Starting phenix.real_space_refine on Wed Mar 4 13:16:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ocd_12804/03_2026/7ocd_12804.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ocd_12804/03_2026/7ocd_12804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ocd_12804/03_2026/7ocd_12804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ocd_12804/03_2026/7ocd_12804.map" model { file = "/net/cci-nas-00/data/ceres_data/7ocd_12804/03_2026/7ocd_12804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ocd_12804/03_2026/7ocd_12804.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 0.002 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 82 5.16 5 C 8982 2.51 5 N 2194 2.21 5 O 2366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13624 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2773 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 381} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 22, 'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2773 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 381} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 22, 'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 203 Chain: "D" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2777 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 21, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 13, 'ARG:plan': 7, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 180 Chain: "I" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1153 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'GLU:plan': 5, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1153 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'GLU:plan': 5, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2777 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 21, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 13, 'ARG:plan': 7, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 180 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'E2Q': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'E2Q': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'E2Q': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'E2Q': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.02, per 1000 atoms: 0.22 Number of scatterers: 13624 At special positions: 0 Unit cell: (129.47, 110.21, 131.61, 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 82 16.00 O 2366 8.00 N 2194 7.00 C 8982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.04 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.35 Conformation dependent library (CDL) restraints added in 528.9 milliseconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3496 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 19 sheets defined 57.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.700A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.655A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.537A pdb=" N LEU A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 623 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.565A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.724A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.675A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.652A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.552A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 removed outlier: 3.511A pdb=" N PHE C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 623 Processing helix chain 'C' and resid 631 through 637 removed outlier: 3.502A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.566A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 709 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.752A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.584A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.518A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.543A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.531A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 768 Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.589A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 41 Processing helix chain 'I' and resid 118 through 127 Processing helix chain 'I' and resid 128 through 150 Processing helix chain 'I' and resid 156 through 184 removed outlier: 3.918A pdb=" N GLY I 160 " --> pdb=" O ASN I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 231 removed outlier: 3.666A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 41 Processing helix chain 'J' and resid 118 through 127 Processing helix chain 'J' and resid 128 through 150 Processing helix chain 'J' and resid 156 through 184 removed outlier: 3.918A pdb=" N GLY J 160 " --> pdb=" O ASN