Starting phenix.real_space_refine on Tue May 5 10:18:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s8k_54663/05_2026/9s8k_54663.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s8k_54663/05_2026/9s8k_54663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s8k_54663/05_2026/9s8k_54663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s8k_54663/05_2026/9s8k_54663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s8k_54663/05_2026/9s8k_54663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s8k_54663/05_2026/9s8k_54663.map" } resolution = 2.06 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 90 5.16 5 C 17866 2.51 5 N 4897 2.21 5 O 5472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28332 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6473 Classifications: {'peptide': 806} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 26, 'TRANS': 779} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Conformer: "B" Number of residues, atoms: 806, 6473 Classifications: {'peptide': 806} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 26, 'TRANS': 779} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 bond proxies already assigned to first conformer: 6606 Chain: "B" Number of atoms: 6425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6425 Classifications: {'peptide': 803} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 26, 'TRANS': 776} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'LLP:plan-2': 1, 'HIP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 6422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6422 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 775} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'LLP:plan-2': 1, 'HIP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 6471 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 803, 6461 Classifications: {'peptide': 803} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 26, 'TRANS': 776} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'LLP:plan-2': 1, 'HIP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 803, 6461 Classifications: {'peptide': 803} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 26, 'TRANS': 776} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'LLP:plan-2': 1, 'HIP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 6592 Chain: "E" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 620 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 585 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 81} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 584 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 80} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 586 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 19 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 19 " occ=0.50 residue: pdb=" N AHIS D 19 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 19 " occ=0.50 Time building chain proxies: 10.16, per 1000 atoms: 0.36 Number of scatterers: 28332 At special positions: 0 Unit cell: (150.453, 157.68, 147.168, 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 90 16.00 P 7 15.00 O 5472 8.00 N 4897 7.00 C 17866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.07 Conformation dependent library (CDL) restraints added in 1.8 seconds 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6674 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 23 sheets defined 58.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 37 through 68 removed outlier: 3.730A pdb=" N GLU A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.584A pdb=" N GLU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.556A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.614A pdb=" N ALA A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.805A pdb=" N SER A 266 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 306 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.552A pdb=" N GLN A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 378 through 400 Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.508A pdb=" N GLY A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.598A pdb=" N ARG A 494 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 509 through 536 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 557 through 575 removed outlier: 3.604A pdb=" N ASN A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 614 removed outlier: 3.901A pdb=" N ASN A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 657 through 666 removed outlier: 4.087A pdb=" N MET A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 686 Processing helix chain 'A' and resid 687 through 690 removed outlier: 3.570A pdb=" N ILE A 690 " --> pdb=" O ALA A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 687 through 690' Processing helix chain 'A' and resid 696 through 706 Processing helix chain 'A' and resid 709 through 717 removed outlier: 4.163A pdb=" N TYR A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 730 Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 759 through 776 removed outlier: 4.031A pdb=" N LEU A 776 " --> pdb=" O GLU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 790 Processing helix chain 'A' and resid 791 through 794 Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'B' and resid 14 through 28 Processing helix chain 'B' and resid 37 through 68 removed outlier: 3.635A pdb=" N GLU B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 124 through 141 removed outlier: 3.504A pdb=" N ARG B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.546A pdb=" N ALA B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 removed outlier: 3.528A pdb=" N VAL B 265 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 266 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 306 Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.708A pdb=" N GLN B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 371 through 378 Processing helix chain 'B' and resid 378 through 400 Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 450 through 457 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 509 through 536 removed outlier: 3.610A pdb=" N ASN B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 575 removed outlier: 3.643A pdb=" N ASN B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 614 removed outlier: 3.843A pdb=" N ASN B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 658 through 666 Processing helix chain 'B' and resid 677 through 686 Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 709 through 717 removed outlier: 4.018A pdb=" N TYR B 713 " --> pdb=" O LYS B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 729 Processing helix chain 'B' and resid 740 through 749 Processing helix chain 'B' and resid 759 through 776 removed outlier: 3.974A pdb=" N LEU B 776 " --> pdb=" O GLU B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 790 Processing helix chain 'B' and resid 791 through 794 Processing helix chain 'B' and resid 795 through 807 removed outlier: 3.500A pdb=" N THR B 799 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 28 Processing helix chain 'C' and resid 37 through 68 removed outlier: 3.553A pdb=" N GLU C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 124 through 141 removed outlier: 3.514A pdb=" N ARG C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 261 through 267 removed outlier: 3.932A pdb=" N SER C 266 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 306 Processing helix chain 'C' and resid 322 through 325 Processing helix chain 'C' and resid 326 through 338 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 371 through 378 Processing helix chain 'C' and resid 378 through 400 Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.508A pdb=" N GLY C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 431 Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'C' and resid 450 through 457 Processing helix chain 'C' and resid 469 through 476 Processing helix chain 'C' and resid 478 through 490 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.531A pdb=" N ARG C 494 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 499 Processing helix chain 'C' and resid 500 through 505 removed outlier: 4.070A pdb=" N GLN C 504 " --> pdb=" O LEU C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 536 Processing helix chain 'C' and resid 557 