Starting phenix.real_space_refine on Sun Aug 24 08:25:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6a_44251/08_2025/9b6a_44251.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6a_44251/08_2025/9b6a_44251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b6a_44251/08_2025/9b6a_44251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6a_44251/08_2025/9b6a_44251.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b6a_44251/08_2025/9b6a_44251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6a_44251/08_2025/9b6a_44251.map" } resolution = 3.35 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 12029 2.51 5 N 2984 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3190 Chain: "B" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3133 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3215 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.81 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.19 residue: pdb=" N APHE B 623 " occ=0.51 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.49 residue: pdb=" N APHE D 623 " occ=0.73 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.27 Time building chain proxies: 5.10, per 1000 atoms: 0.28 Number of scatterers: 18493 At special positions: 0 Unit cell: (114.8, 108.24, 145.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3352 8.00 N 2984 7.00 C 12029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 781.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4366 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 24 sheets defined 60.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.693A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.599A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 removed outlier: 3.594A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.643A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.917A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.546A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 removed outlier: 3.610A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.704A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.809A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.655A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.602A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.786A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.856A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.543A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.841A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.732A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 792 through 825 removed outlier: 3.631A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.077A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 488 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.897A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 661 removed outlier: 4.287A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 removed outlier: 3.525A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.751A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.701A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 126 removed outlier: 3.986A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.773A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.645A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 removed outlier: 3.603A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.733A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.499A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 399 removed outlier: 6.704A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.521A pdb=" N GLU B 422 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 removed outlier: 5.222A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 480 removed outlier: 5.222A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.446A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AB5, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.546A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AB8, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.805A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.701A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 394 through 399 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'D' and resid 489 through 498 removed outlier: 6.795A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.462A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 78 through 79 Processing sheet with id=AC6, first strand: chain 'G' and resid 77 through 79 1191 hydrogen bonds defined for protein. 