J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 231 removed outlier: 3.666A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.584A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.518A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.543A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.531A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 788 through 819 removed outlier: 3.589A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 440 removed outlier: 5.387A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.673A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 494 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.394A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 700 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 437 through 440 removed outlier: 5.384A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 470 " --> pdb=" O ILE C 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AA7, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AA8, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.692A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 494 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.398A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 700 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 398 through 399 Processing sheet with id=AB2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.653A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.566A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 90 through 91 removed outlier: 3.894A pdb=" N CYS I 90 " --> pdb=" O HIS I 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 90 through 91 removed outlier: 3.894A pdb=" N CYS J 90 " --> pdb=" O HIS J 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 398 through 399 Processing sheet with id=AB8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.653A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.565A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 704 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2439 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: 2.27 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2056 1.31 - 1.43: 3969 1.43 - 1.56: 7773 1.56 - 1.68: 4 1.68 - 1.81: 126 Bond restraints: 13928 Sorted by residual: bond pdb=" C09 E2Q A 901 " pdb=" S11 E2Q A 901 " ideal model delta sigma weight residual 1.799 1.691 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C09 E2Q C 901 " pdb=" S11 E2Q C 901 " ideal model delta sigma weight residual 1.799 1.694 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C09 E2Q D 901 " pdb=" S11 E2Q D 901 " ideal model delta sigma weight residual 1.799 1.699 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C09 E2Q B 901 " pdb=" S11 E2Q B 901 " ideal model delta sigma weight residual 1.799 1.699 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C21 PC1 C 903 " pdb=" O21 PC1 C 903 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 13923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 18506 1.80 - 3.61: 398 3.61 - 5.41: 106 5.41 - 7.21: 12 7.21 - 9.01: 8 Bond angle restraints: 19030 Sorted by residual: angle pdb=" C22 PC1 A 903 " pdb=" C21 PC1 A 903 " pdb=" O21 PC1 A 903 " ideal model delta sigma weight residual 111.12 120.13 -9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" C22 PC1 C 903 " pdb=" C21 PC1 C 903 " pdb=" O21 PC1 C 903 " ideal model delta sigma weight residual 111.12 120.11 -8.99 3.00e+00 1.11e-01 8.97e+00 angle pdb=" C22 PC1 C 902 " pdb=" C21 PC1 C 902 " pdb=" O21 PC1 C 902 " ideal model delta sigma weight residual 111.12 119.96 -8.84 3.00e+00 1.11e-01 8.69e+00 angle pdb=" C22 PC1 A 902 " pdb=" C21 PC1 A 902 " pdb=" O21 PC1 A 902 " ideal model delta sigma weight residual 111.12 119.96 -8.84 3.00e+00 1.11e-01 8.69e+00 angle pdb=" C32 PC1 D 902 " pdb=" C31 PC1 D 902 " pdb=" O31 PC1 D 902 " ideal model delta sigma weight residual 111.44 119.95 -8.51 3.00e+00 1.11e-01 8.05e+00 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 7217 15.93 - 31.85: 564 31.85 - 47.78: 103 47.78 - 63.70: 44 63.70 - 79.63: 4 Dihedral angle restraints: 7932 sinusoidal: 2444 harmonic: 5488 Sorted by residual: dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 161.07 -68.07 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual 93.00 160.30 -67.30 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual 93.00 138.96 -45.96 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 7929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1243 0.027 - 0.055: 619 0.055 - 0.082: 299 0.082 - 0.109: 81 0.109 - 0.137: 28 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CG LEU C 538 " pdb=" CB LEU C 538 " pdb=" CD1 LEU C 538 " pdb=" CD2 LEU C 538 