through 575 removed outlier: 3.772A pdb=" N ASN C 561 " --> pdb=" O ARG C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 614 removed outlier: 3.733A pdb=" N ASN C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 631 through 639 Processing helix chain 'C' and resid 640 through 642 No H-bonds generated for 'chain 'C' and resid 640 through 642' Processing helix chain 'C' and resid 658 through 666 Processing helix chain 'C' and resid 677 through 686 Processing helix chain 'C' and resid 696 through 707 Processing helix chain 'C' and resid 709 through 717 removed outlier: 4.078A pdb=" N TYR C 713 " --> pdb=" O LYS C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 729 Processing helix chain 'C' and resid 740 through 749 Processing helix chain 'C' and resid 759 through 776 removed outlier: 4.046A pdb=" N LEU C 776 " --> pdb=" O GLU C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 789 Processing helix chain 'C' and resid 790 through 794 removed outlier: 4.707A pdb=" N TYR C 793 " --> pdb=" O ASN C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 807 Processing helix chain 'D' and resid 14 through 28 Processing helix chain 'D' and resid 37 through 68 removed outlier: 3.657A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 108 through 116 Processing helix chain 'D' and resid 124 through 141 Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.705A pdb=" N ALA D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 267 removed outlier: 3.613A pdb=" N VAL D 265 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 266 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 306 Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 326 through 340 removed outlier: 3.566A pdb=" N GLN D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 371 through 378 Processing helix chain 'D' and resid 378 through 400 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.608A pdb=" N GLY D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'D' and resid 450 through 457 Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 478 through 490 Processing helix chain 'D' and resid 491 through 495 Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 508 through 536 Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 557 through 575 removed outlier: 3.658A pdb=" N ASN D 561 " --> pdb=" O ARG D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 613 Processing helix chain 'D' and resid 618 through 620 No H-bonds generated for 'chain 'D' and resid 618 through 620' Processing helix chain 'D' and resid 631 through 639 Processing helix chain 'D' and resid 640 through 642 No H-bonds generated for 'chain 'D' and resid 640 through 642' Processing helix chain 'D' and resid 658 through 666 Processing helix chain 'D' and resid 677 through 686 Processing helix chain 'D' and resid 696 through 706 Processing helix chain 'D' and resid 709 through 717 removed outlier: 4.118A pdb=" N TYR D 713 " --> pdb=" O LYS D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 730 Processing helix chain 'D' and resid 740 through 749 Processing helix chain 'D' and resid 759 through 776 removed outlier: 4.081A pdb=" N LEU D 776 " --> pdb=" O GLU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 790 Processing helix chain 'D' and resid 791 through 794 Processing helix chain 'D' and resid 795 through 807 Processing helix chain 'E' and resid 15 through 28 removed outlier: 3.828A pdb=" N GLY E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 71 through 84 Processing helix chain 'F' and resid 15 through 28 removed outlier: 3.599A pdb=" N GLY F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 71 through 84 removed outlier: 3.713A pdb=" N LEU F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 27 Processing helix chain 'G' and resid 46 through 52 Processing helix chain 'G' and resid 69 through 83 Processing helix chain 'H' and resid 15 through 29 removed outlier: 3.830A pdb=" N GLY H 28 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 52 Processing helix chain 'H' and resid 69 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 192 removed outlier: 12.535A pdb=" N LYS A 182 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N ILE A 219 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N HIS A 184 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N ASP A 217 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR A 186 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 144 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ARG A 232 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY A 146 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TRP A 234 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY A 148 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA A 236 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 72 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR A 147 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR A 74 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE A 149 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS A 433 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 434 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 161 removed outlier: 6.452A pdb=" N MET A 155 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A 170 " --> pdb=" O MET A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA5, first strand: chain 'A' and resid 622 through 627 removed outlier: 6.185A pdb=" N LEU A 544 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 586 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP A 546 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY A 588 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 548 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE A 549 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 645 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR A 670 " --> pdb=" O PHE A 691 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 192 removed outlier: 12.649A pdb=" N LYS B 182 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 12.051A pdb=" N ILE B 219 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N HIS B 184 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N ASP B 217 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 186 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY B 144 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ARG B 232 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY B 146 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TRP B 234 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY B 148 " --> pdb=" O TRP B 234 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ALA B 236 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 72 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR B 147 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR B 74 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ILE B 149 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS B 433 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 434 " --> pdb=" O THR B 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 154 through 161 removed outlier: 6.453A pdb=" N MET B 155 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP B 170 " --> pdb=" O MET B 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 195 through 199 Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB1, first strand: chain 'B' and resid 622 through 626 removed outlier: 6.200A pdb=" N LEU B 544 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 586 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 546 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLY B 588 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN B 548 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE B 545 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU B 646 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 547 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR B 670 " --> pdb=" O PHE B 691 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 192 removed outlier: 4.125A pdb=" N ALA C 215 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ASN C 185 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N GLY C 213 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N ARG C 187 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N ILE C 211 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N