Starting phenix.real_space_refine on Fri Jun 5 04:58:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zku_74385/06_2026/9zku_74385.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zku_74385/06_2026/9zku_74385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zku_74385/06_2026/9zku_74385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zku_74385/06_2026/9zku_74385.map" model { file = "/net/cci-nas-00/data/ceres_data/9zku_74385/06_2026/9zku_74385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zku_74385/06_2026/9zku_74385.cif" } resolution = 3.75 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= 0.016 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 114 5.16 5 C 11500 2.51 5 N 2787 2.21 5 O 3084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17486 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2949 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2944 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2962 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2942 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "E" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1090 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1383 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1314 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1361 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Chain: "M" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 283 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 98 Unusual residues: {'OLC': 2, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.50, per 1000 atoms: 0.26 Number of scatterers: 17486 At special positions: 0 Unit cell: (127.05, 109.725, 133.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 1 15.00 O 3084 8.00 N 2787 7.00 C 11500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " 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 F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.06 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 91 " distance=2.02 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " 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: 1.69 Conformation dependent library (CDL) restraints added in 863.7 milliseconds 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4236 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 22 sheets defined 61.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.552A pdb=" N VAL A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 485 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 removed outlier: 3.836A pdb=" N LEU A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.678A pdb=" N LYS A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 773 through 778 removed outlier: 4.432A pdb=" N ASP A 778 " --> pdb=" O SER A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 788 through 813 removed outlier: 4.071A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.700A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 4.512A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 547 removed outlier: 4.071A pdb=" N SER B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) 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 643 removed outlier: 3.586A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 744 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 774 through 780 removed outlier: 4.164A pdb=" N ASP B 779 " --> pdb=" O GLY B 776 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 780 " --> pdb=" O GLY B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 819 Processing helix 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 Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 591 through 626 Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 712 Processing helix chain 'C' and resid 739 through 752 Processing helix chain 'C' and resid 753 through 765 Processing helix chain 'C' and resid 789 through 813 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.526A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 462 through 469 removed outlier: 4.106A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 489 removed outlier: 4.295A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 519 removed outlier: 4.421A pdb=" N PHE D 517 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.549A pdb=" N SER D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.732A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 4.581A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.686A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 743 through 756 removed outlier: 3.795A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 792 through 819 Processing helix chain 'E' and resid 4 through 38 Processing helix chain 'E' and resid 56 through 85 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 87 through 107 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 127 through 159 Processing helix chain 'F' and resid 5 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.515A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.701A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 210 removed outlier: 3.898A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 41 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 128 through 151 removed outlier: 4.039A pdb=" N ILE G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 184 removed outlier: 4.173A pdb=" N LEU G 159 " --> pdb=" O ARG G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 234 removed outlier: 4.084A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 41 removed outlier: 3.504A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 128 through 151 Processing helix chain 'H' and resid 155 through 184 Processing helix chain 'H' and resid 202 through 235 removed outlier: 3.755A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 298 removed outlier: 4.031A pdb=" N GLN M 298 " --> pdb=" O ILE M 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 394 through 395 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 471 through 476 removed outlier: 5.847A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS A 726 " --> pdb=" O MET A 492 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET A 492 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR A 728 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE A 730 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.894A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 698 " --> pdb=" O MET A 499 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 442 through 443 removed outlier: 5.711A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 451 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.541A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 391 through 395 Processing sheet with id=AB3, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB4, first strand: chain 'C' and resid 471 through 472 removed outlier: 3.570A pdb=" N ASP C 486 " --> pdb=" O THR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.645A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 697 through 701 removed outlier: 3.672A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 645 through 646 removed outlier: 6.491A pdb=" N THR C 645 " --> pdb=" O VAL C 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 397 through 398 removed outlier: 5.440A pdb=" N THR D 398 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.311A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 66 through 68 Processing sheet with id=AC3, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AC4, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.661A pdb=" N HIS H 83 " --> pdb=" O CYS H 90 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER H 200 " --> pdb=" O TYR H 46 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 5312 1.34 - 