3466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 5728 1.36 - 1.49: 5064 1.49 - 1.62: 7908 1.62 - 1.75: 2 1.75 - 1.88: 207 Bond restraints: 18909 Sorted by residual: bond pdb=" CG PRO D 548 " pdb=" CD PRO D 548 " ideal model delta sigma weight residual 1.503 1.230 0.273 3.40e-02 8.65e+02 6.45e+01 bond pdb=" N PRO D 548 " pdb=" CD PRO D 548 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" CB PRO D 548 " pdb=" CG PRO D 548 " ideal model delta sigma weight residual 1.492 1.665 -0.173 5.00e-02 4.00e+02 1.19e+01 bond pdb=" CA PRO D 548 " pdb=" CB PRO D 548 " ideal model delta sigma weight residual 1.534 1.483 0.050 1.49e-02 4.50e+03 1.15e+01 bond pdb=" CB CYS G 67 " pdb=" SG CYS G 67 " ideal model delta sigma weight residual 1.808 1.879 -0.071 3.30e-02 9.18e+02 4.61e+00 ... (remaining 18904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 25483 3.04 - 6.08: 72 6.08 - 9.11: 5 9.11 - 12.15: 1 12.15 - 15.19: 4 Bond angle restraints: 25565 Sorted by residual: angle pdb=" N PRO D 548 " pdb=" CD PRO D 548 " pdb=" CG PRO D 548 " ideal model delta sigma weight residual 103.20 88.45 14.75 1.50e+00 4.44e-01 9.67e+01 angle pdb=" CA PRO D 548 " pdb=" CB PRO D 548 " pdb=" CG PRO D 548 " ideal model delta sigma weight residual 104.50 89.31 15.19 1.90e+00 2.77e-01 6.39e+01 angle pdb=" N PRO D 548 " pdb=" CA PRO D 548 " pdb=" CB PRO D 548 " ideal model delta sigma weight residual 103.51 95.87 7.64 9.60e-01 1.09e+00 6.33e+01 angle pdb=" CA CYS G 77 " pdb=" CB CYS G 77 " pdb=" SG CYS G 77 " ideal model delta sigma weight residual 114.40 128.68 -14.28 2.30e+00 1.89e-01 3.86e+01 angle pdb=" CA PRO B 745 " pdb=" N PRO B 745 " pdb=" CD PRO B 745 " ideal model delta sigma weight residual 112.00 103.78 8.22 1.40e+00 5.10e-01 3.45e+01 ... (remaining 25560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 9503 17.81 - 35.61: 1160 35.61 - 53.42: 339 53.42 - 71.23: 43 71.23 - 89.04: 22 Dihedral angle restraints: 11067 sinusoidal: 4227 harmonic: 6840 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 176.71 -83.71 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 173.65 -80.65 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 168.64 -75.64 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 11064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2386 0.051 - 0.101: 422 0.101 - 0.152: 68 0.152 - 0.202: 0 0.202 - 0.253: 1 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA CYS G 77 " pdb=" N CYS G 77 " pdb=" C CYS G 77 " pdb=" CB CYS G 77 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE D 474 " pdb=" N ILE D 474 " pdb=" C ILE D 474 " pdb=" CB ILE D 474 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 2874 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 744 " 0.087 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO B 745 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 678 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO B 679 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 678 " -0.036 5.00e-02 4.00e+02 5.29e-02 4.49e+00 pdb=" N PRO D 679 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 679 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 679 " -0.026 5.00e-02 4.00e+02 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1176 2.74 - 3.28: 18459 3.28 - 3.82: 32517 3.82 - 4.36: 35922 4.36 - 4.90: 63568 Nonbonded interactions: 151642 Sorted by model distance: nonbonded pdb=" O SER D 631 " pdb=" OG SER D 631 " model vdw 2.196 3.040 nonbonded pdb=" O ALA E 20 " pdb=" OG SER E 186 " model vdw 2.222 3.040 nonbonded pdb=" O GLN H 9 " pdb=" OG1 THR H 13 " model vdw 2.225 3.040 nonbonded pdb=" O PHE E 107 " pdb=" OG SER E 148 " model vdw 2.266 3.040 nonbonded pdb=" O PRO C 520 " pdb=" ND2 ASN C 619 " model vdw 2.268 3.120 ... (remaining 151637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 7 \ 63 or resid 765 through 812 or (resid 813 and (name N or name CA or name C or na \ me O or name CB )) or resid 814 through 818 or (resid 819 through 820 and (name \ N or name CA or name C or name O or name CB )) or resid 821 through 825)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 506 or (resid 511 and (name N or name CA or name C or name \ O or name CB )) or resid 512 through 575 or (resid 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 through 593 or (resid 594 and (nam \ e N or name CA or name C or name O or name CB )) or resid 595 through 622 or res \ id 624 through 626 or (resid 627 and (name N or name CA or name C or name O or n \ ame CB )) or resid 628 through 763 or resid 765 through 773 or (resid 784 and (n \ ame N or name CA or name C or name O or name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 763 or resid 765 through 812 \ or (resid 813 and (name