LYS C 189 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N GLU C 209 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLY C 144 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ARG C 232 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY C 146 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N TRP C 234 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C 148 " --> pdb=" O TRP C 234 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ALA C 236 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL C 72 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N TYR C 147 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR C 74 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ILE C 149 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 433 " --> pdb=" O PHE C 354 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 434 " --> pdb=" O THR C 462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 161 removed outlier: 6.422A pdb=" N MET C 155 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP C 170 " --> pdb=" O MET C 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 195 through 199 Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 622 through 627 removed outlier: 6.274A pdb=" N LEU C 544 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE C 586 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP C 546 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLY C 588 " --> pdb=" O ASP C 546 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN C 548 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE C 545 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU C 646 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 547 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 645 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR C 670 " --> pdb=" O PHE C 691 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 199 removed outlier: 12.584A pdb=" N LYS D 182 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 12.051A pdb=" N ILE D 219 " --> pdb=" O LYS D 182 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N HIS D 184 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 10.999A pdb=" N ASP D 217 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 186 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 194 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU D 207 " --> pdb=" O GLY D 194 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE D 196 " --> pdb=" O TRP D 205 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP D 205 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN D 198 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR D 203 " --> pdb=" O GLN D 198 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY D 144 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG D 232 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY D 146 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TRP D 234 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY D 148 " --> pdb=" O TRP D 234 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ALA D 236 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL D 72 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR D 147 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR D 74 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ILE D 149 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS D 433 " --> pdb=" O PHE D 354 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL D 434 " --> pdb=" O THR D 462 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 157 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AC1, first strand: chain 'D' and resid 622 through 627 removed outlier: 6.076A pdb=" N LEU D 544 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE D 586 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP D 546 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY D 588 " --> pdb=" O ASP D 546 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN D 548 " --> pdb=" O GLY D 588 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE D 549 " --> pdb=" O GLU D 646 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 2 through 7 removed outlier: 3.561A pdb=" N PHE E 2 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AC4, first strand: chain 'G' and resid 2 through 7 removed outlier: 3.591A pdb=" N PHE G 2 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU G 32 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.542A pdb=" N GLU H 32 " --> pdb=" O GLU H 66 " (cutoff:3.500A) 1602 hydrogen bonds defined for protein. 4565 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: 6.78 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4931 1.32 - 1.44: 7601 1.44 - 1.57: 16078 1.57 - 1.69: 4 1.69 - 1.81: 167 Bond restraints: 28781 Sorted by residual: bond pdb=" ND1 HIP C 806 " pdb=" P HIP C 806 " ideal model delta sigma weight residual 1.928 1.706 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" ND1 HIP D 806 " pdb=" P HIP D 806 " ideal model delta sigma weight residual 1.928 1.708 0.220 2.00e-02 2.50e+03 1.22e+02 bond pdb=" ND1 HIP B 806 " pdb=" P HIP B 806 " ideal model delta sigma weight residual 1.928 1.708 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" NZ LLP A 662 " pdb=" C4' LLP A 662 " ideal model delta sigma weight residual 1.273 1.428 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" NZ LLP C 662 " pdb=" C4' LLP C 662 " ideal model delta sigma weight residual 1.273 1.428 -0.155 2.00e-02 2.50e+03 5.98e+01 ... (remaining 28776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 39022 4.20 - 8.39: 48 8.39 - 12.59: 9 12.59 - 16.79: 3 16.79 - 20.98: 1 Bond angle restraints: 39083 Sorted by residual: angle pdb=" CE LLP B 662 " pdb=" NZ LLP B 662 " pdb=" C4' LLP B 662 " ideal model delta sigma weight residual 119.26 98.28 20.98 3.00e+00 1.11e-01 4.89e+01 angle pdb=" N PRO A 10 " pdb=" CA PRO A 10 " pdb=" CB PRO A 10 " ideal model delta sigma weight residual 103.00 110.39 -7.39 1.10e+00 8.26e-01 4.51e+01 angle pdb=" CE LLP A 662 " pdb=" NZ LLP A 662 " pdb=" C4' LLP A 662 " ideal model delta sigma weight residual 119.26 102.82 16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" ND1 HIP C 806 " pdb=" P HIP C 806 " pdb=" O1P HIP C 806 " ideal model delta sigma weight residual 98.03 112.28 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" CE LLP C 662 " pdb=" NZ LLP C 662 " pdb=" C4' LLP C 662 " ideal model delta sigma weight residual 119.26 106.53 12.73 3.00e+00 1.11e-01 1.80e+01 ... (remaining 39078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16220 17.98 - 35.96: 711 35.96 - 53.94: 141 53.94 - 71.92: 37 71.92 - 89.90: 17 Dihedral angle restraints: 17126 sinusoidal: 6761 harmonic: 10365 Sorted by residual: dihedral pdb=" CA GLN B 647 " pdb=" C GLN B 647 " pdb=" N ILE B 648 " pdb=" CA ILE B 648 " ideal model delta harmonic sigma weight residual -180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE C 247 " pdb=" C PHE C 247 " pdb=" N ASN C 248 " pdb=" CA ASN C 248 " ideal model delta harmonic sigma weight residual -180.00 -158.39 -21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLN C 647 " pdb=" C GLN C 647 " pdb=" N ILE C 648 " pdb=" CA ILE C 648 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 17123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2744 0.032 - 0.064: 1155 0.064 - 0.096: 249 0.096 - 0.128: 174 0.128 - 0.160: 13 Chirality restraints: 4335 Sorted by residual: chirality pdb=" CA PRO A 10 " pdb=" N PRO A 10 " pdb=" C PRO A 10 " pdb=" CB PRO A 10 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CB ILE D 807 " pdb=" CA ILE D 807 " pdb=" CG1 ILE D 807 " pdb=" CG2 ILE D 807 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA PRO D 458 " pdb=" N PRO D 458 " pdb=" C PRO D 458 " pdb=" CB PRO D 458 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 4332 not shown) Planarity restraints: 5074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 LLP B 662 " 0.012 2.00e-02 2.50e+03 7.38e-02 1.36e+02 pdb=" C2' LLP B 662 " 0.038 2.00e-02 2.50e+03 pdb=" C3 LLP B 662 " -0.049 2.00e-02 2.50e+03 pdb=" C4 LLP B 662 " -0.071 2.00e-02 2.50e+03 pdb=" C4' LLP B 662 " 0.176 2.00e-02 2.50e+03 pdb=" C5 LLP B 662 " -0.033 2.00e-02 2.50e+03 pdb=" C5' LLP B 662 " -0.059 2.00e-02 2.50e+03 pdb=" C6 LLP B 662 " 0.026 2.00e-02 2.50e+03 pdb=" N1 LLP B 662 " 0.046 