m-70) cc_final: 0.5805 (m170) REVERT: F 645 MET cc_start: 0.7221 (mmm) cc_final: 0.6859 (mmm) REVERT: F 680 TYR cc_start: 0.8585 (t80) cc_final: 0.7973 (t80) REVERT: F 682 ARG cc_start: 0.6175 (mtt-85) cc_final: 0.5818 (mtt-85) REVERT: G 471 LEU cc_start: 0.8950 (mt) cc_final: 0.8707 (mm) REVERT: G 534 GLN cc_start: 0.7309 (tt0) cc_final: 0.6980 (tt0) REVERT: G 541 PHE cc_start: 0.8501 (t80) cc_final: 0.8224 (t80) REVERT: H 503 THR cc_start: 0.8538 (t) cc_final: 0.8252 (m) REVERT: H 508 LYS cc_start: 0.8402 (tttp) cc_final: 0.8093 (ttmt) REVERT: H 630 TRP cc_start: 0.7418 (m100) cc_final: 0.7138 (m100) outliers start: 43 outliers final: 37 residues processed: 599 average time/residue: 0.2162 time to fit residues: 200.4808 Evaluate side-chains 629 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 591 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 550 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 470 SER Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 159 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN D 689 HIS E 500 ASN ** E 534 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.095209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078414 restraints weight = 67685.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.082355 restraints weight = 32026.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.085022 restraints weight = 18585.111| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 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 = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4214 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= 0.212 Angle : 0.635 10.826 20594 Z= 0.316 Chirality : 0.039 0.190 2546 Planarity : 0.004 0.113 2716 Dihedral : 3.683 16.392 2398 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.80 % Favored : 95.03 % Rotamer: Outliers : 4.34 % Allowed : 43.54 % Favored : 52.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 2296 helix: 1.53 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.15 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 448 HIS 0.012 0.001 HIS H 636 PHE 0.039 0.002 PHE G 441 TYR 0.029 0.001 TYR A 504 ARG 0.016 0.002 ARG D 693 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4039.43 seconds wall clock time: 73 minutes 6.20 seconds (4386.20 seconds total)