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA VAL D 406 " pdb=" N VAL D 406 " pdb=" C VAL D 406 " pdb=" CB VAL D 406 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 406 " pdb=" N VAL B 406 " pdb=" C VAL B 406 " pdb=" CB VAL B 406 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 2267 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 515 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A 516 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 119 " 0.013 2.00e-02 2.50e+03 8.70e-03 1.51e+00 pdb=" CG TYR I 119 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR I 119 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR I 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR I 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR I 119 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR I 119 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR I 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 119 " -0.013 2.00e-02 2.50e+03 8.66e-03 1.50e+00 pdb=" CG TYR J 119 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR J 119 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR J 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 119 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR J 119 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR J 119 " -0.009 2.00e-02 2.50e+03 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 282 2.69 - 3.24: 14300 3.24 - 3.79: 22018 3.79 - 4.35: 26319 4.35 - 4.90: 45569 Nonbonded interactions: 108488 Sorted by model distance: nonbonded pdb=" N14 E2Q A 901 " pdb=" O16 E2Q A 901 " model vdw 2.132 3.120 nonbonded pdb=" N14 E2Q C 901 " pdb=" O16 E2Q C 901 " model vdw 2.135 3.120 nonbonded pdb=" OD2 ASP C 586 " pdb=" OG SER D 592 " model vdw 2.138 3.040 nonbonded pdb=" N14 E2Q B 901 " pdb=" O16 E2Q B 901 " model vdw 2.140 3.120 nonbonded pdb=" N14 E2Q D 901 " pdb=" O16 E2Q D 901 " model vdw 2.140 3.120 ... (remaining 108483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.008 0.108 13936 Z= 0.335 Angle : 0.710 9.549 19046 Z= 0.353 Chirality : 0.040 0.137 2270 Planarity : 0.003 0.036 2328 Dihedral : 12.732 79.627 4412 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1880 helix: 1.77 (0.16), residues: 1068 sheet: -2.21 (0.44), residues: 146 loop : -1.77 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 467 TYR 0.018 0.001 TYR J 119 PHE 0.011 0.001 PHE C 810 TRP 0.007 0.001 TRP D 767 HIS 0.009 0.003 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00767 (13928) covalent geometry : angle 0.70049 (19030) SS BOND : bond 0.00455 ( 8) SS BOND : angle 4.00727 ( 16) hydrogen bonds : bond 0.12819 ( 834) hydrogen bonds : angle 5.49803 ( 2439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.469 Fit side-chains REVERT: A 701 GLU cc_start: 0.7997 (mp0) cc_final: 0.7683 (mp0) REVERT: C 701 GLU cc_start: 0.8047 (mp0) cc_final: 0.7644 (mp0) REVERT: D 496 MET cc_start: 0.8738 (ttp) cc_final: 0.8535 (ttp) REVERT: D 586 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7479 (ttp80) REVERT: D 709 ASN cc_start: 0.8197 (t0) cc_final: 0.7797 (t0) REVERT: B 496 MET cc_start: 0.8734 (ttp) cc_final: 0.8534 (ttp) REVERT: B 709 ASN cc_start: 0.8160 (t0) cc_final: 0.7748 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1166 time to fit residues: 30.3133 Evaluate side-chains 138 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.083618 restraints weight = 29700.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085729 restraints weight = 19014.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085924 restraints weight = 15470.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.086540 restraints weight = 12940.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086766 restraints weight = 11693.446| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13936 Z= 0.131 Angle : 0.528 8.330 19046 Z= 0.268 Chirality : 0.040 0.140 2270 Planarity : 0.004 0.047 2328 Dihedral : 7.520 57.561 2190 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.95 % Allowed : 8.25 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1880 helix: 2.24 (0.16), residues: 1076 sheet: -2.11 (0.45), residues: 146 loop : -1.32 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 97 TYR 0.011 0.001 TYR C 519 PHE 0.023 0.001 PHE J 32 TRP 0.007 0.001 TRP C 667 HIS 0.002 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00294 (13928) covalent geometry : angle 0.52721 (19030) SS BOND : bond 0.00859 ( 8) SS BOND : angle 1.05798 ( 16) hydrogen bonds : bond 0.03703 ( 834) hydrogen bonds : angle 4.15301 ( 2439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 701 GLU cc_start: 0.8211 (mp0) cc_final: 0.7575 (mp0) REVERT: C 541 