2.00e-02 2.50e+03 pdb=" O3 LLP B 662 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 LLP C 662 " -0.011 2.00e-02 2.50e+03 6.06e-02 9.19e+01 pdb=" C2' LLP C 662 " -0.030 2.00e-02 2.50e+03 pdb=" C3 LLP C 662 " 0.038 2.00e-02 2.50e+03 pdb=" C4 LLP C 662 " 0.060 2.00e-02 2.50e+03 pdb=" C4' LLP C 662 " -0.144 2.00e-02 2.50e+03 pdb=" C5 LLP C 662 " 0.027 2.00e-02 2.50e+03 pdb=" C5' LLP C 662 " 0.048 2.00e-02 2.50e+03 pdb=" C6 LLP C 662 " -0.019 2.00e-02 2.50e+03 pdb=" N1 LLP C 662 " -0.039 2.00e-02 2.50e+03 pdb=" O3 LLP C 662 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 LLP D 662 " 0.012 2.00e-02 2.50e+03 5.73e-02 8.22e+01 pdb=" C2' LLP D 662 " 0.029 2.00e-02 2.50e+03 pdb=" C3 LLP D 662 " -0.037 2.00e-02 2.50e+03 pdb=" C4 LLP D 662 " -0.059 2.00e-02 2.50e+03 pdb=" C4' LLP D 662 " 0.136 2.00e-02 2.50e+03 pdb=" C5 LLP D 662 " -0.026 2.00e-02 2.50e+03 pdb=" C5' LLP D 662 " -0.044 2.00e-02 2.50e+03 pdb=" C6 LLP D 662 " 0.018 2.00e-02 2.50e+03 pdb=" N1 LLP D 662 " 0.035 2.00e-02 2.50e+03 pdb=" O3 LLP D 662 " -0.066 2.00e-02 2.50e+03 ... (remaining 5071 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 184 2.53 - 3.12: 21851 3.12 - 3.71: 45005 3.71 - 4.31: 67436 4.31 - 4.90: 111126 Nonbonded interactions: 245602 Sorted by model distance: nonbonded pdb=" O ALA B 138 " pdb=" O HOH B 901 " model vdw 1.935 3.040 nonbonded pdb=" O ARG A 232 " pdb=" O HOH A 901 " model vdw 1.961 3.040 nonbonded pdb=" OD1 ASP D 152 " pdb=" O HOH D 901 " model vdw 1.980 3.040 nonbonded pdb=" NH1 ARG C 70 " pdb=" O TRP C 808 " model vdw 1.984 3.120 nonbonded pdb=" OG SER G 31 " pdb=" OD1 ASP G 69 " model vdw 2.014 3.040 ... (remaining 245597 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 13 through 18 or resid 20 through 200 or (resid 201 throug \ h 202 and (name N or name CA or name C or name O or name CB )) or resid 203 thro \ ugh 276 or (resid 277 and (name N or name CA or name C or name O or name CB )) o \ r resid 278 through 361 or (resid 362 and (name N or name CA or name C or name O \ or name CB )) or resid 363 through 366 or (resid 367 and (name N or name CA or \ name C or name O or name CB )) or resid 368 through 401 or (resid 402 and (name \ N or name CA or name C or name O or name CB )) or resid 403 through 415 or (resi \ d 416 through 417 and (name N or name CA or name C or name O or name CB )) or re \ sid 418 through 454 or (resid 455 and (name N or name CA or name C or name O or \ name CB )) or resid 456 through 486 or (resid 487 and (name N or name CA or name \ C or name O or name CB )) or resid 488 through 501 or (resid 502 and (name N or \ name CA or name C or name O or name CB )) or resid 503 through 505 or (resid 50 \ 6 through 509 and (name N or name CA or name C or name O or name CB )) or resid \ 510 through 578 or (resid 579 and (name N or name CA or name C or name O or name \ CB )) or resid 580 through 715 or (resid 716 and (name N or name CA or name C o \ r name O or name CB )) or resid 717 through 734 or (resid 735 and (name N or nam \ e CA or name C or name O or name CB )) or resid 736 through 805 or resid 807 thr \ ough 814)) selection = (chain 'B' and (resid 13 through 18 or resid 20 through 247 or (resid 248 and (n \ ame N or name CA or name C or name O or name CB )) or resid 249 through 366 or ( \ resid 367 and (name N or name CA or name C or name O or name CB )) or resid 368 \ through 401 or (resid 402 and (name N or name CA or name C or name O or name CB \ )) or resid 403 through 486 or (resid 487 and (name N or name CA or name C or na \ me O or name CB )) or resid 488 through 501 or (resid 502 and (name N or name CA \ or name C or name O or name CB )) or resid 503 through 510 or (resid 511 and (n \ ame N or name CA or name C or name O or name CB )) or resid 512 through 805 or r \ esid 807 through 814)) selection = (chain 'C' and (resid 13 through 18 or resid 20 through 247 or (resid 248 and (n \ ame N or name CA or name C or name O or name CB )) or resid 249 through 415 or ( \ resid 416 through 417 and (name N or name CA or name C or name O or name CB )) o \ r resid 418 through 454 or (resid 455 and (name N or name CA or name C or name O \ or name CB )) or resid 456 through 504 or (resid 505 through 509 and (name N or \ name CA or name C or name O or name CB )) or resid 510 through 578 or (resid 57 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 580 through \ 715 or (resid 716 and (name N or name CA or name C or name O or name CB )) or re \ sid 717 through 734 or (resid 735 and (name N or name CA or name C or name O or \ name CB )) or resid 736 through 805 or resid 807 through 814)) selection = (chain 'D' and (resid 13 through 18 or resid 20 through 200 or (resid 201 throug \ h 202 and (name N or name CA or name C or name O or name CB )) or resid 203 thro \ ugh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 276 or (resid 277 and (name N or name CA or name C or name O \ or name CB )) or resid 278 through 361 or (resid 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 or (resid 364 through 365 and (name \ N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 and (n \ ame N or name CA or name C or name O or name CB )) or resid 368 through 401 or ( \ resid 402 and (name N or name CA or name C or name O or name CB )) or resid 403 \ through 415 or (resid 416 through 417 and (name N or name CA or name C or name O \ or name CB )) or resid 418 through 454 or (resid 455 and (name N or name CA or \ name C or name O or name CB )) or resid 456 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 501 or (resi \ d 502 and (name N or name CA or name C or name O or name CB )) or resid 503 thro \ ugh 507 or (resid 508 through 509 and (name N or name CA or name C or name O or \ name CB )) or resid 510 through 578 or (resid 579 and (name N or name CA or name \ C or name O or name CB )) or resid 580 through 715 or (resid 716 and (name N or \ name CA or name C or name O or name CB )) or resid 717 through 734 or (resid 73 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 736 through \ 805 or resid 807 through 814)) } ncs_group { reference = (chain 'E' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 or (resid 4 through 5 and (name N or name CA or name C or \ name O or name CB )) or resid 6 through 8 or (resid 9 through 10 and (name N or \ name CA or name C or name O or name CB )) or resid 11 or (resid 12 and (name N \ or name CA or name C or name O or name CB )) or resid 13 through 16 or (resid 17 \ and (name N or name CA or name C or name O or name CB )) or resid 18 through 31 \ or (resid 32 and (name N or name CA or name C or name O or name CB )) or resid \ 33 through 56 or (resid 57 and (name N or name CA or name C or name O or name CB \ )) or resid 58 through 70 or (resid 71 through 73 and (name N or name CA or nam \ e C or name O or name CB )) or resid 74 or (resid 75 and (name N or name CA or n \ ame C or name O or name CB )) or resid 76 through 78 or (resid 79 and (name N or \ name CA or name C or name O or name CB )) or resid 80 through 82 or (resid 83 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 31 or (resid 32 and (name N or name \ CA or name C or name O or name CB )) or resid 33 through 69 or (resid 70 through \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 83)) selection = (chain 'G' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 or (resid 4 through 5 and (name N or name CA or name C or \ name O or name CB )) or resid 6 through 8 or (resid 9 through 10 and (name N or \ name CA or name C or name O or name CB )) or resid 11 or (resid 12 and (name N \ or name CA or name C or name O or name CB )) or resid 13 through 31 or (resid 32 \ and (name N or name CA or name C or name O or name CB )) or resid 33 through 56 \ or (resid 57 and (name N or name CA or name C or name O or name CB )) or resid \ 58 through 69 or (resid 70 through 73 and (name N or name CA or name C or name O \ or name CB )) or resid 74 through 83)) selection = (chain 'H' and (resid 1 through 3 or (resid 4 through 5 and (name N or name CA o \ r name C or name O or name CB )) or resid 6 through 8 or (resid 9 through 10 and \ (name N or name CA or name C or name O or name CB )) or resid 11 through 56 or \ (resid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 t \ hrough 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 82 or (resid 83 and (name N