N or name CA or name C or name O or name CB )) or resid \ 814 through 818 or (resid 819 through 820 and (name N or name CA or name C or n \ ame O or name CB )) or resid 821 through 825)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 506 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 763 or resid \ 765 through 773 or (resid 784 and (name N or name CA or name C or name O or nam \ e CB )) or resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214)) } 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=0.19 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.370 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.273 18921 Z= 0.132 Angle : 0.502 15.190 25589 Z= 0.274 Chirality : 0.038 0.253 2877 Planarity : 0.004 0.127 3155 Dihedral : 16.789 89.036 6665 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.26 % Allowed : 24.74 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.10 (0.18), residues: 2337 helix: 2.81 (0.14), residues: 1393 sheet: -0.66 (0.41), residues: 146 loop : -0.86 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.010 0.001 TYR A 440 PHE 0.015 0.001 PHE C 438 TRP 0.010 0.001 TRP B 671 HIS 0.004 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00340 (18909) covalent geometry : angle 0.49647 (25565) SS BOND : bond 0.00584 ( 12) SS BOND : angle 2.38253 ( 24) hydrogen bonds : bond 0.11317 ( 1189) hydrogen bonds : angle 4.57034 ( 3466) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 291 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: D 619 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7611 (t0) REVERT: G 95 GLU cc_start: 0.5014 (tm-30) cc_final: 0.3985 (tt0) outliers start: 5 outliers final: 3 residues processed: 293 average time/residue: 0.1210 time to fit residues: 52.9463 Evaluate side-chains 281 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 713 GLU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 642 GLN B 756 GLN A 756 GLN D 756 GLN E 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.178450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142506 restraints weight = 49549.510| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.38 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18921 Z= 0.101 Angle : 0.451 10.139 25589 Z= 0.240 Chirality : 0.038 0.142 2877 Planarity : 0.004 0.086 3155 Dihedral : 3.636 53.303 2571 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.85 % Allowed : 23.46 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.39 (0.18), residues: 2337 helix: 3.07 (0.14), residues: 1405 sheet: -0.66 (0.41), residues: 146 loop : -0.83 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 99 TYR 0.012 0.001 TYR A 647 PHE 0.012 0.001 PHE C 682 TRP 0.008 0.001 TRP B 671 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00220 (18909) covalent geometry : angle 0.44875 (25565) SS BOND : bond 0.00272 ( 12) SS BOND : angle 1.49938 ( 24) hydrogen bonds : bond 0.03414 ( 1189) hydrogen bonds : angle 3.55884 ( 3466) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 313 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 490 ASP cc_start: 0.6530 (p0) cc_final: 0.5997 (t0) outliers start: 36 outliers final: 27 residues processed: 334 average time/residue: 0.1244 time to fit residues: 62.3057 Evaluate side-chains 311 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 284 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 197 optimal weight: 7.9990 chunk 142 optimal weight: 0.0970 chunk 207 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 76 optimal weight: 0.1980 chunk 141 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN D 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.177192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.143918 restraints weight = 40585.181| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.51 r_work: 0.3171 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18921 Z= 0.116 Angle : 0.470 14.153 25589 Z= 0.245 Chirality : 0.038 0.157 2877 Planarity : 0.004 0.075 3155 Dihedral : 3.729 58.824 2567 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.57 % Allowed : 23.46 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.34 (0.18), residues: 2337 helix: 3.03 (0.14), residues: 1403 sheet: -0.68 (0.40), residues: 146 loop : -0.84 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 660 TYR 0.013 0.001 TYR C 424 PHE 0.013 0.001 PHE C 682 TRP 0.007 0.001 TRP G 178 HIS 0.004 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00264 (18909) covalent geometry : angle 0.46705 (25565) SS BOND : bond 0.00324 ( 12) SS BOND : angle 1.84831 ( 24) hydrogen bonds : bond 0.03554 ( 1189) hydrogen