Starting phenix.real_space_refine on Fri Mar 6 03:00:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lve_0991/03_2026/6lve_0991.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lve_0991/03_2026/6lve_0991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lve_0991/03_2026/6lve_0991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lve_0991/03_2026/6lve_0991.map" model { file = "/net/cci-nas-00/data/ceres_data/6lve_0991/03_2026/6lve_0991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lve_0991/03_2026/6lve_0991.cif" } resolution = 3.1 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= 0.011 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 96 5.16 5 C 17476 2.51 5 N 4856 2.21 5 O 5268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27696 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5907 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 2 Chain: "B" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1017 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5907 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 2 Chain: "D" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1017 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5907 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 2 Chain: "F" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1017 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5907 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 2 Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1017 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 6.52, per 1000 atoms: 0.24 Number of scatterers: 27696 At special positions: 0 Unit cell: (120.91, 155.15, 105.93, 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 96 16.00 O 5268 8.00 N 4856 7.00 C 17476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 34 sheets defined 23.9% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.899A pdb=" N GLY A 227 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.514A pdb=" N ARG A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.543A pdb=" N GLN A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.525A pdb=" N TYR A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.871A pdb=" N ILE A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.706A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 4.038A pdb=" N ARG A 462 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 4.276A pdb=" N LEU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.159A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.818A pdb=" N ASP A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 599 through 605 removed outlier: 3.965A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 631 removed outlier: 3.775A pdb=" N GLN A 626 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG A 629 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.832A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 Processing helix chain 'B' and resid 19 through 41 Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.697A pdb=" N GLY B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.577A pdb=" N GLY C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.890A pdb=" N TYR C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.517A pdb=" N ALA C 408 " --> pdb=" O MET C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.683A pdb=" N LEU C 428 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 435 Processing helix chain 'C' and resid 458 through 462 removed outlier: 4.120A pdb=" N ARG C 462 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 removed outlier: 4.352A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.086A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 537 removed outlier: 3.961A pdb=" N ASP C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 597 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 662 through 666 removed outlier: 3.527A pdb=" N LEU C 665 " --> pdb=" O ASP C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 726 through 730 removed outlier: 3.629A pdb=" N TRP C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 730 " --> pdb=" O ILE C 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 726 through 730' Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'D' and resid 18 through 41 removed outlier: 4.225A pdb=" N TRP D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 72 through 78 removed outlier: 6.227A pdb=" N THR D 75 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.686A pdb=" N ALA D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 removed outlier: 3.578A pdb=" N GLY E 227 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 258 Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 393 through 399 removed outlier: 3.890A pdb=" N TYR E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.558A pdb=" N ALA E 408 " --> pdb=" O MET E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 431 removed outlier: 3.682A pdb=" N LEU E 428 " --> pdb=" O ASN E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 435 Processing helix chain 'E' and resid 458 through 462 removed outlier: 4.119A pdb=" N ARG E 462 " --> pdb=" O MET E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 488 removed outlier: 4.351A pdb=" N LEU E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 504 through 509 removed outlier: 4.087A pdb=" N LEU E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 537 removed outlier: 4.007A pdb=" N ASP E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 597 Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 623 through 627 Processing helix chain 'E' and resid 662 through 666 removed outlier: 3.527A pdb=" N LEU E 665 " --> pdb=" O ASP E 662 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 