or name CA or name C or name O o \ r name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.220 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: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.970 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.006 0.222 28781 Z= 0.284 Angle : 0.591 20.981 39083 Z= 0.301 Chirality : 0.041 0.160 4335 Planarity : 0.004 0.074 5074 Dihedral : 11.465 89.904 10452 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 0.98 % Allowed : 3.41 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.14), residues: 3520 helix: 1.08 (0.12), residues: 1872 sheet: 0.36 (0.22), residues: 578 loop : -0.53 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 798 TYR 0.018 0.002 TYR D 569 PHE 0.014 0.002 PHE D 794 TRP 0.016 0.001 TRP D 808 HIS 0.007 0.001 HIS H 15 Details of bonding type rmsd covalent geometry : bond 0.00610 (28781) covalent geometry : angle 0.59097 (39083) hydrogen bonds : bond 0.14910 ( 1602) hydrogen bonds : angle 6.00061 ( 4565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 448 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.5835 (t70) REVERT: A 533 GLN cc_start: 0.7420 (mt0) cc_final: 0.6903 (mt0) REVERT: A 546 ASP cc_start: 0.7987 (t0) cc_final: 0.7029 (t0) REVERT: B 444 LEU cc_start: 0.8348 (mp) cc_final: 0.8065 (tt) REVERT: B 796 SER cc_start: 0.8513 (t) cc_final: 0.8306 (p) REVERT: D 331 MET cc_start: 0.8580 (tpp) cc_final: 0.8346 (tpp) REVERT: D 533 GLN cc_start: 0.7396 (mt0) cc_final: 0.7003 (mt0) REVERT: G 15 HIS cc_start: 0.7489 (p90) cc_final: 0.7237 (p-80) outliers start: 29 outliers final: 14 residues processed: 470 average time/residue: 0.8304 time to fit residues: 446.1110 Evaluate side-chains 275 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 425 TRP Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 766 CYS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 425 TRP Chi-restraints excluded: chain D residue 766 CYS Chi-restraints excluded: chain F residue 15 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 2.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 417 ASN A 435 ASN A 617 GLN A 749 ASN B 108 ASN B 305 HIS B 352 GLN B 435 ASN B 504 GLN B 600 HIS B 617 GLN B 790 ASN C 185 ASN C 352 GLN C 432 HIS C 435 ASN C 488 HIS C 504 GLN C 514 HIS C 518 GLN C 660 ASN ** C 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 61 ASN D 305 HIS D 435 ASN D 617 GLN D 660 ASN D 706 GLN E 4 GLN E 71 GLN G 15 HIS G 21 GLN H 15 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060735 restraints weight = 84395.929| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.82 r_work: 0.2695 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28781 Z= 0.132 Angle : 0.536 10.092 39083 Z= 0.291 Chirality : 0.042 0.170 4335 Planarity : 0.004 0.049 5074 Dihedral : 7.178 88.635 3940 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 1.79 % Allowed : 8.84 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.14), residues: 3520 helix: 1.55 (0.12), residues: 1879 sheet: 0.72 (0.22), residues: 532 loop : -0.37 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 705 TYR 0.020 0.001 TYR D 555 PHE 0.018 0.001 PHE G 2 TRP 0.018 0.001 TRP A 473 HIS 0.007 0.001 HIS H 15 Details of bonding type rmsd covalent geometry : bond 0.00281 (28781) covalent geometry : angle 0.53621 (39083) hydrogen bonds : bond 0.04640 ( 1602) hydrogen bonds : angle 4.99177 ( 4565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.6478 (t70) REVERT: A 706 GLN cc_start: 0.8276 (pp30) cc_final: 0.8010 (pp30) REVERT: B 444 LEU cc_start: 0.8773 (mp) cc_final: 0.8426 (tt) REVERT: B 533 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8590 (mm110) REVERT: B 546 ASP cc_start: 0.8682 (m-30) cc_final: 0.8404 (t0) REVERT: B 688 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8459 (t0) REVERT: C 171 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8911 (m-80) REVERT: C 204 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8365 (mtm110) REVERT: C 505 GLN cc_start: 0.7551 (mp10) cc_final: 0.6893 (mp10) REVERT: C 775 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: D 259 LYS cc_start: 0.9297 (mptp) cc_final: 0.8855 (mppt) REVERT: D 362 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8439 (mmm) REVERT: D 504 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: D 508 ASP cc_start: 0.4102 (OUTLIER) cc_final: 0.3265 (m-30) REVERT: D 579 LYS cc_start: 0.9146 (tppt) cc_final: 0.8927 (ptmm) REVERT: D 706 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8128 (pp30) REVERT: D 775 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: E 78 VAL cc_start: 0.9409 (t) cc_final: 0.9016 (m) REVERT: F 70 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: G 24 LYS cc_start: 0.9258 (tppt) cc_final: 0.9013 (pttp) outliers start: 53 outliers final: 11 residues processed: 301 average time/residue: 0.7524 time to fit residues: 262.6817 Evaluate side-chains 262 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 425 TRP Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain B residue 766 CYS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 425 TRP Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 70 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 214 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 307 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 417 ASN A 660 ASN B 660 ASN C 159 ASN C 197 GLN C 305 HIS C 504 GLN C 614 ASN D 295 GLN D 447 GLN G 21 GLN H 15 HIS H 57 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.057938 restraints weight = 79286.761| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.74 r_work: 0.2633 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28781 Z= 0.207 Angle : 0.557 9.993 39083 Z= 0.302 Chirality : 0.043 0.169 4335 Planarity : 0.004 0.054 5074 Dihedral : 6.830 89.992 3925 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 1.92 % Allowed : 9.38 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3520 helix: 1.50 (0.12), residues: 1880 sheet: 0.52 (0.21), residues: 565 loop : -0.32 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 17 TYR 0.016 0.002 TYR D 287 PHE 0.013 0.002 PHE D 794 TRP 0.018 0.001 TRP D 473 HIS 0.013 0.001 HIS B 600 Details of bonding type rmsd covalent geometry : bond 0.00474 (28781) covalent geometry : angle 0.55720 (39083) hydrogen bonds : bond 0.05304 ( 1602) hydrogen bonds : angle 4.98129 ( 4565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8616 (tt0) REVERT: A 447 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8579 (mm110) REVERT: A 506 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6368 (t70) REVERT: A 706 GLN cc_start: 0.8276 (pp30) cc_final: 0.8020 (pp30) REVERT: A 775 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: B 103 GLU cc_start: 0.9123 (tt0) cc_final: 0.8869 (tp30) REVERT: B 155 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7325 (tpt) REVERT: B 444 LEU cc_start: 0.8779 (mp) cc_final: 0.8467 (tt) REVERT: B 447 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: B 533 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8561 (mm110) REVERT: B 546 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8384 (t0) REVERT: C 96 GLU cc_start: 0.8548 (mp0) cc_final: 0.8265 (pm20) REVERT: C 505 GLN cc_start: 0.7634 (mp10) cc_final: 0.6948 (mp10) REVERT: D 362 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8421 (mmm) REVERT: D 444 LEU cc_start: 0.9075 (tp) cc_final: 0.8824 (mm) REVERT: D 504 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: D 706 GLN cc_start: 0.8790 (pp30) cc_final: 0.8497 (pp30) REVERT: D 775 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: E 78 VAL cc_start: 0.9379 (t) cc_final: 0.8992 (m) REVERT: F 70 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8077 (tt0) outliers start: 57 outliers final: 18 residues processed: 274 average time/residue: 0.7069 time to fit residues: 225.5950 Evaluate side-chains 258 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 425 TRP Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 425 TRP Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain H residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 122 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 255 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 417 ASN B 504 GLN B 600 HIS D 488 HIS F 21 GLN G 21 GLN H 15 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.060382 