bonds : angle 3.60109 ( 3466) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 209 ARG cc_start: 0.6008 (mmm-85) cc_final: 0.5582 (mmm-85) REVERT: D 490 ASP cc_start: 0.6925 (p0) cc_final: 0.6174 (t0) outliers start: 50 outliers final: 33 residues processed: 323 average time/residue: 0.1225 time to fit residues: 59.7518 Evaluate side-chains 313 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 280 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 96 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.171997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.138790 restraints weight = 61942.924| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.08 r_work: 0.3138 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18921 Z= 0.146 Angle : 0.500 10.418 25589 Z= 0.263 Chirality : 0.040 0.180 2877 Planarity : 0.004 0.067 3155 Dihedral : 3.888 53.932 2567 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.44 % Allowed : 23.05 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.07 (0.18), residues: 2337 helix: 2.80 (0.14), residues: 1403 sheet: -0.84 (0.39), residues: 146 loop : -0.91 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 6 TYR 0.015 0.001 TYR C 424 PHE 0.019 0.001 PHE C 682 TRP 0.010 0.001 TRP C 551 HIS 0.005 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00343 (18909) covalent geometry : angle 0.49660 (25565) SS BOND : bond 0.00328 ( 12) SS BOND : angle 1.96621 ( 24) hydrogen bonds : bond 0.03902 ( 1189) hydrogen bonds : angle 3.73177 ( 3466) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 298 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 204 ARG cc_start: 0.7240 (mtt180) cc_final: 0.7028 (mtt180) REVERT: H 209 ARG cc_start: 0.5953 (mmm-85) cc_final: 0.5120 (ttp-110) REVERT: F 59 THR cc_start: 0.8554 (p) cc_final: 0.8345 (p) REVERT: B 745 PRO cc_start: 0.7619 (Cg_exo) cc_final: 0.7310 (Cg_endo) REVERT: E 211 THR cc_start: 0.7298 (t) cc_final: 0.7046 (p) outliers start: 67 outliers final: 45 residues processed: 342 average time/residue: 0.1179 time to fit residues: 60.8220 Evaluate side-chains 328 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 122 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 435 HIS B ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.173009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135015 restraints weight = 42652.611| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.07 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18921 Z= 0.122 Angle : 0.466 8.150 25589 Z= 0.247 Chirality : 0.039 0.213 2877 Planarity : 0.003 0.062 3155 Dihedral : 3.766 53.995 2567 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.39 % Allowed : 23.72 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.15 (0.18), residues: 2337 helix: 2.87 (0.14), residues: 1403 sheet: -0.82 (0.40), residues: 146 loop : -0.90 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 99 TYR 0.013 0.001 TYR C 424 PHE 0.015 0.001 PHE C 682 TRP 0.008 0.001 TRP E 178 HIS 0.006 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00283 (18909) covalent geometry : angle 0.46316 (25565) SS BOND : bond 0.00517 ( 12) SS BOND : angle 1.86583 ( 24) hydrogen bonds : bond 0.03594 ( 1189) hydrogen bonds : angle 3.64631 ( 3466) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 298 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 209 ARG cc_start: 0.5644 (mmm-85) cc_final: 0.4998 (ttp-110) REVERT: B 745 PRO cc_start: 0.7368 (Cg_exo) cc_final: 0.7168 (Cg_endo) REVERT: A 627 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: G 85 GLU cc_start: 0.0170 (OUTLIER) cc_final: -0.0054 (mt-10) outliers start: 66 outliers final: 48 residues processed: 344 average time/residue: 0.1190 time to fit residues: 62.0720 Evaluate side-chains 333 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 189 optimal weight: 0.0070 chunk 80 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.176519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.143659 restraints weight = 61924.037| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.08 r_work: 0.3186 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 18921 Z= 0.095 Angle : 0.454 10.785 25589 Z= 0.237 Chirality : 0.038 0.216 2877 Planarity : 0.003 0.058 3155 Dihedral : 3.591 52.673 2567 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.52 % Allowed : 24.54 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.42 (0.18), residues: 2337 helix: 3.16 (0.14), residues: 1391 sheet: -0.80 (0.40), residues: 146 loop : -0.86 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 37 TYR 0.014 0.001 TYR A 440 PHE 0.011 0.001 PHE C 682 TRP 0.009 