1.48: 4861 1.48 - 1.63: 7508 1.63 - 1.77: 2 1.77 - 1.91: 172 Bond restraints: 17855 Sorted by residual: bond pdb=" CB CYS F 67 " pdb=" SG CYS F 67 " ideal model delta sigma weight residual 1.808 1.909 -0.101 3.30e-02 9.18e+02 9.30e+00 bond pdb=" CB MET E 153 " pdb=" CG MET E 153 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.57e+00 bond pdb=" O12 POV B1003 " pdb=" P POV B1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" C11 POV B1003 " pdb=" O12 POV B1003 " ideal model delta sigma weight residual 1.408 1.455 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 POV B1003 " pdb=" O11 POV B1003 " ideal model delta sigma weight residual 1.410 1.454 -0.044 2.00e-02 2.50e+03 4.73e+00 ... (remaining 17850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 23850 3.06 - 6.12: 271 6.12 - 9.18: 49 9.18 - 12.24: 15 12.24 - 15.30: 1 Bond angle restraints: 24186 Sorted by residual: angle pdb=" CB MET E 153 " pdb=" CG MET E 153 " pdb=" SD MET E 153 " ideal model delta sigma weight residual 112.70 97.40 15.30 3.00e+00 1.11e-01 2.60e+01 angle pdb=" CA LYS E 66 " pdb=" CB LYS E 66 " pdb=" CG LYS E 66 " ideal model delta sigma weight residual 114.10 124.01 -9.91 2.00e+00 2.50e-01 2.45e+01 angle pdb=" CA ARG A 467 " pdb=" CB ARG A 467 " pdb=" CG ARG A 467 " ideal model delta sigma weight residual 114.10 123.45 -9.35 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CA CYS F 77 " pdb=" CB CYS F 77 " pdb=" SG CYS F 77 " ideal model delta sigma weight residual 114.40 125.02 -10.62 2.30e+00 1.89e-01 2.13e+01 angle pdb=" CA MET A 704 " pdb=" CB MET A 704 " pdb=" CG MET A 704 " ideal model delta sigma weight residual 114.10 121.92 -7.82 2.00e+00 2.50e-01 1.53e+01 ... (remaining 24181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 10208 34.71 - 69.41: 138 69.41 - 104.12: 13 104.12 - 138.82: 6 138.82 - 173.53: 1 Dihedral angle restraints: 10366 sinusoidal: 3728 harmonic: 6638 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 93.00 177.00 -84.00 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS F 67 " pdb=" SG CYS F 67 " pdb=" SG CYS F 77 " pdb=" CB CYS F 77 " ideal model delta sinusoidal sigma weight residual 93.00 28.83 64.17 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS H 52 " pdb=" SG CYS H 52 " pdb=" SG CYS H 91 " pdb=" CB CYS H 91 " ideal model delta sinusoidal sigma weight residual 93.00 50.55 42.45 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 10363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2422 0.070 - 0.140: 346 0.140 - 0.210: 29 0.210 - 0.279: 5 0.279 - 0.349: 3 Chirality restraints: 2805 Sorted by residual: chirality pdb=" CG LEU H 137 " pdb=" CB LEU H 137 " pdb=" CD1 LEU H 137 " pdb=" CD2 LEU H 137 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB VAL E 120 " pdb=" CA VAL E 120 " pdb=" CG1 VAL E 120 " pdb=" CG2 VAL E 120 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CG LEU F 63 " pdb=" CB LEU F 63 " pdb=" CD1 LEU F 63 " pdb=" CD2 LEU F 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2802 not shown) Planarity restraints: 2959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 763 " 0.030 2.00e-02 2.50e+03 2.53e-02 1.61e+01 pdb=" CG TRP A 763 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 763 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 763 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 763 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 763 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 763 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 763 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 763 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 763 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 643 " -0.019 2.00e-02 2.50e+03 2.13e-02 9.08e+00 pdb=" CG TYR C 643 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 643 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 643 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 643 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 643 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR C 643 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 643 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 531 " 0.017 2.00e-02 2.50e+03 1.91e-02 6.37e+00 pdb=" CG PHE B 531 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 531 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 531 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 531 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 531 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 531 " -0.001 2.00e-02 2.50e+03 ... (remaining 2956 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3450 2.77 - 3.30: 17719 3.30 - 3.84: 29791 3.84 - 4.37: 32830 4.37 - 4.90: 56129 Nonbonded interactions: 139919 Sorted by model distance: nonbonded pdb=" O TRP A 456 " pdb=" OH TYR A 465 " model vdw 2.239 3.040 nonbonded pdb=" O LEU C 635 " pdb=" OH TYR C 643 " model vdw 2.248 3.040 nonbonded pdb=" O TYR E 155 " pdb=" OG SER E 159 " model vdw 2.264 3.040 nonbonded pdb=" O LEU E 16 " pdb=" OG SER E 19 " model vdw 2.280 3.040 nonbonded pdb=" O PRO D 520 " pdb=" ND2 ASN D 619 " model vdw 2.284 3.120 ... (remaining 139914 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 461 or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 through 46 \ 6 or (resid 468 through 469 and (name N or name CA or name C or name O or name C \ B )) or resid 471 or resid 473 through 481 or (resid 482 through 483 and (name N \ or name CA or name C or name O or name CB )) or resid 484 through 543 or (resid \ 565 and (name N or name CA or name C or name O or name CB )) or resid 566 throu \ gh 581 or resid 583 through 629 or (resid 630 and (name N or name CA or name C o \ r name O or name CB )) or resid 631 through 635 or (resid 637 through 640 and (n \ ame N or name CA or name C or name O or name CB )) or resid 641 through 646 or r \ esid 649 or (resid 650 and (name N or name CA or name C or name O or name CB )) \ or resid 651 or (resid 652 through 653 and (name N or name CA or name C or name \ O or name CB )) or resid 654 through 663 or resid 665 through 669 or (resid 670 \ and (name N or name CA or name C or name O or name CB )) or resid 672 through 67 \ 5 or (resid 676 and (name N or name CA or name C or name O or name CB )) or resi \ d 677 through 682 or resid 684 through 685 or resid 688 through 689 or (resid 69 \ 0 through 693 and (name N or name CA or name C or name O or name CB )) or resid \ 694 through 733 or (resid 734 and (name N or name CA or name C or name O or name \ CB )) or resid 735 through 736 or resid 738 or (resid 739 and (name N or name C \ A or name C or name O or name CB )) or resid 742 through 749 or resid 751 throug \ h 753 or resid 755 through 759 or resid 761 through 771 or resid 776 through 777 \ or resid 779 through 795 or resid 797 through 811 or (resid 812 through 813 and \ (name N or name CA or name C or name O or name CB )) or (resid 1002 and (name C \ 1 or name C10 or name C11 or name C12 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name C9 or name O19 or name O20)))) selection = (chain 'B' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through 4 \ 54 or (resid 456 through 458 and (name N or name CA or name C or name O or name \ CB )) or resid 460 through 462 or (resid 463 and (name N or name CA or name C or \ name O or name CB )) or resid 464 through 470 or resid 472 through 473 or resid \ 475 or resid 477 through 486 or (resid 487 and (name N or name CA or name C or \ name O or name CB )) or resid 488 through 507 or (resid 508 through 509 and (nam \ e N or name CA or name C or name O or name CB )) or resid 510 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 585 or \ resid 587 through 639 or resid 641 through 650 or resid 653 through 659 or (res \ id 660 through 661 and (name N or