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7986 (tpp-160) REVERT: D 496 MET cc_start: 0.8667 (ttp) cc_final: 0.8416 (ttp) REVERT: D 508 GLN cc_start: 0.8410 (mt0) cc_final: 0.8102 (mt0) REVERT: D 586 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.7753 (mmm160) REVERT: D 709 ASN cc_start: 0.8409 (t0) cc_final: 0.8038 (t0) REVERT: B 496 MET cc_start: 0.8666 (ttp) cc_final: 0.8413 (ttp) REVERT: B 508 GLN cc_start: 0.8425 (mt0) cc_final: 0.8207 (mt0) REVERT: B 709 ASN cc_start: 0.8412 (t0) cc_final: 0.8043 (t0) outliers start: 11 outliers final: 9 residues processed: 177 average time/residue: 0.1380 time to fit residues: 34.0764 Evaluate side-chains 150 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 119 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076820 restraints weight = 30235.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079476 restraints weight = 16869.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081126 restraints weight = 12180.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082123 restraints weight = 10160.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082574 restraints weight = 9097.512| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13936 Z= 0.202 Angle : 0.560 8.391 19046 Z= 0.286 Chirality : 0.041 0.135 2270 Planarity : 0.004 0.043 2328 Dihedral : 7.259 59.257 2190 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.15 % Allowed : 13.66 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1880 helix: 2.12 (0.16), residues: 1064 sheet: -2.22 (0.43), residues: 146 loop : -1.25 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 97 TYR 0.009 0.001 TYR C 519 PHE 0.011 0.001 PHE J 32 TRP 0.009 0.001 TRP D 578 HIS 0.002 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00474 (13928) covalent geometry : angle 0.55992 (19030) SS BOND : bond 0.00476 ( 8) SS BOND : angle 0.97125 ( 16) hydrogen bonds : bond 0.04278 ( 834) hydrogen bonds : angle 4.17390 ( 2439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.476 Fit side-chains REVERT: A 541 ARG cc_start: 0.8295 (tpp80) cc_final: 0.8051 (tpp80) REVERT: A 701 GLU cc_start: 0.8340 (mp0) cc_final: 0.7592 (mp0) REVERT: C 541 ARG cc_start: 0.8360 (tpp80) cc_final: 0.7950 (tpp80) REVERT: C 701 GLU cc_start: 0.8333 (mp0) cc_final: 0.7569 (mp0) REVERT: D 586 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.7891 (mmm160) REVERT: B 496 MET cc_start: 0.8958 (ttp) cc_final: 0.8706 (ttp) outliers start: 25 outliers final: 17 residues processed: 169 average time/residue: 0.1307 time to fit residues: 31.5289 Evaluate side-chains 158 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 161 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.103698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.077773 restraints weight = 29991.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080446 restraints weight = 16751.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.082125 restraints weight = 12104.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083111 restraints weight = 10081.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.083323 restraints weight = 9050.603| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13936 Z= 0.145 Angle : 0.515 10.157 19046 Z= 0.259 Chirality : 0.039 0.129 2270 Planarity : 0.004 0.045 2328 Dihedral : 7.125 59.708 2190 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.49 % Allowed : 15.12 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1880 helix: 2.27 (0.16), residues: 1064 sheet: -2.13 (0.44), residues: 140 loop : -1.18 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 97 TYR 0.015 0.001 TYR I 119 PHE 0.020 0.001 PHE J 207 TRP 0.006 0.001 TRP B 766 HIS 0.001 0.000 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00340 (13928) covalent geometry : angle 0.51510 (19030) SS BOND : bond 0.00402 ( 8) SS BOND : angle 0.76511 ( 16) hydrogen bonds : bond 0.03761 ( 834) hydrogen bonds : angle 3.97380 ( 2439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.535 Fit side-chains REVERT: A 701 GLU cc_start: 0.8290 (mp0) cc_final: 0.7517 (mp0) REVERT: C 701 GLU cc_start: 0.8296 (mp0) cc_final: 0.7579 (mp0) REVERT: D 586 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7933 (mmm160) REVERT: J 140 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8247 (tt) outliers start: 29 outliers final: 18 residues processed: 172 average time/residue: 0.1219 time to fit residues: 30.2373 Evaluate side-chains 167 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 93 optimal weight: 0.0030 chunk 11 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 1 optimal weight: 0.0170 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN D 508 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.073588 restraints weight = 31232.