restraints weight = 68930.157| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.57 r_work: 0.2693 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28781 Z= 0.123 Angle : 0.499 8.442 39083 Z= 0.270 Chirality : 0.041 0.178 4335 Planarity : 0.003 0.055 5074 Dihedral : 6.695 89.946 3924 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 1.65 % Allowed : 10.16 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.14), residues: 3520 helix: 1.65 (0.12), residues: 1879 sheet: 0.63 (0.21), residues: 545 loop : -0.34 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 70 TYR 0.016 0.001 TYR D 555 PHE 0.012 0.001 PHE A 181 TRP 0.017 0.001 TRP A 473 HIS 0.007 0.001 HIS H 15 Details of bonding type rmsd covalent geometry : bond 0.00268 (28781) covalent geometry : angle 0.49903 (39083) hydrogen bonds : bond 0.04308 ( 1602) hydrogen bonds : angle 4.78818 ( 4565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: A 506 HIS cc_start: 0.7120 (OUTLIER) cc_final: 0.6502 (t70) REVERT: A 706 GLN cc_start: 0.8291 (pp30) cc_final: 0.8014 (pp30) REVERT: A 775 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: B 103 GLU cc_start: 0.9075 (tt0) cc_final: 0.8817 (tp30) REVERT: B 444 LEU cc_start: 0.8759 (mp) cc_final: 0.8424 (tt) REVERT: B 546 ASP cc_start: 0.8704 (m-30) cc_final: 0.8254 (t0) REVERT: B 688 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8477 (t0) REVERT: B 706 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8244 (mm110) REVERT: C 96 GLU cc_start: 0.8586 (mp0) cc_final: 0.8259 (pm20) REVERT: C 171 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8811 (m-80) REVERT: C 204 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8313 (mtm110) REVERT: C 505 GLN cc_start: 0.7667 (mp10) cc_final: 0.6894 (mp10) REVERT: C 600 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8199 (t-170) REVERT: C 775 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: D 259 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8829 (mppt) REVERT: D 362 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8375 (mmm) REVERT: D 444 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8804 (mm) REVERT: D 504 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: D 529 GLU cc_start: 0.8730 (tp30) cc_final: 0.8423 (mm-30) REVERT: D 706 GLN cc_start: 0.8621 (pp30) cc_final: 0.8236 (pp30) REVERT: D 775 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: D 785 MET cc_start: 0.8858 (mtp) cc_final: 0.8578 (mtm) REVERT: E 78 VAL cc_start: 0.9373 (t) cc_final: 0.8986 (m) REVERT: F 70 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: G 59 THR cc_start: 0.8918 (m) cc_final: 0.8616 (t) outliers start: 49 outliers final: 14 residues processed: 271 average time/residue: 0.7417 time to fit residues: 233.8594 Evaluate side-chains 259 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 425 TRP Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 70 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN B 790 ASN D 533 GLN H 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.058810 restraints weight = 82481.402| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.77 r_work: 0.2653 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28781 Z= 0.162 Angle : 0.511 8.615 39083 Z= 0.276 Chirality : 0.042 0.193 4335 Planarity : 0.004 0.055 5074 Dihedral : 6.632 89.166 3922 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.79 % Allowed : 10.66 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.14), residues: 3520 helix: 1.65 (0.12), residues: 1878 sheet: 0.56 (0.21), residues: 565 loop : -0.27 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 705 TYR 0.016 0.002 TYR D 555 PHE 0.058 0.002 PHE A 509 TRP 0.017 0.001 TRP A 473 HIS 0.007 0.001 HIS B 600 Details of bonding type rmsd covalent geometry : bond 0.00368 (28781) covalent geometry : angle 0.51140 (39083) hydrogen bonds : bond 0.04626 ( 1602) hydrogen bonds : angle 4.79977 ( 4565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7323 (tmm) REVERT: A 210 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8558 (tt0) REVERT: A 506 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6335 (t70) REVERT: A 706 GLN cc_start: 0.8336 (pp30) cc_final: 0.8046 (pp30) REVERT: A 775 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: B 103 GLU cc_start: 0.9135 (tt0) cc_final: 0.8870 (tp30) REVERT: B 155 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6646 (tmm) REVERT: B 444 LEU cc_start: 0.8821 (mp) cc_final: 0.8494 (tt) REVERT: B 529 GLU cc_start: 0.8955 (tp30) cc_final: 0.8687 (tm-30) REVERT: B 546 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8379 (t0) REVERT: B 688 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8526 (t0) REVERT: C 96 GLU cc_start: 0.8608 (mp0) cc_final: 0.8289 (pm20) REVERT: C 171 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8794 (m-80) REVERT: C 204 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8375 (mtm110) REVERT: C 505 GLN cc_start: 0.7669 (mp10) cc_final: 0.6879 (mp10) REVERT: C 600 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8268 (t-170) REVERT: D 64 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8155 (tm-30) REVERT: D 259 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8848 (mppt) REVERT: D 362 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8398 (mmm) REVERT: D 444 LEU cc_start: 0.9088 (tp) cc_final: 0.8854 (mm) REVERT: D 504 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: D 529 GLU cc_start: 0.8816 (tp30) cc_final: 0.8483 (mm-30) REVERT: D 600 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8178 (t70) REVERT: D 706 GLN cc_start: 0.8619 (pp30) cc_final: 0.8218 (pp30) REVERT: D 775 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: D 785 MET cc_start: 0.8898 (mtp) cc_final: 0.8610 (mtm) REVERT: E 78 VAL cc_start: 0.9391 (t) cc_final: 0.9032 (m) REVERT: E 79 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8785 (pttt) REVERT: F 70 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: G 59 THR cc_start: 0.8939 (m) cc_final: 0.8632 (t) REVERT: H 79 LYS cc_start: 0.8883 (pttm) cc_final: 0.8568 (ttpp) outliers start: 53 outliers final: 18 residues processed: 277 average time/residue: 0.7292 time to fit residues: 235.0785 Evaluate side-chains 271 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 425 TRP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain H residue 56 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 209 optimal weight: 0.0770 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN B 504 GLN B 614 ASN B 706 GLN C 504 GLN D 533 GLN F 21 GLN H 15 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.057892 restraints weight = 98958.049| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.00 r_work: 0.2623 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28781 Z= 0.182 Angle : 0.525 9.492 39083 Z= 0.283 Chirality : 0.042 0.201 4335 Planarity : 0.004 0.054 5074 Dihedral : 6.674 89.140 3922 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.99 % Allowed : 10.66 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.14), residues: 3520 helix: 1.60 (0.12), residues: 1878 sheet: 0.54 (0.21), residues: 565 loop : -0.28 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 705 TYR 0.019 0.002 TYR D 555 PHE 0.045 0.002 PHE A 509 TRP 0.017 0.001 TRP D 473 HIS 0.007 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00414 (28781) covalent geometry : angle 0.52456 (39083) hydrogen bonds : bond 0.04841 ( 1602) hydrogen bonds : angle 4.82457 ( 4565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7272 (tmm) REVERT: A 210 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: A 506 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6423 (t70) REVERT: A 529 GLU cc_start: 0.8588 (tp30) cc_final: 0.8187 (mm-30) REVERT: A 706 GLN cc_start: 0.8273 (pp30) cc_final: 0.7992 (pp30) REVERT: A 775 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: B 103 GLU cc_start: 0.8969 (tt0) cc_final: 0.8763 (tp30) REVERT: B 155 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.6657 (tmm) REVERT: B 444 LEU cc_start: 0.8789 (mp) cc_final: 0.8471 (tt) REVERT: B 498 SER cc_start: 0.9342 (m) cc_final: 0.9133 (p) REVERT: B 529 GLU cc_start: 0.8789 (tp30) cc_final: 0.8564 (tm-30) REVERT: B 546 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8212 (t0) REVERT: B 688 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8463 (t0) REVERT: C 96 GLU cc_start: 0.8456 (mp0) cc_final: 0.8128 (pm20) REVERT: C 505 GLN cc_start: 0.7715 (mp10) cc_final: 0.6914 (mp10) REVERT: C 600 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.8215 (t-170) REVERT: D 64 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8125 (tm-30) REVERT: D 444 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8804 (mm) REVERT: D 504 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: D 529 GLU cc_start: 0.8620 (tp30) cc_final: 0.8370 (mm-30) REVERT: D 600 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8092 (t70) REVERT: D 706 GLN cc_start: 0.8524 (pp30) cc_final: 0.8159 (pp30) REVERT: D 775 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: E 79 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8749 (pttt) REVERT: F 70 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: G 59 THR cc_start: 0.8923 (m) cc_final: 0.8612 (t) REVERT: H 79 LYS cc_start: 0.8912 (pttm) cc_final: 0.8592 (ttpp) outliers start: 59 outliers final: 26 residues processed: 278 average time/residue: 0.6870 time to fit residues: 223.3538 Evaluate side-chains 273 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 425 TRP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain H residue 56 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 287 optimal weight: 5.9990 chunk 333 optimal weight: 0.3980 chunk 190 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 322 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 315 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN B 600 HIS D 305 HIS H 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.060674 restraints weight = 81604.125| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.78 r_work: 0.2697 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28781 Z= 0.109 Angle : 0.482 9.619 39083 Z= 0.258 Chirality : 0.040 0.206 4335 Planarity : 0.003 0.053 5074 Dihedral : 6.534 89.132 3922 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 1.52 % Allowed : 11.37 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3520 helix: 1.77 (0.12), residues: 1871 sheet: 0.55 (0.21), residues: 568 loop : -0.25 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 705 TYR 0.022 0.001 TYR D 555 PHE 0.028 0.001 PHE A 509 TRP 0.016 0.001 TRP D 473 HIS 0.007 0.001 HIS H 15 Details of bonding type rmsd covalent geometry : bond 0.00225 (28781) covalent geometry : angle 0.48167 (39083) hydrogen bonds : bond 0.03928 ( 1602) hydrogen bonds : angle 4.64740 ( 4565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: A 506 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6410 (t70) REVERT: A 529 GLU cc_start: 0.8714 (tp30) cc_final: 0.8274 (mm-30) REVERT: A 706 GLN cc_start: 0.8382 (pp30) cc_final: 0.8083 (pp30) REVERT: A 775 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: B 103 GLU cc_start: 0.9075 (tt0) cc_final: 0.8822 (tp30) REVERT: B 444 LEU cc_start: 0.8795 (mp) cc_final: 0.8461 (tt) REVERT: B 498 SER cc_start: 0.9322 (m) cc_final: 0.9105 (p) REVERT: B 529 GLU cc_start: 0.8974 (tp30) cc_final: 0.8722 (tm-30) REVERT: B 546 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8294 (t0) REVERT: B 688 ASP cc_start: 0.9128 (OUTLIER) cc_final: 0.8514 (t0) REVERT: B 706 GLN cc_start: 0.8224 (mm-40) cc_final: 0.8006 (mm-40) REVERT: C 171 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: C 505 GLN cc_start: 0.7664 (mp10) cc_final: 0.6842 (mp10) REVERT: C 600 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.8231 (t-170) REVERT: C 706 GLN cc_start: 0.8753 (mt0) cc_final: 0.8225 (tm-30) REVERT: C 775 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: D 362 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8205 (mpp) REVERT: D 444 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8809 (mm) REVERT: D 504 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: D 529 GLU cc_start: 0.8817 (tp30) cc_final: 0.8440 (mm-30) REVERT: D 600 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8036 (t70) REVERT: D 706 GLN cc_start: 0.8582 (pp30) cc_final: 0.8192 (pp30) REVERT: D 775 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: D 785 MET cc_start: 0.8886 (mtp) cc_final: 0.8579 (mtm) REVERT: E 24 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8442 (pttm) REVERT: E 78 VAL cc_start: 0.9380 (t) cc_final: 0.9028 (m) REVERT: E 79 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8790 (pttt) REVERT: F 70 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: G 59 THR cc_start: 0.8899 (m) cc_final: 0.8624 (t) REVERT: H 24 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8895 (ttpp) REVERT: H 79 LYS cc_start: 0.8933 (pttm) cc_final: 0.8586 (ttpp) outliers start: 45 outliers final: 16 residues processed: 269 average time/residue: 0.6975 time to fit residues: 219.0267 Evaluate side-chains 265 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain H residue 56 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 11 optimal weight: 8.9990 chunk 349 optimal weight: 0.0060 chunk 102 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 308 optimal weight: 0.0000 chunk 343 optimal weight: 20.0000 chunk 346 optimal weight: 0.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN D 533 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN H 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.060199 restraints weight = 89939.130| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.90 r_work: 0.2684 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28781 Z= 0.116 Angle : 0.485 10.132 39083 Z= 0.260 Chirality : 0.040 0.229 4335 Planarity : 0.003 0.053 5074 Dihedral : 6.340 89.394 3918 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 1.42 % Allowed : 11.95 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.14), residues: 3520 helix: 1.82 (0.12), residues: 1869 sheet: 0.56 (0.21), residues: 570 loop : -0.23 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 705 TYR 0.021 0.001 TYR D 555 PHE 0.025 0.001 PHE A 509 TRP 0.016 0.001 TRP D 473 HIS 0.006 0.001 HIS H 15 Details of bonding type rmsd covalent geometry : bond 0.00254 (28781) covalent geometry : angle 0.48545 (39083) hydrogen bonds : bond 0.04011 ( 1602) hydrogen bonds : angle 4.60735 ( 4565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: A 506 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.6464 (t70) REVERT: A 529 GLU cc_start: 0.8479 (tp30) cc_final: 0.8143 (mm-30) REVERT: A 600 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.7972 (t70) REVERT: A 706 GLN cc_start: 0.8276 (pp30) cc_final: 0.7984 (pp30) REVERT: A 775 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: B 103 GLU cc_start: 0.8952 (tt0) cc_final: 0.8747 (tp30) REVERT: B 105 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (mtm) REVERT: B 444 LEU cc_start: 0.8756 (mp) cc_final: 0.8425 (tt) REVERT: B 498 SER cc_start: 0.9299 (m) cc_final: 0.9074 (p) REVERT: B 529 GLU cc_start: 0.8765 (tp30) cc_final: 0.8555 (tm-30) REVERT: B 546 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8097 (t0) REVERT: B 688 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8436 (t0) REVERT: B 706 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7946 (mm-40) REVERT: C 171 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8854 (m-80) REVERT: C 505 GLN cc_start: 0.7732 (mp10) cc_final: 0.6898 (mp10) REVERT: C 529 GLU cc_start: 0.8526 (tp30) cc_final: 0.8265 (tm-30) REVERT: C 600 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8144 (t-170) REVERT: C 706 GLN cc_start: 0.8632 (mt0) cc_final: 0.8148 (tm-30) REVERT: C 775 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: D 362 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8156 (mpp) REVERT: D 444 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8759 (mm) REVERT: D 529 GLU cc_start: 0.8563 (tp30) cc_final: 0.8326 (mm-30) REVERT: D 600 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.7967 (t70) REVERT: D 706 GLN cc_start: 0.8495 (pp30) cc_final: 0.8111 (pp30) REVERT: D 775 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: E 24 LYS cc_start: 0.8788 (pttt) cc_final: 0.8554 (pttm) REVERT: E 78 VAL cc_start: 0.9387 (t) cc_final: 0.9044 (m) REVERT: E 79 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8782 (pttt) REVERT: G 59 THR cc_start: 0.8917 (m) cc_final: 0.8655 (t) outliers start: 42 outliers final: 15 residues processed: 265 average