name CA or name C or name O or name CB )) or r \ esid 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) \ or resid 664 through 667 or resid 669 through 674 or resid 676 through 684 or (r \ esid 685 and (name N or name CA or name C or name O or name CB )) or resid 686 o \ r (resid 688 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 89 or (resid 692 and (name N or name CA or name C or name O or name CB )) or res \ id 693 through 695 or (resid 696 through 697 and (name N or name CA or name C or \ name O or name CB )) or resid 698 through 714 or (resid 715 through 716 and (na \ me N or name CA or name C or name O or name CB )) or resid 717 through 740 or re \ sid 742 or (resid 743 and (name N or name CA or name C or name O or name CB )) o \ r resid 746 through 753 or resid 755 through 757 or resid 759 through 763 or res \ id 765 through 768 or (resid 769 through 770 and (name N or name CA or name C or \ name O or name CB )) or resid 771 through 775 or resid 780 through 781 or (resi \ d 783 through 784 and (name N or name CA or name C or name O or name CB )) or re \ sid 785 through 799 or resid 801 through 817 or resid 1004)) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 458 or (resid 459 \ and (name N or name CA or name C or name O or name CB )) or resid 460 through 46 \ 1 or (resid 462 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 481 or (resid 482 through \ 483 and (name N or name CA or name C or name O or name CB )) or resid 484 throu \ gh 543 or (resid 565 and (name N or name CA or name C or name O or name CB )) or \ resid 566 through 581 or resid 583 through 629 or (resid 630 and (name N or nam \ e CA or name C or name O or name CB )) or resid 631 through 635 or (resid 637 th \ rough 640 and (name N or name CA or name C or name O or name CB )) or resid 641 \ through 646 or resid 649 or (resid 650 and (name N or name CA or name C or name \ O or name CB )) or resid 651 or (resid 652 through 653 and (name N or name CA or \ name C or name O or name CB )) or resid 654 through 663 or resid 665 through 66 \ 9 or (resid 670 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 675 or (resid 676 and (name N or name CA or name C or name O or na \ me CB )) or resid 677 through 682 or resid 684 through 685 or resid 688 through \ 689 or (resid 690 through 693 and (name N or name CA or name C or name O or name \ CB )) or resid 694 through 733 or (resid 734 and (name N or name CA or name C o \ r name O or name CB )) or resid 735 through 736 or resid 738 or (resid 739 and ( \ name N or name CA or name C or name O or name CB )) or resid 742 through 749 or \ resid 751 through 753 or resid 755 through 759 or resid 761 through 765 or (resi \ d 766 and (name N or name CA or name C or name O or name CB )) or resid 767 thro \ ugh 771 or resid 776 through 777 or resid 779 through 795 or resid 797 through 8 \ 11 or (resid 812 through 813 and (name N or name CA or name C or name O or name \ CB )) or (resid 1002 and (name C1 or name C10 or name C11 or name C12 or name C2 \ or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or \ name O19 or name O20)))) selection = (chain 'D' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through 4 \ 54 or (resid 456 through 458 and (name N or name CA or name C or name O or name \ CB )) or resid 460 through 462 or (resid 463 and (name N or name CA or name C or \ name O or name CB )) or resid 464 through 470 or resid 472 through 473 or resid \ 475 or resid 477 through 486 or (resid 487 and (name N or name CA or name C or \ name O or name CB )) or resid 488 through 507 or (resid 508 through 509 and (nam \ e N or name CA or name C or name O or name CB )) or resid 510 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 585 or \ resid 587 through 639 or resid 641 through 650 or resid 653 through 659 or (res \ id 660 through 661 and (name N or name CA or name C or name O or name CB )) or r \ esid 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) \ or resid 664 through 667 or resid 669 through 674 or resid 676 through 684 or (r \ esid 685 and (name N or name CA or name C or name O or name CB )) or resid 686 o \ r (resid 688 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 89 or (resid 692 and (name N or name CA or name C or name O or name CB )) or res \ id 693 through 695 or (resid 696 through 697 and (name N or name CA or name C or \ name O or name CB )) or resid 698 through 714 or (resid 715 through 716 and (na \ me N or name CA or name C or name O or name CB )) or resid 717 through 740 or re \ sid 742 through 743 or resid 746 through 753 or resid 755 through 757 or resid 7 \ 59 through 763 or resid 765 through 768 or (resid 769 through 770 and (name N or \ name CA or name C or name O or name CB )) or resid 771 through 775 or resid 780 \ through 781 or (resid 783 through 784 and (name N or name CA or name C or name \ O or name CB )) or resid 785 through 799 or resid 801 through 817 or (resid 1003 \ and (name C1 or name C10 or name C11 or name C12 or name C2 or name C3 or name \ C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O19 or name O2 \ 0)))) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 15 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 107 or (resid 108 and ( \ name N or name CA or name C or name O or name CB )) or resid 115 through 117 or \ (resid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ through 149 or (resid 150 through 155 and (name N or name CA or name C or name \ O or name CB )) or resid 156 through 185 or resid 197 through 235)) } 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.150 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.005 0.101 17865 Z= 0.213 Angle : 0.880 15.296 24206 Z= 0.438 Chirality : 0.050 0.349 2805 Planarity : 0.005 0.062 2959 Dihedral : 13.664 173.531 6100 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.66 (0.16), residues: 2269 helix: 0.56 (0.13), residues: 1371 sheet: -1.99 (0.45), residues: 110 loop : -1.96 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 590 TYR 0.050 0.002 TYR C 643 PHE 0.044 0.002 PHE B 531 TRP 0.068 0.002 TRP A 763 HIS 0.010 0.001 HIS H 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (17855) covalent geometry : angle 0.87463 / 0.44 (24186) SS BOND : bond 0.01040 / 0.64 ( 10) SS BOND : angle 3.36315 / 1.92 ( 20) hydrogen bonds : bond 0.12809 / 8.42 ( 1140) hydrogen bonds : angle 5.72402 / 4.02 ( 3330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7910 (tp30) REVERT: A 479 LEU cc_start: 0.9301 (tp) cc_final: 0.9084 (pt) REVERT: A 499 MET cc_start: 0.8405 (ppp) cc_final: 0.7943 (ppp) REVERT: A 623 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8655 (mm-30) REVERT: B 427 ASP cc_start: 0.8764 (m-30) cc_final: 0.8550 (m-30) REVERT: B 490 ASP cc_start: 0.7282 (t0) cc_final: 0.6448 (t0) REVERT: B 523 TYR cc_start: 0.8162 (t80) cc_final: 0.7944 (t80) REVERT: B 688 GLU cc_start: 0.8864 (tt0) cc_final: 0.8383 (tt0) REVERT: B 702 TYR cc_start: 0.8268 (t80) cc_final: 0.8067 (t80) REVERT: B 769 ASP cc_start: 0.9125 (m-30) cc_final: 0.8647 (m-30) REVERT: C 456 TRP cc_start: 0.7930 (m100) cc_final: 0.7650 (m100) REVERT: C 485 ILE cc_start: 0.8334 (tp) cc_final: 0.7914 (tp) REVERT: C 499 MET cc_start: 0.8851 (tmm) cc_final: 0.8104 (tmm) REVERT: C 717 MET cc_start: 0.8691 (ttp) cc_final: 0.8464 (ttp) REVERT: D 408 MET cc_start: 0.5754 (tpt) cc_final: 0.5284 (ttt) REVERT: D 599 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7811 (mtt90) REVERT: D 629 MET cc_start: 0.7789 (mtp) cc_final: 0.6902 (ptm) REVERT: E 63 LEU cc_start: 0.8947 (pp) cc_final: 0.8685 (mm) REVERT: E 82 PHE cc_start: 0.8785 (m-10) cc_final: 0.8029 (m-80) REVERT: E 84 CYS cc_start: 0.9016 (m) cc_final: 0.8566 (m) REVERT: E 95 ILE cc_start: 0.9156 (tp) cc_final: 0.8469 (tp) REVERT: E 133 LYS cc_start: 