691 removed outlier: 3.749A pdb=" N LYS E 691 " --> pdb=" O PRO E 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 688 through 691' Processing helix chain 'E' and resid 716 through 718 No H-bonds generated for 'chain 'E' and resid 716 through 718' Processing helix chain 'E' and resid 726 through 730 removed outlier: 3.626A pdb=" N TRP E 729 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 730 " --> pdb=" O ILE E 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 726 through 730' Processing helix chain 'E' and resid 740 through 754 Processing helix chain 'F' and resid 18 through 41 removed outlier: 4.225A pdb=" N TRP F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 72 through 78 removed outlier: 6.227A pdb=" N THR F 75 " --> pdb=" O MET F 72 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY F 77 " --> pdb=" O PRO F 74 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG F 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 130 removed outlier: 3.654A pdb=" N ALA F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 removed outlier: 3.960A pdb=" N GLY G 227 " --> pdb=" O ALA G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 259 removed outlier: 3.515A pdb=" N ARG G 259 " --> pdb=" O GLU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 327 removed outlier: 3.543A pdb=" N GLN G 326 " --> pdb=" O CYS G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 399 removed outlier: 3.525A pdb=" N TYR G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 3.919A pdb=" N ILE G 410 " --> pdb=" O LYS G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 431 removed outlier: 3.706A pdb=" N GLU G 427 " --> pdb=" O GLU G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 462 removed outlier: 4.032A pdb=" N ARG G 462 " --> pdb=" O MET G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 488 removed outlier: 4.275A pdb=" N LEU G 481 " --> pdb=" O ALA G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 504 through 509 removed outlier: 4.162A pdb=" N LEU G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 537 removed outlier: 3.818A pdb=" N ASP G 537 " --> pdb=" O ASP G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 593 through 597 Processing helix chain 'G' and resid 599 through 605 removed outlier: 3.966A pdb=" N ILE G 603 " --> pdb=" O ALA G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 631 removed outlier: 3.774A pdb=" N GLN G 626 " --> pdb=" O PRO G 623 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU G 628 " --> pdb=" O SER G 625 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG G 629 " --> pdb=" O GLN G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 726 through 733 removed outlier: 3.832A pdb=" N TRP G 729 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 730 " --> pdb=" O ILE G 727 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 733 " --> pdb=" O LEU G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 740 through 754 Processing helix chain 'H' and resid 19 through 41 Processing helix chain 'H' and resid 43 through 51 Processing helix chain 'H' and resid 60 through 71 Processing helix chain 'H' and resid 73 through 78 removed outlier: 3.692A pdb=" N GLY H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG H 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.941A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU A 41 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU A 56 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.941A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 64 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.924A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 95 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.924A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 330 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.748A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N PHE A 611 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 12.534A pdb=" N ARG A 660 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE A 613 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 12.506A pdb=" N LEU A 658 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N HIS A 615 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 656 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 654 " --> pdb=" O GLY A 617 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.748A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.694A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.940A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 38 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS C 54 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.940A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 36 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 64 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 3.522A pdb=" N SER C 122 " --> pdb=" O ASN C 117 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 128 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY C 111 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 288 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.063A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL C 239 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TRP C 101 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.613A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 12.449A pdb=" N PHE C 611 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 12.255A pdb=" N ARG C 660 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 11.857A pdb=" N PHE C 613 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 12.650A pdb=" N LEU C 658 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N HIS C 615 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR C 656 " --> pdb=" O HIS C 615 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.613A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB8, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.166A pdb=" N GLN C 523 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL C 555 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 6 through 10 removed outlier: 3.686A pdb=" N PHE E 346 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.946A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU E 38 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS E 54 " --> pdb=" O ILE E 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.946A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 36 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 64 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 144 through 148 removed outlier: 3.521A pdb=" N SER E 122 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE E 128 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY E 111 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 288 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.612A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 12.448A pdb=" N PHE E 611 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 12.257A pdb=" N ARG E 660 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N PHE E 613 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 12.649A pdb=" N LEU E 658 " --> pdb=" O PHE E 613 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N HIS E 615 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR E 656 " --> pdb=" O HIS E 615 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 642 through 643 removed outlier: 3.575A pdb=" N PHE E 611 " --> pdb=" O THR E 685 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 420 through 421 Processing sheet with id=AC7, first strand: chain 'E' and resid 451 through 453 removed outlier: 6.166A pdb=" N GLN E 523 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL E 555 " --> pdb=" O GLN E 523 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 6 through 10 Processing sheet with id=AC9, first strand: chain 'G' and resid 14 through 15 removed outlier: 4.941A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU G 41 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU G 56 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 14 through 15 removed outlier: 4.941A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY G 64 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.923A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL G 239 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TRP G 101 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA G 241 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE G 99 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER G 95 " --> pdb=" O TYR G 245 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.923A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU G 330 " --> pdb=" O VAL G 239 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.748A pdb=" N ILE G 387 " --> pdb=" O ASP G 493 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA G 495 " --> pdb=" O ILE G 387 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL G 389 " --> pdb=" O ALA G 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 514 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) removed outlier: 12.376A pdb=" N PHE G 611 " --> pdb=" O ARG G 660 " (cutoff:3.500A) removed outlier: 12.540A pdb=" N ARG G 660 " --> pdb=" O PHE G 611 " (cutoff:3.500A) removed outlier: 11.933A pdb=" N PHE G 613 " --> pdb=" O LEU G 658 " (cutoff:3.500A) removed outlier: 12.477A pdb=" N LEU G 658 " --> pdb=" O PHE G 613 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N HIS G 615 " --> pdb=" O TYR G 656 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR G 656 " --> pdb=" O HIS G 615 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY G 654 " --> pdb=" O GLY G 617 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.748A pdb=" N ILE G 387 " --> pdb=" O ASP G 493 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA G 495 " --> pdb=" O ILE G 387 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL G 389 " --> pdb=" O ALA G 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 514 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 420 through 421 Processing sheet with id=AD7, first strand: chain 'G' and resid 451 through 453 1035 hydrogen bonds defined for protein. 2730 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.97 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7094 1.33 - 1.45: 6337 1.45 - 1.57: 14889 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28476 Sorted by residual: bond pdb=" CA PRO A 668 " pdb=" C PRO A 668 " ideal model delta sigma weight residual 1.514 1.501 0.013 5.50e-03 3.31e+04 5.81e+00 bond pdb=" CG LEU C 330 " pdb=" CD1 LEU C 330 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.24e+00 bond pdb=" CG LEU E 330 " pdb=" CD1 LEU E 330 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.24e+00 bond pdb=" CG1 ILE A 161 " pdb=" CD1 ILE A 161 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.56e+00 bond pdb=" CG1 ILE C 552 " pdb=" CD1 ILE C 552 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.46e+00 ... (remaining 28471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 36517 1.96 - 3.91: 1828 3.91 - 5.87: 270 5.87 - 7.83: 55 7.83 - 9.78: 22 Bond angle restraints: 38692 Sorted by residual: angle pdb=" N PHE E 332 " pdb=" CA PHE E 332 " pdb=" C PHE E 332 " ideal model delta sigma weight residual 110.91 117.62 -6.71 1.17e+00 7.31e-01 3.29e+01 angle pdb=" N PHE C 332 " pdb=" CA PHE C 332 " pdb=" C PHE C 332 " ideal model delta sigma weight