0.001 TRP E 178 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00208 (18909) covalent geometry : angle 0.44805 (25565) SS BOND : bond 0.00433 ( 12) SS BOND : angle 2.47231 ( 24) hydrogen bonds : bond 0.03160 ( 1189) hydrogen bonds : angle 3.50171 ( 3466) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 209 ARG cc_start: 0.5967 (mmm-85) cc_final: 0.5161 (ttp-110) REVERT: A 408 MET cc_start: 0.6193 (mmm) cc_final: 0.5787 (mmt) REVERT: A 627 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 641 LYS cc_start: 0.7542 (mtmt) cc_final: 0.6461 (mmtm) REVERT: D 407 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5349 (ptp) REVERT: G 73 PHE cc_start: 0.2956 (OUTLIER) cc_final: 0.2695 (p90) REVERT: G 85 GLU cc_start: 0.0335 (OUTLIER) cc_final: 0.0046 (mt-10) REVERT: G 95 GLU cc_start: 0.5048 (tm-30) cc_final: 0.4263 (tt0) outliers start: 49 outliers final: 29 residues processed: 337 average time/residue: 0.1155 time to fit residues: 59.0824 Evaluate side-chains 318 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 155 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.174530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143082 restraints weight = 54288.737| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.84 r_work: 0.3180 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18921 Z= 0.138 Angle : 0.502 10.061 25589 Z= 0.262 Chirality : 0.040 0.237 2877 Planarity : 0.004 0.058 3155 Dihedral : 3.746 52.929 2567 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.23 % Allowed : 23.87 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.14 (0.18), residues: 2337 helix: 2.86 (0.14), residues: 1403 sheet: -0.74 (0.38), residues: 156 loop : -0.92 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 37 TYR 0.013 0.001 TYR A 440 PHE 0.012 0.001 PHE C 584 TRP 0.010 0.001 TRP A 671 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00325 (18909) covalent geometry : angle 0.49658 (25565) SS BOND : bond 0.00544 ( 12) SS BOND : angle 2.51903 ( 24) hydrogen bonds : bond 0.03750 ( 1189) hydrogen bonds : angle 3.66093 ( 3466) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 296 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 209 ARG cc_start: 0.5852 (mmm-85) cc_final: 0.5008 (ttp-110) REVERT: C 453 ARG cc_start: 0.6595 (tpp80) cc_final: 0.6180 (ttp-170) REVERT: B 745 PRO cc_start: 0.7515 (Cg_exo) cc_final: 0.7246 (Cg_endo) REVERT: A 627 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: A 641 LYS cc_start: 0.7587 (mtmt) cc_final: 0.6406 (mmtm) REVERT: G 73 PHE cc_start: 0.3061 (OUTLIER) cc_final: 0.2639 (p90) REVERT: G 85 GLU cc_start: 0.0256 (OUTLIER) cc_final: 0.0018 (mt-10) outliers start: 63 outliers final: 49 residues processed: 344 average time/residue: 0.1188 time to fit residues: 62.0643 Evaluate side-chains 334 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 131 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.171607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138526 restraints weight = 62941.329| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.05 r_work: 0.3119 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18921 Z= 0.142 Angle : 0.504 11.003 25589 Z= 0.264 Chirality : 0.040 0.234 2877 Planarity : 0.004 0.057 3155 Dihedral : 3.759 52.467 2565 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.39 % Allowed : 23.61 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.03 (0.18), residues: 2337 helix: 2.77 (0.14), residues: 1403 sheet: -0.82 (0.38), residues: 156 loop : -0.96 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 37 TYR 0.014 0.001 TYR C 424 PHE 0.012 0.001 PHE D 584 TRP 0.011 0.001 TRP A 551 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00336 (18909) covalent geometry : angle 0.49939 (25565) SS BOND : bond 0.00550 ( 12) SS BOND : angle 2.37810 ( 24) hydrogen bonds : bond 0.03768 ( 1189) hydrogen bonds : angle 3.70269 ( 3466) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 292 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 209 ARG cc_start: 0.5845 (mmm-85) cc_final: 0.5418 (mmm-85) REVERT: C 453 ARG cc_start: 0.6636 (tpp80) cc_final: 0.6209 (ttp-170) REVERT: B 745 PRO cc_start: 0.7635 (Cg_exo) cc_final: 0.7330 (Cg_endo) REVERT: A 627 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: A 641 LYS cc_start: 0.7595 (mtmt) cc_final: 0.6328 (mmtm) REVERT: G 73 PHE cc_start: 0.2968 (OUTLIER) cc_final: 0.2699 (p90) REVERT: G 85 GLU cc_start: 0.0325 (OUTLIER) cc_final: 0.0014 (mt-10) outliers start: 66 outliers final: 55 residues processed: 342 average time/residue: 0.1146 time to fit residues: 59.9629 Evaluate side-chains 345 