0.7858 (pttm) cc_final: 0.6894 (pttt) REVERT: F 32 TYR cc_start: 0.5302 (m-10) cc_final: 0.4789 (m-10) REVERT: F 58 MET cc_start: 0.6138 (tpt) cc_final: 0.5165 (mtt) REVERT: F 192 MET cc_start: 0.7844 (mmp) cc_final: 0.7548 (mmm) REVERT: G 177 ILE cc_start: 0.8801 (pt) cc_final: 0.8456 (mt) REVERT: G 199 TYR cc_start: 0.7510 (t80) cc_final: 0.7214 (t80) REVERT: H 39 ILE cc_start: 0.9026 (pt) cc_final: 0.8814 (pt) REVERT: H 105 HIS cc_start: 0.7345 (m-70) cc_final: 0.7144 (m170) REVERT: H 118 GLU cc_start: 0.8574 (pp20) cc_final: 0.8309 (pp20) REVERT: H 154 LYS cc_start: 0.7261 (mttt) cc_final: 0.6589 (mmmt) REVERT: H 164 LEU cc_start: 0.8758 (tp) cc_final: 0.8524 (tp) REVERT: H 205 PHE cc_start: 0.8970 (t80) cc_final: 0.8740 (t80) REVERT: H 207 PHE cc_start: 0.8420 (m-80) cc_final: 0.8201 (m-80) REVERT: H 231 ARG cc_start: 0.8095 (tpm170) cc_final: 0.7661 (tpm170) REVERT: M 283 MET cc_start: 0.8350 (tpt) cc_final: 0.8113 (tpp) outliers start: 1 outliers final: 0 residues processed: 489 average time/residue: 0.1268 time to fit residues: 96.0470 Evaluate side-chains 361 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0670 chunk 212 optimal weight: 5.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 744 ASN C 565 ASN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 GLN D 764 ASN F 149 ASN G 105 HIS G 172 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.122608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095049 restraints weight = 51078.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.097350 restraints weight = 28512.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098825 restraints weight = 20231.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099730 restraints weight = 16723.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099943 restraints weight = 14981.366| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17865 Z= 0.164 Angle : 0.632 10.978 24206 Z= 0.329 Chirality : 0.042 0.272 2805 Planarity : 0.004 0.045 2959 Dihedral : 7.829 139.613 2682 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.94 % Allowed : 11.09 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.20 (0.17), residues: 2269 helix: 1.40 (0.14), residues: 1382 sheet: -2.50 (0.40), residues: 144 loop : -1.75 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 715 TYR 0.034 0.002 TYR B 440 PHE 0.042 0.002 PHE E 22 TRP 0.026 0.001 TRP H 203 HIS 0.010 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (17855) covalent geometry : angle 0.62899 / 0.33 (24186) SS BOND : bond 0.00700 / 0.38 ( 10) SS BOND : angle 2.31679 / 1.33 ( 20) hydrogen bonds : bond 0.04161 / 2.76 ( 1140) hydrogen bonds : angle 4.50033 / 3.17 ( 3330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 375 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8040 (ppp) cc_final: 0.7828 (ppp) REVERT: A 623 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8394 (mm-30) REVERT: B 490 ASP cc_start: 0.6761 (t0) cc_final: 0.6501 (t0) REVERT: B 769 ASP cc_start: 0.9204 (m-30) cc_final: 0.8938 (m-30) REVERT: B 788 SER cc_start: 0.8760 (t) cc_final: 0.8517 (m) REVERT: C 485 ILE cc_start: 0.8221 (tp) cc_final: 0.7847 (tp) REVERT: C 499 MET cc_start: 0.8702 (tmm) cc_final: 0.8155 (tmm) REVERT: D 408 MET cc_start: 0.5402 (tpt) cc_final: 0.5071 (ttt) REVERT: D 463 MET cc_start: 0.7870 (mtt) cc_final: 0.7440 (mtp) REVERT: D 629 MET cc_start: 0.7200 (mtp) cc_final: 0.6607 (ptm) REVERT: D 639 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8558 (mm) REVERT: D 708 MET cc_start: 0.8195 (tpp) cc_final: 0.7991 (tpp) REVERT: E 84 CYS cc_start: 0.8998 (m) cc_final: 0.8677 (m) REVERT: E 95 ILE cc_start: 0.9139 (tp) cc_final: 0.8782 (tp) REVERT: E 99 PHE cc_start: 0.8192 (m-10) cc_final: 0.7984 (m-10) REVERT: E 133 LYS cc_start: 0.7625 (pttm) cc_final: 0.6466 (pttt) REVERT: F 24 MET cc_start: 0.8005 (ptm) cc_final: 0.7761 (ppp) REVERT: F 35 TYR cc_start: 0.3517 (m-10) cc_final: 0.3175 (m-10) REVERT: F 58 MET cc_start: 0.6142 (tpt) cc_final: 0.5425 (mtp) REVERT: F 97 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8381 (t80) REVERT: F 110 LEU cc_start: 0.9167 (pp) cc_final: 0.8913 (tp) REVERT: F 149 ASN cc_start: 0.8654 (t0) cc_final: 0.8378 (t0) REVERT: F 192 MET cc_start: 0.7605 (mmp) cc_final: 0.7369 (mmm) REVERT: F 204 ARG cc_start: 0.4491 (tpm170) cc_final: 0.4182 (tpp-160) REVERT: G 22 LEU cc_start: 0.8434 (mm) cc_final: 0.8119 (pp) REVERT: G 42 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6554 (t0) REVERT: G 122 ARG cc_start: 0.7257 (mtm180) cc_final: 0.6778 (mtm180) REVERT: G 125 ARG cc_start: 0.8037 (tmm160) cc_final: 0.7568 (tmm160) REVERT: G 137 LEU cc_start: 0.8638 (mm) cc_final: 0.8322 (mm) REVERT: G 177 ILE cc_start: 0.9052 (pt) cc_final: 0.8577 (mt) REVERT: G 216 GLU cc_start: 0.8879 (mp0) cc_final: 0.8449 (mp0) REVERT: H 154 LYS cc_start: 0.7009 (mttt) cc_final: 0.6374 (mmmt) REVERT: H 224 ASN cc_start: 0.8760 (m110) cc_final: 0.8555 (m110) REVERT: H 231 ARG cc_start: 0.7473 (tpm170) cc_final: 0.7203 (tpm170) REVERT: M 283 MET cc_start: 0.8098 (tpt) cc_final: 0.7882 (tpp) outliers start: 33 outliers final: 23 residues processed: 393 average time/residue: 0.1232 time to fit residues: 75.8523 Evaluate side-chains 377 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 351 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 171 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 128 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 108 optimal weight: 0.1980 chunk 183 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN B 726 ASN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.118420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090927 restraints weight = 52358.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092691 restraints weight = 32118.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093359 restraints weight = 22430.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093396 restraints weight = 20328.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093556 restraints weight = 20223.842| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17865 Z= 0.256 Angle : 0.678 10.051 24206 Z= 0.358 Chirality : 0.043 0.222 2805 Planarity : 0.004 0.050 2959 Dihedral : 8.085 115.753 2682 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.05 % Allowed : 15.26 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.26 (0.17), residues: 2269 helix: 1.43 (0.13), residues: 1396 sheet: -2.03 (0.39), residues: 151 loop : -1.86 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 715 TYR 0.039 0.002 TYR C 643 PHE 0.033 0.002 PHE E 22 TRP 0.017 0.002 TRP C 456 HIS 0.012 0.002 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.26 (17855) covalent geometry : angle 0.67641 / 0.36 (24186) SS BOND : bond 0.00352 / 0.18 ( 10) SS BOND : angle 1.84104 / 1.10 ( 20) hydrogen bonds : bond 0.04458 / 2.97 ( 1140) hydrogen bonds : angle 4.60258 / 3.25 ( 3330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 351 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8345 (ppp) cc_final: 0.8026 (ppp) REVERT: A 590 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7993 (ttm110) REVERT: A 785 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9077 (tp) REVERT: B 769 ASP cc_start: 0.9416 (m-30) cc_final: 0.9102 (m-30) REVERT: C 485 ILE cc_start: 0.8382 (tp) cc_final: 0.7997 (tp) REVERT: C 499 MET cc_start: 0.8772 (tmm) cc_final: 0.8239 (tmm) REVERT: C 590 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8388 (ttm-80) REVERT: C 630 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7696 (mm-30) REVERT: D 408 MET cc_start: 0.5460 (tpt) cc_final: 0.5148 (ttt) REVERT: D 463 MET cc_start: 0.8246 (mtt) cc_final: 0.7695 (mtp) REVERT: D 629 MET cc_start: 0.7772 (mtp) cc_final: 0.7279 (ptm) REVERT: E 81 MET cc_start: 0.9003 (mtp) cc_final: 0.8502 (mtp) REVERT: E 95 ILE cc_start: 0.9169 (tp) cc_final: 0.8955 (tp) REVERT: E 99 PHE cc_start: 0.8382 (m-10) cc_final: 0.8161 (m-10) REVERT: E 133 LYS cc_start: 0.7687 (pttm) cc_final: 0.6682 (pttt) REVERT: F 58 MET cc_start: 0.6417 (tpt) cc_final: 0.5704 (mtt) REVERT: F 97 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8415 (t80) REVERT: F 192 MET cc_start: 0.7575 (mmp) cc_final: 0.7330 (mmm) REVERT: G 22 LEU cc_start: 0.8504 (mm) cc_final: 0.8171 (pp) REVERT: G 35 MET cc_start: 0.8492 (tmm) cc_final: 0.8257 (tmm) REVERT: G 42 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6658 (t0) REVERT: G 125 ARG cc_start: 0.8045 (tmm160) cc_final: 0.7604 (ttp80) REVERT: G 177 ILE cc_start: 0.9092 (pt) cc_final: 0.8597 (mt) REVERT: H 154 LYS cc_start: 0.7055 (mttt) cc_final: 0.6432 (mmpt) REVERT: H 199 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6686 (t80) REVERT: H 224 ASN cc_start: 0.8880 (m110) cc_final: 0.8608 (m110) REVERT: H 231 ARG cc_start: 0.7642 (tpm170) cc_final: 0.7333 (tpm170) outliers start: 52 outliers final: 31 residues processed: 377 average time/residue: 0.1239 time to fit residues: 72.7731 Evaluate side-chains 363 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 328 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 199 TYR Chi-restraints excluded: chain H residue 234 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 102 optimal weight: 0.0870 chunk 185 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN B 726 ASN G 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.120154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095097 restraints weight = 53039.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096595 restraints weight = 33426.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096795 restraints weight = 24021.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097084 restraints weight = 21883.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.097210 restraints weight = 20938.291| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17865 Z= 0.148 Angle : 0.601 11.475 24206 Z= 0.309 Chirality : 0.041 0.205 2805 Planarity : 0.004 0.045 2959 Dihedral : 7.505 109.713 2682 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.52 % Allowed : 18.72 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.55 (0.18), residues: 2269 helix: 1.69 (0.14), residues: 1395 sheet: -2.12 (0.39), residues: 153 loop : -1.77 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 149 TYR 0.037 0.002 TYR C 643 PHE 0.048 0.002 PHE B 531 TRP 0.024 0.001 TRP C 456 HIS 0.012 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (17855) covalent geometry : angle 0.59996 / 0.31 (24186) SS BOND : bond 0.00128 / 0.07 ( 10) SS BOND : angle 1.19091 / 0.66 ( 20) hydrogen bonds : bond 0.03902 / 2.58 ( 1140) hydrogen bonds : angle 4.34999 / 3.07 ( 3330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 362 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8227 (ppp) cc_final: 0.7975 (ppp) REVERT: A 704 MET cc_start: 0.8711 (tpt) cc_final: 0.8508 (tpp) REVERT: A 785 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9018 (tp) REVERT: A 807 LEU cc_start: 0.8805 (tt) cc_final: 0.8506 (mm) REVERT: B 635 SER cc_start: 0.8683 (t) cc_final: 0.8188 (m) REVERT: B 769 ASP cc_start: 0.9372 (m-30) cc_final: 0.9065 (m-30) REVERT: B 798 ILE cc_start: 0.9034 (tp) cc_final: 0.8815 (tp) REVERT: C 485 ILE cc_start: 0.8224 (tp) cc_final: 0.7897 (tp) REVERT: C 499 MET cc_start: 0.8796 (tmm) cc_final: 0.8308 (tmm) REVERT: C 595 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8385 (mmt90) REVERT: D 408 MET cc_start: 0.5414 (tpt) cc_final: 0.5078 (ttt) REVERT: D 463 MET cc_start: 0.7910 (mtt) cc_final: 0.7482 (mtp) REVERT: D 629 MET cc_start: 0.7741 (mtp) cc_final: 0.7036 (ptm) REVERT: E 82 PHE cc_start: 0.8264 (m-10) cc_final: 0.7796 (m-80) REVERT: E 95 ILE cc_start: 0.9042 (tp) cc_final: 0.8383 (tp) REVERT: E 99 PHE cc_start: 0.8177 (m-10) cc_final: 0.7928 (m-10) REVERT: E 133 LYS cc_start: 0.7695 (pttm) cc_final: 0.6685 (pttt) REVERT: F 58 MET cc_start: 0.6131 (tpt) cc_final: 0.5796 (mtt) REVERT: F 97 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8313 (t80) REVERT: F 204 ARG cc_start: 0.4681 (tpm170) cc_final: 0.4113 (tpp-160) REVERT: G 22 LEU cc_start: 0.8506 (mm) cc_final: 0.8213 (pp) REVERT: G 42 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6521 (t0) REVERT: G 177 ILE cc_start: 0.9059 (pt) cc_final: 0.8544 (mt) REVERT: G 216 GLU cc_start: 0.8823 (mp0) cc_final: 0.8503 (mp0) REVERT: H 154 LYS cc_start: 0.6854 (mttt) cc_final: 0.6400 (mmpt) REVERT: H 224 ASN cc_start: 0.8824 (m110) cc_final: 0.8526 (m110) REVERT: H 231 ARG cc_start: 0.7494 (tpm170) cc_final: 0.7161 (tpm170) outliers start: 43 outliers final: 30 residues processed: 385 average time/residue: 0.1267 time to fit residues: 75.9170 Evaluate side-chains 373 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 340 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 280 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 174 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 173 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 0.0060 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.120979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.095454 restraints weight = 52689.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.096649 restraints weight = 31717.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097437 restraints weight = 22405.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097622 restraints weight = 20439.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.097755 restraints weight = 19314.775| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17865 Z= 0.135 Angle : 0.598 11.793 24206 Z= 0.305 Chirality : 0.041 0.207 2805 Planarity : 0.004 0.044 2959 Dihedral : 7.330 105.583 2682 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 20.01 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.68 (0.18), residues: 2269 helix: 1.80 (0.14), residues: 1396 sheet: -2.08 (0.40), residues: 151 loop : -1.73 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 739 TYR 0.036 0.001 TYR C 643 PHE 0.037 0.002 PHE B 531 TRP 0.025 0.001 TRP H 203 HIS 0.014 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (17855) covalent geometry : angle 0.59790 / 0.30 (24186) SS BOND : bond 0.00273 / 0.16 ( 10) SS BOND : angle 1.07932 / 0.59 ( 20) hydrogen bonds : bond 0.03757 / 2.47 ( 1140) hydrogen bonds : angle 4.26335 / 3.00 ( 3330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 368 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8314 (ppp) cc_final: 0.7979 (ppp) REVERT: A 586 ASP cc_start: 0.7650 (p0) cc_final: 0.7450 (p0) REVERT: A 793 TYR cc_start: 0.9137 (m-80) cc_final: 0.8797 (m-80) REVERT: B 635 SER cc_start: 0.8648 (t) cc_final: 0.8334 (m) REVERT: B 769 ASP cc_start: 0.9316 (m-30) cc_final: 0.8999 (m-30) REVERT: B 798 ILE cc_start: 0.9043 (tp) cc_final: 0.8838 (tp) REVERT: C 485 ILE cc_start: 0.8207 (tp) cc_final: 0.7883 (tp) REVERT: C 499 MET cc_start: 0.8831 (tmm) cc_final: 0.8345 (tmm) REVERT: C 595 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8348 (mmt90) REVERT: C 630 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7697 (mm-30) REVERT: D 408 MET cc_start: 0.5424 (tpt) cc_final: 0.5093 (ttt) REVERT: D 463 MET cc_start: 0.7983 (mtt) cc_final: 0.7552 (mtp) REVERT: D 629 MET cc_start: 0.7659 (mtp) cc_final: 0.6997 (ptm) REVERT: D 708 MET cc_start: 0.8195 (tpp) cc_final: 0.7976 (tpp) REVERT: E 82 PHE cc_start: 0.8233 (m-80) cc_final: 0.7747 (m-80) REVERT: E 95 ILE cc_start: 0.9052 (tp) cc_final: 0.8377 (tp) REVERT: E 99 PHE cc_start: 0.8265 (m-10) cc_final: 0.8018 (m-10) REVERT: E 133 LYS cc_start: 0.7621 (pttm) cc_final: 0.6631 (pttt) REVERT: F 10 MET cc_start: 0.6067 (mtt) cc_final: 0.5786 (mpp) REVERT: F 58 MET cc_start: 0.6226 (tpt) cc_final: 0.5793 (mtt) REVERT: F 97 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8416 (t80) REVERT: F 192 MET cc_start: 0.7299 (mmm) cc_final: 0.7078 (mmm) REVERT: G 22 LEU cc_start: 0.8530 (mm) cc_final: 0.8231 (pp) REVERT: G 42 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6607 (t0) REVERT: G 125 ARG cc_start: 0.8124 (tmm160) cc_final: 0.7801 (tmm160) REVERT: G 177 ILE cc_start: 0.9063 (pt) cc_final: 0.8528 (mt) REVERT: G 214 LEU cc_start: 0.9077 (tp) cc_final: 0.8801 (tt) REVERT: H 154 LYS cc_start: 0.6825 (mttt) cc_final: 0.6373 (mmpt) REVERT: H 224 ASN cc_start: 0.8852 (m110) cc_final: 0.8533 (m110) REVERT: H 231 ARG cc_start: 0.7576 (tpm170) cc_final: 0.7145 (tpm170) outliers start: 45 outliers final: 33 residues processed: 390 average time/residue: 0.1242 time to fit residues: 76.4126 Evaluate side-chains 385 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 350 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 280 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.119871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092439 restraints weight = 52078.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094890 restraints weight = 30304.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095564 restraints weight = 20312.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095967 restraints weight = 18498.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095983 restraints weight = 17796.686| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17865 Z= 0.174 Angle : 0.624 11.793 24206 Z= 0.320 Chirality : 0.042 0.234 2805 Planarity : 0.004 0.045 2959 Dihedral : 7.563 100.205 2682 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.05 % Allowed : 21.36 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.66 (0.18), residues: 2269 helix: 1.77 (0.14), residues: 1398 sheet: -2.14 (0.42), residues: 138 loop : -1.72 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 586 TYR 0.028 0.002 TYR B 440 PHE 0.037 0.002 PHE E 22 TRP 0.018 0.001 TRP H 203 HIS 0.015 0.002 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (17855) covalent geometry : angle 0.62363 / 0.32 (24186) SS BOND : bond 0.00228 / 0.13 ( 10) SS BOND : angle 1.06646 / 0.60 ( 20) hydrogen bonds : bond 0.03909 / 2.57 ( 1140) hydrogen bonds : angle 4.31809 / 3.05 ( 3330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 355 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8479 (ppp) cc_final: 0.8066 (ppp) REVERT: A 785 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9012 (tp) REVERT: B 503 MET cc_start: 0.8913 (tmm) cc_final: 0.8651 (tmm) REVERT: B 635 SER cc_start: 0.8719 (t) cc_final: 0.8382 (m) REVERT: B 769 ASP cc_start: 0.9378 (m-30) cc_final: 0.9050 (m-30) REVERT: B 798 ILE cc_start: 0.9067 (tp) cc_final: 0.8844 (tp) REVERT: C 485 ILE cc_start: 0.8299 (tp) cc_final: 0.7921 (tp) REVERT: C 499 MET cc_start: 0.8901 (tmm) cc_final: 0.8379 (tmm) REVERT: C 595 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8349 (mmt90) REVERT: C 630 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7622 (mm-30) REVERT: D 408 MET cc_start: 0.5374 (tpt) cc_final: 0.5072 (ttt) REVERT: D 463 MET cc_start: 0.8225 (mtt) cc_final: 0.7744 (mtp) REVERT: D 476 ILE cc_start: 0.9025 (mm) cc_final: 0.8704 (mm) REVERT: D 585 MET cc_start: 0.9323 (mmt) cc_final: 0.8715 (mtt) REVERT: D 629 MET cc_start: 0.7704 (mtp) cc_final: 0.7127 (ptm) REVERT: E 81 MET cc_start: 0.9239 (mmm) cc_final: 0.9000 (mmm) REVERT: E 82 PHE cc_start: 0.8357 (m-80) cc_final: 0.7883 (m-80) REVERT: E 99 PHE cc_start: 0.8458 (m-10) cc_final: 0.8243 (m-10) REVERT: E 133 LYS cc_start: 0.7673 (pttm) cc_final: 0.6752 (pttt) REVERT: F 10 MET cc_start: 0.6150 (mtt) cc_final: 0.5856 (mpp) REVERT: F 58 MET cc_start: 0.6369 (tpt) cc_final: 0.5844 (mtt) REVERT: F 97 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8462 (t80) REVERT: F 192 MET cc_start: 0.7403 (mmm) cc_final: 0.7122 (mmm) REVERT: G 22 LEU cc_start: 0.8543 (mm) cc_final: 0.8246 (pp) REVERT: G 42 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6732 (t0) REVERT: G 125 ARG cc_start: 0.8010 (tmm160) cc_final: 0.7623 (tmm160) REVERT: G 177 ILE cc_start: 0.9096 (pt) cc_final: 0.8601 (mt) REVERT: G 197 ASN cc_start: 0.8130 (t0) cc_final: 0.7593 (p0) REVERT: H 105 HIS cc_start: 0.6824 (m90) cc_final: 0.6483 (m170) REVERT: H 154 LYS cc_start: 0.6859 (mttt) cc_final: 0.6347 (mmpt) REVERT: H 199 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6528 (t80) REVERT: H 224 ASN cc_start: 0.8929 (m110) cc_final: 0.8590 (m110) REVERT: H 231 ARG cc_start: 0.7589 (tpm170) cc_final: 0.7090 (tpm170) outliers start: 52 outliers final: 39 residues processed: 382 average time/residue: 0.1229 time to fit residues: 74.0268 Evaluate side-chains 381 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 338 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 199 TYR Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain H residue 234 HIS Chi-restraints excluded: chain M residue 280 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 108 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** 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 = 0.3888 r_free = 0.3888 target = 0.120697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093038 restraints weight = 52010.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095355 restraints weight = 28971.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096789 restraints weight = 20727.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097465 restraints weight = 17166.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098062 restraints weight = 15586.819| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17865 Z= 0.147 Angle : 0.634 11.615 24206 Z= 0.319 Chirality : 0.042 0.253 2805 Planarity : 0.004 0.045 2959 Dihedral : 7.414 94.846 2682 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.88 % Allowed : 22.83 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.71 (0.18), residues: 2269 helix: 1.81 (0.14), residues: 1399 sheet: -2.11 (0.42), residues: 138 loop : -1.71 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 590 TYR 0.028 0.001 TYR B 440 PHE 0.051 0.002 PHE G 165 TRP 0.017 0.001 TRP F 178 HIS 0.016 0.002 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (17855) covalent geometry : angle 0.63351 / 0.32 (24186) SS BOND : bond 0.00220 / 0.13 ( 10) SS BOND : angle 1.00542 / 0.56 ( 20) hydrogen bonds : bond 0.03801 / 2.50 ( 1140) hydrogen bonds : angle 4.25906 / 3.01 ( 3330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8344 (ppp) cc_final: 0.7987 (ppp) REVERT: A 704 MET cc_start: 0.8771 (tpp) cc_final: 0.8473 (tpt) REVERT: A 793 TYR cc_start: 0.9144 (m-80) cc_final: 0.8839 (m-80) REVERT: B 620 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9048 (tt) REVERT: B 635 SER cc_start: 0.8676 (t) cc_final: 0.8329 (m) REVERT: B 769 ASP cc_start: 0.9322 (m-30) cc_final: 0.9022 (m-30) REVERT: B 798 ILE cc_start: 0.9049 (tp) cc_final: 0.8820 (tp) REVERT: C 485 ILE cc_start: 0.8230 (tp) cc_final: 0.7885 (tp) REVERT: C 499 MET cc_start: 0.8850 (tmm) cc_final: 0.8310 (tmm) REVERT: C 595 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8318 (mmt90) REVERT: C 630 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7610 (mm-30) REVERT: D 408 MET cc_start: 0.5353 (tpt) cc_final: 0.5067 (ttt) REVERT: D 463 MET cc_start: 0.7943 (mtt) cc_final: 0.7554 (mtp) REVERT: D 476 ILE cc_start: 0.8968 (mm) cc_final: 0.8660 (mm) REVERT: D 585 MET cc_start: 0.9321 (mmt) cc_final: 0.8555 (mtt) REVERT: D 629 MET cc_start: 0.7506 (mtp) cc_final: 0.6893 (ptm) REVERT: E 81 MET cc_start: 0.9141 (mmm) cc_final: 0.8861 (mmm) REVERT: E 82 PHE cc_start: 0.8256 (m-80) cc_final: 0.7781 (m-80) REVERT: E 95 ILE cc_start: 