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075670 restraints weight = 19231.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.076666 restraints weight = 14665.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077674 restraints weight = 12724.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.078041 restraints weight = 11509.649| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13936 Z= 0.241 Angle : 0.587 10.854 19046 Z= 0.299 Chirality : 0.041 0.143 2270 Planarity : 0.004 0.093 2328 Dihedral : 7.472 59.878 2190 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.35 % Allowed : 16.58 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1880 helix: 1.99 (0.16), residues: 1064 sheet: -2.16 (0.44), residues: 140 loop : -1.14 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 97 TYR 0.014 0.001 TYR C 417 PHE 0.014 0.002 PHE J 207 TRP 0.010 0.001 TRP B 578 HIS 0.002 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00571 (13928) covalent geometry : angle 0.58707 (19030) SS BOND : bond 0.00438 ( 8) SS BOND : angle 0.93011 ( 16) hydrogen bonds : bond 0.04496 ( 834) hydrogen bonds : angle 4.19703 ( 2439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.316 Fit side-chains REVERT: A 701 GLU cc_start: 0.8279 (mp0) cc_final: 0.7642 (mp0) REVERT: C 541 ARG cc_start: 0.8417 (tpp-160) cc_final: 0.7161 (tpp-160) REVERT: C 701 GLU cc_start: 0.8267 (mp0) cc_final: 0.7679 (mp0) REVERT: D 400 ILE cc_start: 0.7399 (mp) cc_final: 0.7150 (tt) REVERT: D 586 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7996 (mmm160) REVERT: B 400 ILE cc_start: 0.7394 (mp) cc_final: 0.7158 (tt) outliers start: 39 outliers final: 27 residues processed: 177 average time/residue: 0.1106 time to fit residues: 28.3728 Evaluate side-chains 167 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 144 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 166 optimal weight: 0.0770 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076706 restraints weight = 30863.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.078862 restraints weight = 18882.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080079 restraints weight = 14332.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.080961 restraints weight = 12300.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081421 restraints weight = 11157.505| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13936 Z= 0.121 Angle : 0.514 10.666 19046 Z= 0.257 Chirality : 0.039 0.151 2270 Planarity : 0.004 0.051 2328 Dihedral : 7.336 59.986 2190 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.58 % Allowed : 18.04 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1880 helix: 2.30 (0.17), residues: 1066 sheet: -2.14 (0.44), residues: 140 loop : -1.01 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 97 TYR 0.011 0.001 TYR A 417 PHE 0.016 0.001 PHE I 32 TRP 0.008 0.001 TRP D 767 HIS 0.002 0.000 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00278 (13928) covalent geometry : angle 0.51365 (19030) SS BOND : bond 0.00338 ( 8) SS BOND : angle 0.64583 ( 16) hydrogen bonds : bond 0.03624 ( 834) hydrogen bonds : angle 3.90394 ( 2439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.504 Fit side-chains REVERT: A 701 GLU cc_start: 0.8201 (mp0) cc_final: 0.7524 (mp0) REVERT: A 803 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: C 701 GLU cc_start: 0.8203 (mp0) cc_final: 0.7638 (mp0) REVERT: D 408 MET cc_start: 0.7635 (mmt) cc_final: 0.7425 (mmm) REVERT: D 586 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.7890 (mmm160) REVERT: J 144 CYS cc_start: 0.8263 (t) cc_final: 0.8050 (t) REVERT: B 408 MET cc_start: 0.7658 (mmt) cc_final: 0.7409 (mmm) outliers start: 30 outliers final: 17 residues processed: 183 average time/residue: 0.1243 time to fit residues: 32.6522 Evaluate side-chains 172 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 181 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.099864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.075507 restraints weight = 30916.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077622 restraints weight = 18921.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.078959 restraints weight = 14346.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079613 restraints weight = 12253.