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 713 GLU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 137 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 203 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.175357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.141990 restraints weight = 54015.015| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.19 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 18921 Z= 0.100 Angle : 0.466 13.002 25589 Z= 0.242 Chirality : 0.038 0.226 2877 Planarity : 0.003 0.055 3155 Dihedral : 3.559 52.196 2565 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.21 % Allowed : 25.00 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 2.35 (0.18), residues: 2337 helix: 3.11 (0.14), residues: 1391 sheet: -0.80 (0.39), residues: 156 loop : -0.90 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.014 0.001 TYR A 647 PHE 0.009 0.001 PHE C 546 TRP 0.012 0.001 TRP A 551 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00222 (18909) covalent geometry : angle 0.46262 (25565) SS BOND : bond 0.00480 ( 12) SS BOND : angle 1.96647 ( 24) hydrogen bonds : bond 0.03262 ( 1189) hydrogen bonds : angle 3.55797 ( 3466) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 209 ARG cc_start: 0.5574 (mmm-85) cc_final: 0.4937 (ttp-110) REVERT: A 408 MET cc_start: 0.4975 (mmm) cc_final: 0.4642 (mmt) REVERT: A 627 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: A 641 LYS cc_start: 0.7510 (mtmt) cc_final: 0.6408 (mmtm) REVERT: G 95 GLU cc_start: 0.4735 (tm-30) cc_final: 0.4083 (tt0) outliers start: 43 outliers final: 38 residues processed: 323 average time/residue: 0.1266 time to fit residues: 62.6201 Evaluate side-chains 320 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 225 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.172160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137389 restraints weight = 45497.112| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.10 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18921 Z= 0.198 Angle : 0.574 12.121 25589 Z= 0.300 Chirality : 0.042 0.229 2877 Planarity : 0.004 0.041 3155 Dihedral : 3.968 51.161 2565 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.98 % Allowed : 24.28 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 1.73 (0.18), residues: 2337 helix: 2.55 (0.14), residues: 1403 sheet: -0.89 (0.36), residues: 180 loop : -1.10 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 37 TYR 0.017 0.002 TYR C 424 PHE 0.017 0.002 PHE C 495 TRP 0.012 0.002 TRP A 671 HIS 0.005 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00478 (18909) covalent geometry : angle 0.56791 (25565) SS BOND : bond 0.00669 ( 12) SS BOND : angle 2.73906 ( 24) hydrogen bonds : bond 0.04291 ( 1189) hydrogen bonds : angle 3.86569 ( 3466) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 281 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 151 ILE cc_start: 0.8783 (mm) cc_final: 0.8569 (mm) REVERT: F 127 PHE cc_start: 0.6506 (m-10) cc_final: 0.6270 (m-10) REVERT: C 453 ARG cc_start: 0.6148 (tpp80) cc_final: 0.5852 (ttp-170) REVERT: A 627 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7315 (tt0) outliers start: 58 outliers final: 52 residues processed: 327 average time/residue: 0.1317 time to fit residues: 64.6735 Evaluate side-chains 324 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 713 GLU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 738 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.173395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.146498 restraints weight = 39614.279| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 4.36 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18921 Z= 0.149 Angle : 0.522 11.689 25589 Z= 0.273 Chirality : 0.040 0.213 2877 Planarity : 0.003 0.040 3155 Dihedral : 3.865 51.197 2565 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.87 % Allowed : 24.08 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 aren not related in a simple way. whole: 1.77 (0.18), residues: 2337 helix: 2.60 (0.14), residues: 1403 sheet: -0.88 (0.36), residues: 180 loop : -1.14 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.015 0.001 TYR A 647 PHE 0.014 0.001 PHE C 495 TRP 0.012 0.001 TRP A 551 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00354 (18909) covalent geometry : angle 0.51834 (25565) SS BOND : bond 0.00512 ( 12) SS BOND : angle 2.09077 ( 24) hydrogen bonds : bond 0.03886 ( 1189) hydrogen bonds : angle 3.78355 ( 3466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3070.34 seconds wall clock time: 53 minutes 45.10 seconds (3225.10 seconds total)