0.8927 (tp) cc_final: 0.8086 (tp) REVERT: E 133 LYS cc_start: 0.7625 (pttm) cc_final: 0.6681 (pttt) REVERT: F 10 MET cc_start: 0.6185 (mtt) cc_final: 0.5889 (mpp) REVERT: F 58 MET cc_start: 0.6331 (tpt) cc_final: 0.5850 (mtt) REVERT: F 97 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8462 (t80) REVERT: F 192 MET cc_start: 0.7302 (mmm) cc_final: 0.6995 (mmm) REVERT: G 22 LEU cc_start: 0.8514 (mm) cc_final: 0.8228 (pp) REVERT: G 42 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6569 (t0) REVERT: G 125 ARG cc_start: 0.7951 (tmm160) cc_final: 0.7577 (tmm160) REVERT: G 177 ILE cc_start: 0.9087 (pt) cc_final: 0.8569 (mt) REVERT: H 105 HIS cc_start: 0.6750 (m90) cc_final: 0.6389 (m170) REVERT: H 154 LYS cc_start: 0.6640 (mttt) cc_final: 0.6284 (mmpt) REVERT: H 231 ARG cc_start: 0.7472 (tpm170) cc_final: 0.7083 (tpm170) outliers start: 49 outliers final: 38 residues processed: 391 average time/residue: 0.1231 time to fit residues: 75.6913 Evaluate side-chains 388 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain M residue 280 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 61 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 224 optimal weight: 0.0070 chunk 155 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 2 optimal weight: 0.0000 chunk 6 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN B 756 GLN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS G 172 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.122757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097641 restraints weight = 51426.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098719 restraints weight = 30235.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099620 restraints weight = 21560.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099780 restraints weight = 20048.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099827 restraints weight = 18642.712| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17865 Z= 0.120 Angle : 0.634 12.572 24206 Z= 0.317 Chirality : 0.041 0.234 2805 Planarity : 0.003 0.044 2959 Dihedral : 7.006 90.293 2682 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.58 % Allowed : 23.53 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.18), residues: 2269 helix: 1.94 (0.14), residues: 1387 sheet: -2.16 (0.41), residues: 142 loop : -1.59 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 590 TYR 0.029 0.001 TYR D 797 PHE 0.053 0.001 PHE G 165 TRP 0.016 0.001 TRP F 178 HIS 0.017 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17855) covalent geometry : angle 0.63389 / 0.32 (24186) SS BOND : bond 0.00223 / 0.13 ( 10) SS BOND : angle 0.94188 / 0.51 ( 20) hydrogen bonds : bond 0.03639 / 2.39 ( 1140) hydrogen bonds : angle 4.18605 / 2.96 ( 3330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 371 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 TYR cc_start: 0.8305 (t80) cc_final: 0.7892 (t80) REVERT: A 499 MET cc_start: 0.8308 (ppp) cc_final: 0.7986 (ppp) REVERT: A 704 MET cc_start: 0.8661 (tpp) cc_final: 0.8307 (tpt) REVERT: A 793 TYR cc_start: 0.9095 (m-80) cc_final: 0.8789 (m-80) REVERT: B 503 MET cc_start: 0.8908 (tmm) cc_final: 0.8658 (tmm) REVERT: B 620 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8896 (tt) REVERT: B 635 SER cc_start: 0.8628 (t) cc_final: 0.8326 (m) REVERT: B 743 ARG cc_start: 0.8538 (tmm-80) cc_final: 0.8252 (ptp-170) REVERT: B 769 ASP cc_start: 0.9287 (m-30) cc_final: 0.9050 (m-30) REVERT: B 797 TYR cc_start: 0.7925 (m-80) cc_final: 0.7598 (m-80) REVERT: B 798 ILE cc_start: 0.8958 (tp) cc_final: 0.8656 (tp) REVERT: C 485 ILE cc_start: 0.8213 (tp) cc_final: 0.7897 (tp) REVERT: C 499 MET cc_start: 0.8821 (tmm) cc_final: 0.8277 (tmm) REVERT: C 595 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8260 (mmt90) REVERT: C 630 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7633 (mm-30) REVERT: D 408 MET cc_start: 0.5337 (tpt) cc_final: 0.5026 (ttt) REVERT: D 463 MET cc_start: 0.7961 (mtt) cc_final: 0.7594 (mtp) REVERT: D 585 MET cc_start: 0.9235 (mmt) cc_final: 0.8343 (mtt) REVERT: D 629 MET cc_start: 0.7527 (mtp) cc_final: 0.6801 (ptm) REVERT: E 81 MET cc_start: 0.9169 (mmm) cc_final: 0.8953 (mmm) REVERT: E 82 PHE cc_start: 0.8184 (m-80) cc_final: 0.7712 (m-80) REVERT: E 84 CYS cc_start: 0.8794 (m) cc_final: 0.8388 (m) REVERT: E 133 LYS cc_start: 0.7586 (pttm) cc_final: 0.6662 (pttt) REVERT: F 10 MET cc_start: 0.6292 (mtt) cc_final: 0.6002 (mpp) REVERT: F 58 MET cc_start: 0.6266 (tpt) cc_final: 0.5868 (mtt) REVERT: F 97 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8412 (t80) REVERT: F 178 TRP cc_start: 0.5639 (m-10) cc_final: 0.4202 (m100) REVERT: F 192 MET cc_start: 0.7207 (mmm) cc_final: 0.6931 (mmm) REVERT: G 22 LEU cc_start: 0.8476 (mm) cc_final: 0.8199 (pp) REVERT: G 42 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6458 (t0) REVERT: G 125 ARG cc_start: 0.7946 (tmm160) cc_final: 0.7609 (tmm160) REVERT: G 177 ILE cc_start: 0.9081 (pt) cc_final: 0.8570 (mt) REVERT: G 197 ASN cc_start: 0.8130 (t0) cc_final: 0.7649 (p0) REVERT: G 214 LEU cc_start: 0.9071 (tp) cc_final: 0.8787 (tt) REVERT: H 105 HIS cc_start: 0.6709 (m90) cc_final: 0.6314 (m170) REVERT: H 154 LYS cc_start: 0.6622 (mttt) cc_final: 0.6257 (mmpt) REVERT: H 231 ARG cc_start: 0.7496 (tpm170) cc_final: 0.7053 (tpm170) outliers start: 44 outliers final: 34 residues processed: 394 average time/residue: 0.1227 time to fit residues: 75.9383 Evaluate side-chains 396 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 359 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain M residue 280 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.121723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094176 restraints weight = 52044.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096519 restraints weight = 29133.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097970 restraints weight = 20788.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098752 restraints weight = 17202.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098941 restraints weight = 15524.714| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17865 Z= 0.144 Angle : 0.662 13.432 24206 Z= 0.332 Chirality : 0.043 0.366 2805 Planarity : 0.004 0.060 2959 Dihedral : 7.025 85.816 2682 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.58 % Allowed : 24.18 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.79 (0.18), residues: 2269 helix: 1.86 (0.14), residues: 1396 sheet: -2.10 (0.41), residues: 142 loop : -1.62 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 586 TYR 0.029 0.001 TYR D 797 PHE 0.055 0.002 PHE G 165 TRP 0.014 0.001 TRP F 178 HIS 0.019 0.002 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (17855) covalent geometry : angle 0.66202 / 0.33 (24186) SS BOND : bond 0.00171 / 0.09 ( 10) SS BOND : angle 0.93547 / 0.52 ( 20) hydrogen bonds : bond 0.03702 / 2.44 ( 1140) hydrogen bonds : angle 4.26092 / 3.02 ( 3330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 TYR cc_start: 0.8393 (t80) cc_final: 0.7967 (t80) REVERT: A 499 MET cc_start: 0.8408 (ppp) cc_final: 0.8037 (ppp) REVERT: A 704 MET cc_start: 0.8749 (tpp) cc_final: 0.8409 (tpt) REVERT: A 793 TYR cc_start: 0.9090 (m-80) cc_final: 0.8820 (m-80) REVERT: B 620 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8999 (tt) REVERT: B 635 SER cc_start: 0.8691 (t) cc_final: 0.8335 (p) REVERT: B 769 ASP cc_start: 0.9312 (m-30) cc_final: 0.9060 (m-30) REVERT: B 798 ILE cc_start: 0.9024 (tp) cc_final: 0.8808 (tp) REVERT: B 805 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8796 (tt) REVERT: C 485 ILE cc_start: 0.8247 (tp) cc_final: 0.7891 (tp) REVERT: C 492 MET cc_start: 0.8373 (ptm) cc_final: 0.8150 (ttp) REVERT: C 499 MET cc_start: 0.8752 (tmm) cc_final: 0.8305 (tmm) REVERT: C 595 