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080196 restraints weight = 11230.808| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13936 Z= 0.165 Angle : 0.552 11.172 19046 Z= 0.272 Chirality : 0.039 0.148 2270 Planarity : 0.004 0.051 2328 Dihedral : 7.362 59.879 2190 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.18 % Allowed : 17.78 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1880 helix: 2.26 (0.16), residues: 1064 sheet: -2.17 (0.44), residues: 140 loop : -1.07 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 97 TYR 0.015 0.001 TYR J 119 PHE 0.017 0.001 PHE I 32 TRP 0.009 0.001 TRP D 767 HIS 0.001 0.000 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00390 (13928) covalent geometry : angle 0.55175 (19030) SS BOND : bond 0.00356 ( 8) SS BOND : angle 0.68293 ( 16) hydrogen bonds : bond 0.03878 ( 834) hydrogen bonds : angle 3.93970 ( 2439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.499 Fit side-chains REVERT: A 581 MET cc_start: 0.8597 (tpp) cc_final: 0.7997 (mmm) REVERT: A 701 GLU cc_start: 0.8238 (mp0) cc_final: 0.7500 (mp0) REVERT: A 803 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7658 (mtm) REVERT: C 701 GLU cc_start: 0.8237 (mp0) cc_final: 0.7610 (mp0) REVERT: D 400 ILE cc_start: 0.7138 (mp) cc_final: 0.6751 (tt) REVERT: D 586 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7901 (mmm160) REVERT: B 400 ILE cc_start: 0.7134 (mp) cc_final: 0.6749 (tt) outliers start: 37 outliers final: 25 residues processed: 179 average time/residue: 0.1214 time to fit residues: 31.1240 Evaluate side-chains 176 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 0.0370 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 0.0050 overall best weight: 0.5872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.101890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079454 restraints weight = 30465.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080407 restraints weight = 19068.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080444 restraints weight = 15464.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.080651 restraints weight = 15733.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081273 restraints weight = 14158.015| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13936 Z= 0.108 Angle : 0.513 11.452 19046 Z= 0.251 Chirality : 0.038 0.130 2270 Planarity : 0.004 0.055 2328 Dihedral : 7.230 59.999 2190 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.06 % Allowed : 18.81 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1880 helix: 2.43 (0.17), residues: 1068 sheet: -2.16 (0.44), residues: 140 loop : -1.00 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 97 TYR 0.010 0.001 TYR A 417 PHE 0.022 0.001 PHE A 810 TRP 0.007 0.001 TRP J 203 HIS 0.002 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00244 (13928) covalent geometry : angle 0.51267 (19030) SS BOND : bond 0.00315 ( 8) SS BOND : angle 0.58969 ( 16) hydrogen bonds : bond 0.03352 ( 834) hydrogen bonds : angle 3.78560 ( 2439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.511 Fit side-chains REVERT: A 581 MET cc_start: 0.8557 (tpp) cc_final: 0.7859 (mmm) REVERT: A 701 GLU cc_start: 0.8174 (mp0) cc_final: 0.7585 (mp0) REVERT: A 803 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: C 541 ARG cc_start: 0.8423 (tpp-160) cc_final: 0.7013 (tpp-160) REVERT: C 701 GLU cc_start: 0.8198 (mp0) cc_final: 0.7584 (mp0) REVERT: D 400 ILE cc_start: 0.7013 (mp) cc_final: 0.6585 (tt) REVERT: D 586 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.7892 (mmm160) REVERT: B 400 ILE cc_start: 0.6992 (mp) cc_final: 0.6771 (mp) outliers start: 24 outliers final: 18 residues processed: 177 average time/residue: 0.1230 time to fit residues: 31.1852 Evaluate side-chains 166 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075420 restraints weight = 31005.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.077539 restraints weight = 19091.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078691 restraints weight = 14570.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079561 restraints weight = 12514.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079965 restraints weight = 11372.819| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13936 Z= 0.181 Angle : 0.559 12.052 19046 Z= 0.276 Chirality : 0.039 0.145 2270 Planarity : 0.004 0.055 2328 Dihedral : 7.283 59.920 2190 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.15 % Allowed : 18.99 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1880 helix: 2.28 (0.16), residues: 1066 sheet: -2.20 (0.44), residues: 140 loop : -0.94 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 97 TYR 0.012 0.001 TYR C 417 PHE 0.019 0.001 PHE A 810 TRP 0.011 0.001 TRP B 767 HIS 0.001 0.000 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00430 (13928) covalent geometry : angle 0.55859 (19030) SS BOND : bond 0.00291 ( 8) SS BOND : angle 0.75591 ( 16) hydrogen bonds : bond 0.03974 ( 834) hydrogen bonds : angle 3.91863 ( 2439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.483 Fit side-chains REVERT: A 581 MET cc_start: 0.8672 (tpp) cc_final: 0.7934 (mmm) REVERT: A 701 GLU cc_start: 0.8227 (mp0) cc_final: 0.7647 (mp0) REVERT: A 803 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7659 (mtm) REVERT: C 541 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.6928 (tpp-160) REVERT: C 701 GLU cc_start: 0.8229 (mp0) cc_final: 0.7608 (mp0) REVERT: C 704 MET cc_start: 0.8536 (tpp) cc_final: 0.8313 (tpp) REVERT: D 400 ILE cc_start: 0.6966 (mp) cc_final: 0.6672 (tt) REVERT: D 496 MET cc_start: 0.8875 (ttp) cc_final: 0.8574 (ttp) REVERT: D 586 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7871 (mmm160) REVERT: D 685 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8476 (m) REVERT: B 400 ILE cc_start: 0.6963 (mp) cc_final: 0.6673 (tt) REVERT: B 496 MET cc_start: 0.8862 (ttp) cc_final: 0.8547 (ttp) outliers start: 25 outliers final: 19 residues processed: 167 average time/residue: 0.1318 time to fit residues: 30.9495 Evaluate side-chains 168 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 161 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN D 508 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.079182 restraints weight = 30734.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081076 restraints weight = 21866.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081269 restraints weight = 16547.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.081573 restraints weight = 14908.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081739 restraints weight = 13976.682| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13936 Z= 0.140 Angle : 0.539 12.546 19046 Z= 0.264 Chirality : 0.039 0.141 2270 Planarity : 0.004 0.065 2328 Dihedral : 7.189 59.743 2190 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.98 % Allowed : 19.33 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1880 helix: 2.36 (0.17), residues: 1066 sheet: -2.16 (0.44), residues: 140 loop : -0.86 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 97 TYR 0.011 0.001 TYR A 417 PHE 0.019 0.001 PHE A 810 TRP 0.009 0.001 TRP B 767 HIS 0.001 0.000 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00330 (13928) covalent geometry : angle 0.53861 (19030) SS BOND : bond 0.00312 ( 8) SS BOND : angle 0.65708 ( 16) hydrogen bonds : bond 0.03667 ( 834) hydrogen bonds : angle 3.82944 ( 2439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.491 Fit side-chains REVERT: A 581 MET cc_start: 0.8650 (tpp) cc_final: 0.7895 (mmm) REVERT: A 701 GLU cc_start: 0.8172 (mp0) cc_final: 0.7701 (mp0) REVERT: A 803 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7689 (mtm) REVERT: C 541 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8162 (tpp80) REVERT: C 701 GLU cc_start: 0.8215 (mp0) cc_final: 0.7704 (mp0) REVERT: D 400 ILE cc_start: 0.6956 (mp) cc_final: 0.6677 (tt) REVERT: D 586 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7855 (mmm160) REVERT: D 685 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8418 (m) REVERT: B 400 ILE cc_start: 0.6971 (mp) cc_final: 0.6640 (tt) outliers start: 23 outliers final: 20 residues processed: 166 average time/residue: 0.1303 time to fit residues: 30.4450 Evaluate side-chains 168 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 27 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075727 restraints weight = 31050.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077839 restraints weight = 19098.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079182 restraints weight = 14470.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079924 restraints weight = 12334.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.080267 restraints weight = 11309.485| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13936 Z= 0.159 Angle : 0.548 13.307 19046 Z= 0.269 Chirality : 0.039 0.153 2270 Planarity : 0.004 0.059 2328 Dihedral : 7.226 59.904 2190 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.23 % Allowed : 19.16 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1880 helix: 2.34 (0.16), residues: 1066 sheet: -2.20 (0.44), residues: 140 loop : -0.86 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 97 TYR 0.012 0.001 TYR C 417 PHE 0.018 0.001 PHE A 810 TRP 0.011 0.001 TRP B 767 HIS 0.001 0.000 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00376 (13928) covalent geometry : angle 0.54792 (19030) SS BOND : bond 0.00324 ( 8) SS BOND : angle 0.65249 ( 16) hydrogen bonds : bond 0.03854 ( 834) hydrogen bonds : angle 3.86673 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.10 seconds wall clock time: 38 minutes 34.26 seconds (2314.26 seconds total)