time/residue: 0.7479 time to fit residues: 230.7535 Evaluate side-chains 266 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 81 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 349 optimal weight: 0.1980 chunk 160 optimal weight: 0.0000 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 533 GLN D 533 GLN E 21 GLN H 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061498 restraints weight = 83921.672| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.81 r_work: 0.2716 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28781 Z= 0.102 Angle : 0.477 10.819 39083 Z= 0.254 Chirality : 0.040 0.241 4335 Planarity : 0.003 0.053 5074 Dihedral : 6.279 89.618 3918 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 1.15 % Allowed : 12.25 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.14), residues: 3520 helix: 1.88 (0.12), residues: 1868 sheet: 0.59 (0.21), residues: 576 loop : -0.19 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 17 TYR 0.020 0.001 TYR D 555 PHE 0.025 0.001 PHE A 509 TRP 0.016 0.001 TRP D 473 HIS 0.006 0.001 HIS F 15 Details of bonding type rmsd covalent geometry : bond 0.00217 (28781) covalent geometry : angle 0.47742 (39083) hydrogen bonds : bond 0.03698 ( 1602) hydrogen bonds : angle 4.52574 ( 4565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: A 506 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6386 (t70) REVERT: A 529 GLU cc_start: 0.8673 (tp30) cc_final: 0.8238 (mm-30) REVERT: A 600 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8017 (t70) REVERT: A 706 GLN cc_start: 0.8418 (pp30) cc_final: 0.8112 (pp30) REVERT: A 775 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: B 103 GLU cc_start: 0.9085 (tt0) cc_final: 0.8814 (tp30) REVERT: B 444 LEU cc_start: 0.8787 (mp) cc_final: 0.8418 (tt) REVERT: B 501 ASN cc_start: 0.8650 (m-40) cc_final: 0.8413 (t0) REVERT: B 529 GLU cc_start: 0.8972 (tp30) cc_final: 0.8729 (tm-30) REVERT: B 546 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8296 (t0) REVERT: B 688 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8472 (t0) REVERT: C 505 GLN cc_start: 0.7748 (mp10) cc_final: 0.6959 (mp10) REVERT: C 600 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8228 (t-170) REVERT: C 706 GLN cc_start: 0.8746 (mt0) cc_final: 0.8233 (tm-30) REVERT: C 775 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: D 105 MET cc_start: 0.8922 (mtm) cc_final: 0.8703 (mtp) REVERT: D 362 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8198 (mpp) REVERT: D 444 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8827 (mm) REVERT: D 529 GLU cc_start: 0.8756 (tp30) cc_final: 0.8377 (mm-30) REVERT: D 600 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8067 (t70) REVERT: D 706 GLN cc_start: 0.8568 (pp30) cc_final: 0.8184 (pp30) REVERT: D 775 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: D 785 MET cc_start: 0.8860 (mtp) cc_final: 0.8603 (mtm) REVERT: E 24 LYS cc_start: 0.8874 (pttt) cc_final: 0.8605 (pttm) REVERT: E 78 VAL cc_start: 0.9388 (t) cc_final: 0.9077 (m) REVERT: E 79 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8787 (pttt) REVERT: G 59 THR cc_start: 0.8918 (m) cc_final: 0.8657 (t) REVERT: H 24 LYS cc_start: 0.8783 (ttpp) cc_final: 0.8382 (pttm) REVERT: H 79 LYS cc_start: 0.8778 (pttt) cc_final: 0.8396 (ttpp) outliers start: 34 outliers final: 15 residues processed: 265 average time/residue: 0.7203 time to fit residues: 221.9891 Evaluate side-chains 265 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain F residue 15 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 184 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 165 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 533 GLN C 533 GLN D 533 GLN E 21 GLN H 15 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.061195 restraints weight = 91735.358| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.93 r_work: 0.2707 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 28781 Z= 0.124 Angle : 0.618 59.199 39083 Z= 0.350 Chirality : 0.040 0.220 4335 Planarity : 0.003 0.052 5074 Dihedral : 6.207 89.602 3916 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.98 % Allowed : 12.86 % Favored : 86.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.14), residues: 3520 helix: 1.88 (0.12), residues: 1868 sheet: 0.60 (0.21), residues: 576 loop : -0.19 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 17 TYR 0.020 0.001 TYR D 555 PHE 0.025 0.001 PHE A 509 TRP 0.015 0.001 TRP D 473 HIS 0.006 0.001 HIS F 15 Details of bonding type rmsd covalent geometry : bond 0.00265 (28781) covalent geometry : angle 0.61819 (39083) hydrogen bonds : bond 0.03732 ( 1602) hydrogen bonds : angle 4.52732 ( 4565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: A 506 HIS cc_start: 0.7315 (OUTLIER) cc_final: 0.6372 (t70) REVERT: A 529 GLU cc_start: 0.8461 (tp30) cc_final: 0.8114 (mm-30) REVERT: A 600 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.7948 (t70) REVERT: A 706 GLN cc_start: 0.8297 (pp30) cc_final: 0.7998 (pp30) REVERT: A 775 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: B 103 GLU cc_start: 0.8950 (tt0) cc_final: 0.8742 (tp30) REVERT: B 444 LEU cc_start: 0.8746 (mp) cc_final: 0.8383 (tt) REVERT: B 501 ASN cc_start: 0.8579 (m-40) cc_final: 0.8350 (t0) REVERT: B 546 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8087 (t0) REVERT: B 688 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8420 (t0) REVERT: C 505 GLN cc_start: 0.7735 (mp10) cc_final: 0.6938 (mp10) REVERT: C 600 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.8140 (t-170) REVERT: C 706 GLN cc_start: 0.8638 (mt0) cc_final: 0.8177 (tm-30) REVERT: C 775 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: D 105 MET cc_start: 0.8867 (mtm) cc_final: 0.8641 (mtp) REVERT: D 362 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: D 444 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8774 (mm) REVERT: D 529 GLU cc_start: 0.8538 (tp30) cc_final: 0.8290 (mm-30) REVERT: D 600 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.7990 (t70) REVERT: D 706 GLN cc_start: 0.8483 (pp30) cc_final: 0.8100 (pp30) REVERT: D 775 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: D 785 MET cc_start: 0.8684 (mtp) cc_final: 0.8409 (mtm) REVERT: E 21 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7950 (mm-40) REVERT: E 24 LYS cc_start: 0.8716 (pttt) cc_final: 0.8201 (pttm) REVERT: E 78 VAL cc_start: 0.9407 (t) cc_final: 0.9073 (m) REVERT: E 79 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8775 (pttt) REVERT: G 59 THR cc_start: 0.8921 (m) cc_final: 0.8668 (t) REVERT: H 24 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8380 (pttm) REVERT: H 79 LYS cc_start: 0.8777 (pttt) cc_final: 0.8414 (ttpp) outliers start: 29 outliers final: 13 residues processed: 253 average time/residue: 0.7162 time to fit residues: 210.8654 Evaluate side-chains 260 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 337 optimal weight: 0.0020 chunk 278 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 314 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 271 optimal weight: 0.4980 chunk 170 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 154 optimal weight: 0.0770 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 533 GLN C 533 GLN D 533 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.061781 restraints weight = 72468.231| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.63 r_work: 0.2726 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 28781 Z= 0.125 Angle : 0.611 55.118 39083 Z= 0.350 Chirality : 0.040 0.220 4335 Planarity : 0.003 0.052 5074 Dihedral : 6.207 89.602 3916 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.94 % Allowed : 12.96 % Favored : 86.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.14), residues: 3520 helix: 1.88 (0.12), residues: 1868 sheet: 0.60 (0.21), residues: 576 loop : -0.19 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 17 TYR 0.020 0.001 TYR D 555 PHE 0.025 0.001 PHE A 509 TRP 0.015 0.001 TRP D 473 HIS 0.006 0.001 HIS F 15 Details of bonding type rmsd covalent geometry : bond 0.00267 (28781) covalent geometry : angle 0.61113 (39083) hydrogen bonds : bond 0.03732 ( 1602) hydrogen bonds : angle 4.52732 ( 4565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19253.81 seconds wall clock time: 326 minutes 29.83 seconds (19589.83 seconds total)