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8263 (mmt90) REVERT: C 630 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7574 (mm-30) REVERT: D 408 MET cc_start: 0.5311 (tpt) cc_final: 0.5034 (ttt) REVERT: D 463 MET cc_start: 0.7909 (mtt) cc_final: 0.7559 (mtp) REVERT: D 476 ILE cc_start: 0.8878 (mm) cc_final: 0.8599 (mm) REVERT: D 585 MET cc_start: 0.9295 (mmt) cc_final: 0.8446 (mtt) REVERT: D 629 MET cc_start: 0.7470 (mtp) cc_final: 0.6791 (ptm) REVERT: E 82 PHE cc_start: 0.8156 (m-80) cc_final: 0.7602 (m-80) REVERT: E 84 CYS cc_start: 0.8873 (m) cc_final: 0.8550 (m) REVERT: E 133 LYS cc_start: 0.7547 (pttm) cc_final: 0.6600 (pttt) REVERT: F 10 MET cc_start: 0.6281 (mtt) cc_final: 0.5982 (mpp) REVERT: F 58 MET cc_start: 0.6382 (tpt) cc_final: 0.5820 (mtt) REVERT: F 97 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8470 (t80) REVERT: F 178 TRP cc_start: 0.5655 (m-10) cc_final: 0.4263 (m100) REVERT: F 192 MET cc_start: 0.7312 (mmm) cc_final: 0.6998 (mmm) REVERT: G 22 LEU cc_start: 0.8482 (mm) cc_final: 0.8187 (pp) REVERT: G 42 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6593 (t0) REVERT: G 125 ARG cc_start: 0.7955 (tmm160) cc_final: 0.7557 (tmm160) REVERT: G 177 ILE cc_start: 0.9086 (pt) cc_final: 0.8610 (mt) REVERT: G 214 LEU cc_start: 0.9112 (tp) cc_final: 0.8829 (tt) REVERT: H 105 HIS cc_start: 0.6799 (m90) cc_final: 0.6438 (m170) REVERT: H 154 LYS cc_start: 0.6559 (mttt) cc_final: 0.6230 (mmpt) REVERT: H 231 ARG cc_start: 0.7447 (tpm170) cc_final: 0.7004 (tpm170) outliers start: 44 outliers final: 35 residues processed: 383 average time/residue: 0.1253 time to fit residues: 75.1507 Evaluate side-chains 386 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 347 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain M residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 226 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 36 optimal weight: 40.0000 chunk 60 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 167 optimal weight: 0.1980 chunk 55 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.122776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095554 restraints weight = 51391.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097875 restraints weight = 28586.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099325 restraints weight = 20475.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100065 restraints weight = 16939.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.100476 restraints weight = 15333.176| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17865 Z= 0.133 Angle : 0.665 15.032 24206 Z= 0.331 Chirality : 0.043 0.484 2805 Planarity : 0.004 0.057 2959 Dihedral : 6.872 81.653 2682 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.35 % Allowed : 24.47 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.80 (0.18), residues: 2269 helix: 1.87 (0.14), residues: 1394 sheet: -2.09 (0.42), residues: 142 loop : -1.61 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 590 TYR 0.031 0.001 TYR B 440 PHE 0.053 0.002 PHE E 99 TRP 0.013 0.001 TRP C 456 HIS 0.020 0.002 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (17855) covalent geometry : angle 0.66513 / 0.33 (24186) SS BOND : bond 0.00188 / 0.11 ( 10) SS BOND : angle 0.90379 / 0.50 ( 20) hydrogen bonds : bond 0.03687 / 2.42 ( 1140) hydrogen bonds : angle 4.25052 / 3.01 ( 3330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 TYR cc_start: 0.8368 (t80) cc_final: 0.7959 (t80) REVERT: A 499 MET cc_start: 0.8385 (ppp) cc_final: 0.8023 (ppp) REVERT: A 704 MET cc_start: 0.8754 (tpp) cc_final: 0.8407 (tpt) REVERT: A 710 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8251 (mm110) REVERT: A 793 TYR cc_start: 0.9082 (m-80) cc_final: 0.8773 (m-80) REVERT: B 620 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9001 (tt) REVERT: B 635 SER cc_start: 0.8638 (t) cc_final: 0.8209 (p) REVERT: B 769 ASP cc_start: 0.9295 (m-30) cc_final: 0.9012 (m-30) REVERT: B 797 TYR cc_start: 0.8029 (m-80) cc_final: 0.7725 (m-80) REVERT: B 798 ILE cc_start: 0.8960 (tp) cc_final: 0.8655 (tp) REVERT: B 805 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8799 (tt) REVERT: C 485 ILE cc_start: 0.8238 (tp) cc_final: 0.7894 (tp) REVERT: C 492 MET cc_start: 0.8452 (ptm) cc_final: 0.8212 (ttp) REVERT: C 499 MET cc_start: 0.8780 (tmm) cc_final: 0.8324 (tmm) REVERT: C 595 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8246 (mmt90) REVERT: D 408 MET cc_start: 0.5291 (tpt) cc_final: 0.5010 (ttt) REVERT: D 463 MET cc_start: 0.7915 (mtt) cc_final: 0.7573 (mtp) REVERT: D 476 ILE cc_start: 0.8840 (mm) cc_final: 0.8623 (mm) REVERT: D 585 MET cc_start: 0.9274 (mmt) cc_final: 0.8358 (mtt) REVERT: D 629 MET cc_start: 0.7376 (mtp) cc_final: 0.6729 (ptm) REVERT: E 82 PHE cc_start: 0.8033 (m-80) cc_final: 0.7516 (m-80) REVERT: E 133 LYS cc_start: 0.7533 (pttm) cc_final: 0.6595 (pttt) REVERT: E 138 LYS cc_start: 0.9081 (tttm) cc_final: 0.8504 (tttm) REVERT: F 10 MET cc_start: 0.6270 (mtt) cc_final: 0.5971 (mpp) REVERT: F 58 MET cc_start: 0.6356 (tpt) cc_final: 0.5800 (mtt) REVERT: F 97 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8472 (t80) REVERT: F 178 TRP cc_start: 0.5714 (m-10) cc_final: 0.4350 (m100) REVERT: F 192 MET cc_start: 0.7315 (mmm) cc_final: 0.6994 (mmm) REVERT: G 22 LEU cc_start: 0.8466 (mm) cc_final: 0.8173 (pp) REVERT: G 42 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6538 (t0) REVERT: G 125 ARG cc_start: 0.7867 (tmm160) cc_final: 0.7535 (tmm160) REVERT: G 197 ASN cc_start: 0.8037 (t0) cc_final: 0.7578 (p0) REVERT: G 214 LEU cc_start: 0.9102 (tp) cc_final: 0.8806 (tt) REVERT: H 154 LYS cc_start: 0.6542 (mttt) cc_final: 0.6226 (mmpt) REVERT: H 231 ARG cc_start: 0.7342 (tpm170) cc_final: 0.6910 (tpm170) REVERT: M 295 ILE cc_start: 0.9024 (pt) cc_final: 0.8810 (mm) outliers start: 40 outliers final: 34 residues processed: 380 average time/residue: 0.1157 time to fit residues: 69.0869 Evaluate side-chains 389 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 351 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 234 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain M residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 208 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 150 optimal weight: 0.1980 chunk 204 optimal weight: 0.2980 chunk 136 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.123564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098626 restraints weight = 51724.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099711 restraints weight = 29944.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100116 restraints weight = 21437.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100420 restraints weight = 20570.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.100690 restraints weight = 18856.693| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17865 Z= 0.126 Angle : 0.675 14.634 24206 Z= 0.333 Chirality : 0.043 0.507 2805 Planarity : 0.004 0.055 2959 Dihedral : 6.600 78.295 2682 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.41 % Allowed : 24.88 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.89 (0.18), residues: 2269 helix: 1.94 (0.14), residues: 1385 sheet: -2.05 (0.42), residues: 142 loop : -1.52 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 586 TYR 0.031 0.001 TYR D 797 PHE 0.055 0.002 PHE G 165 TRP 0.013 0.001 TRP B 578 HIS 0.020 0.002 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17855) covalent geometry : angle 0.67438 / 0.33 (24186) SS BOND : bond 0.00174 / 0.10 ( 10) SS BOND : angle 0.84807 / 0.47 ( 20) hydrogen bonds : bond 0.03646 / 2.39 ( 1140) hydrogen bonds : angle 4.19434 / 2.97 ( 3330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.91 seconds wall clock time: 58 minutes 14.44 seconds (3494.44 seconds total)