residual 110.91 117.58 -6.67 1.17e+00 7.31e-01 3.25e+01 angle pdb=" C TYR C 656 " pdb=" N GLU C 657 " pdb=" CA GLU C 657 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C TYR E 656 " pdb=" N GLU E 657 " pdb=" CA GLU E 657 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C TYR G 656 " pdb=" N GLU G 657 " pdb=" CA GLU G 657 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 ... (remaining 38687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 15636 15.36 - 30.72: 804 30.72 - 46.08: 119 46.08 - 61.44: 17 61.44 - 76.80: 8 Dihedral angle restraints: 16584 sinusoidal: 6624 harmonic: 9960 Sorted by residual: dihedral pdb=" CA GLU E 19 " pdb=" C GLU E 19 " pdb=" N THR E 20 " pdb=" CA THR E 20 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA GLU C 19 " pdb=" C GLU C 19 " pdb=" N THR C 20 " pdb=" CA THR C 20 " ideal model delta harmonic sigma weight residual 180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO C 577 " pdb=" C PRO C 577 " pdb=" N PRO C 578 " pdb=" CA PRO C 578 " ideal model delta harmonic sigma weight residual 180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 16581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3472 0.097 - 0.193: 440 0.193 - 0.290: 18 0.290 - 0.386: 6 0.386 - 0.483: 4 Chirality restraints: 3940 Sorted by residual: chirality pdb=" CB ILE A 283 " pdb=" CA ILE A 283 " pdb=" CG1 ILE A 283 " pdb=" CG2 ILE A 283 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CB ILE G 283 " pdb=" CA ILE G 283 " pdb=" CG1 ILE G 283 " pdb=" CG2 ILE G 283 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CB ILE E 283 " pdb=" CA ILE E 283 " pdb=" CG1 ILE E 283 " pdb=" CG2 ILE E 283 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.47e+00 ... (remaining 3937 not shown) Planarity restraints: 5132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 331 " -0.026 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP A 331 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 331 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 331 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 331 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 331 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 331 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 331 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 331 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 331 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 331 " -0.025 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP G 331 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP G 331 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP G 331 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP G 331 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP G 331 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 331 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 331 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 331 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP G 331 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 331 " 0.028 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP E 331 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP E 331 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 331 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP E 331 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 331 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 331 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 331 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 331 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 331 " 0.002 2.00e-02 2.50e+03 ... (remaining 5129 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5805 2.77 - 3.30: 23548 3.30 - 3.84: 47114 3.84 - 4.37: 58855 4.37 - 4.90: 101465 Nonbonded interactions: 236787 Sorted by model distance: nonbonded pdb=" O HIS E 615 " pdb=" OH TYR E 684 " model vdw 2.239 3.040 nonbonded pdb=" O HIS C 615 " pdb=" OH TYR C 684 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR E 396 " pdb=" OD2 ASP E 478 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR C 396 " pdb=" OD2 ASP C 478 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR G 396 " pdb=" OD2 ASP G 478 " model vdw 2.282 3.040 ... (remaining 236782 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.120 Process input model: 27.890 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.011 0.083 28476 Z= 0.448 Angle : 0.999 9.784 38692 Z= 0.555 Chirality : 0.065 0.483 3940 Planarity : 0.008 0.068 5132 Dihedral : 9.727 76.803 10264 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.42 % Allowed : 1.46 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.12), residues: 3440 helix: -2.61 (0.15), residues: 652 sheet: -1.07 (0.21), residues: 628 loop : -2.46 (0.11), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG E 592 TYR 0.054 0.004 TYR G 684 PHE 0.037 0.005 PHE C 332 TRP 0.057 0.004 TRP A 331 HIS 0.019 0.004 HIS G 556 Details of bonding type rmsd covalent geometry : bond 0.01080 (28476) covalent geometry : angle 0.99949 (38692) hydrogen bonds : bond 0.22813 ( 880) hydrogen bonds : angle 8.87493 ( 2730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 493 time to evaluate : 0.712 Fit side-chains REVERT: A 486 ASN cc_start: 0.8739 (m-40) cc_final: 0.8447 (m-40) REVERT: A 499 ASP cc_start: 0.7817 (m-30) cc_final: 0.7545 (m-30) REVERT: A 638 ASP cc_start: 0.7016 (t70) cc_final: 0.6401 (t70) REVERT: B 17 ASP cc_start: 0.8585 (t0) cc_final: 0.8381 (t70) REVERT: B 111 THR cc_start: 0.8175 (p) cc_final: 0.7915 (t) REVERT: B 116 MET cc_start: 0.8104 (mtt) cc_final: 0.7842 (mtm) REVERT: C 12 ARG cc_start: 0.8066 (ptm160) cc_final: 0.7843 (ptp-170) REVERT: C 58 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8603 (mp) REVERT: C 69 ARG cc_start: 0.7858 (ptt180) cc_final: 0.7607 (ptt180) REVERT: C 200 SER cc_start: 0.8854 (p) cc_final: 0.8570 (m) REVERT: C 638 ASP cc_start: 0.7045 (t70) cc_final: 0.6586 (m-30) REVERT: D 32 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7930 (mttm) REVERT: D 36 ASP cc_start: 0.7185 (m-30) cc_final: 0.6745 (m-30) REVERT: E 12 ARG cc_start: 0.8058 (ptm160) cc_final: 0.7844 (ptp-170) REVERT: E 58 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8601 (mp) REVERT: E 69 ARG cc_start: 0.7861 (ptt180) cc_final: 0.7613 (ptt180) REVERT: E 200 SER cc_start: 0.8856 (p) cc_final: 0.8568 (m) REVERT: E 286 ASP cc_start: 0.8293 (p0) cc_final: 0.8092 (p0) REVERT: E 638 ASP cc_start: 0.7050 (t70) cc_final: 0.6612 (m-30) REVERT: F 32 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7930 (mttm) REVERT: F 36 ASP cc_start: 0.7188 (m-30) cc_final: 0.6748 (m-30) REVERT: G 486 ASN cc_start: 0.8743 (m-40) cc_final: 0.8439 (m-40) REVERT: G 499 ASP cc_start: 0.7817 (m-30) cc_final: 0.7546 (m-30) REVERT: G 638 ASP cc_start: 0.7001 (t70) cc_final: 0.6395 (t70) REVERT: H 17 ASP cc_start: 0.8590 (t0) cc_final: 0.8383 (t70) REVERT: H 111 THR cc_start: 0.8179 (p) cc_final: 0.7913 (t) REVERT: H 116 MET cc_start: 0.8153 (mtt) cc_final: 0.7881 (mtm) outliers start: 12 outliers final: 4 residues processed: 503 average time/residue: 0.2131 time to fit residues: 159.5639 Evaluate side-chains 276 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 270 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain G residue 309 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 251 GLN A 287 HIS A 417 HIS A 480 HIS A 626 GLN C 403 GLN C 429 HIS C 465 HIS C 695 HIS D 14 ASN E 403 GLN E 429 HIS E 465 HIS E 695 HIS F 14 ASN G 171 GLN G 251 GLN G 287 HIS G 480 HIS G 626 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091685 restraints weight = 38252.716| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.65 r_work: 0.2883 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28476 Z= 0.140 Angle : 0.592 7.221 38692 Z= 0.321 Chirality : 0.046 0.231 3940 Planarity : 0.006 0.055 5132 Dihedral : 5.888 48.898 3884 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.08 % Allowed : 5.33 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.13), residues: 3440 helix: -1.03 (0.18), residues: 656 sheet: -1.06 (0.20), residues: 684 loop : -1.82 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 588 TYR 0.019 0.001 TYR E 684 PHE 0.014 0.002 PHE C 332 TRP 0.017 0.001 TRP F 22 HIS 0.007 0.001 HIS G 465 Details of bonding type rmsd covalent geometry : bond 0.00308 (28476) covalent geometry : angle 0.59178 (38692) hydrogen bonds : bond 0.04772 ( 880) hydrogen bonds : angle 5.59689 ( 2730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 338 time to evaluate : 0.857 Fit side-chains REVERT: A 406 HIS cc_start: 0.7716 (t70) cc_final: 0.7498 (t-170) REVERT: A 499 ASP cc_start: 0.8237 (m-30) cc_final: 0.8000 (m-30) REVERT: B 116 MET cc_start: 0.8397 (mtt) cc_final: 0.8141 (mtm) REVERT: C 53 TYR cc_start: 0.8324 (t80) cc_final: 0.8090 (t80) REVERT: C 58 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8664 (mp) REVERT: C 69 ARG cc_start: 0.7842 (ptt180) cc_final: 0.7487 (ptt180) REVERT: C 200 SER cc_start: 0.8897 (p) cc_final: 0.8561 (m) REVERT: C 343 GLU cc_start: 0.8190 (tt0) cc_final: 0.7932 (tt0) REVERT: C 642 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7716 (mtm-85) REVERT: C 657 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: D 32 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7909 (mttm) REVERT: D 36 ASP cc_start: 0.7379 (m-30) cc_final: 0.6907 (m-30) REVERT: D 53 PHE cc_start: 0.9045 (m-80) cc_final: 0.8735 (m-80) REVERT: E 53 TYR cc_start: 0.8347 (t80) cc_final: 0.8104 (t80) REVERT: E 58 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8660 (mp) REVERT: E 69 ARG cc_start: 0.7839 (ptt180) cc_final: 0.7478 (ptt180) REVERT: E 200 SER cc_start: 0.8885 (p) cc_final: 0.8543 (m) REVERT: E 286 ASP cc_start: 0.8796 (p0) cc_final: 0.8588 (p0) REVERT: E 343 GLU cc_start: 0.8197 (tt0) cc_final: 0.7934 (tt0) REVERT: E 638 ASP cc_start: 0.7975 (t70) cc_final: 0.7738 (m-30) REVERT: F 32 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7918 (mttm) REVERT: F 36 ASP cc_start: 0.7402 (m-30) cc_final: 0.6931 (m-30) REVERT: F 53 PHE cc_start: 0.9045 (m-80) cc_final: 0.8774 (m-80) REVERT: G 406 HIS cc_start: 0.7672 (t70) cc_final: 0.7447 (t-170) REVERT: G 499 ASP cc_start: 0.8242 (m-30) cc_final: 0.8005 (m-30) REVERT: H 116 MET cc_start: 0.8415 (mtt) cc_final: 0.8167 (mtm) outliers start: 31 outliers final: 15 residues processed: 362 average time/residue: 0.1883 time to fit residues: 108.0017 Evaluate side-chains 299 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 281 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 84 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 424 ASN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN C 28 ASN ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN E 28 ASN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN G 171 GLN G 424 ASN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 626 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.083299 restraints weight = 38968.180| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.65 r_work: 0.2743 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.071 28476 Z= 0.454 Angle : 0.804 9.633 38692 Z= 0.427 Chirality : 0.056 0.256 3940 Planarity : 0.007 0.070 5132 Dihedral : 6.227 43.167 3882 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.88 % Allowed : 7.07 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.13), residues: 3440 helix: -0.36 (0.19), residues: 636 sheet: -0.96 (0.19), residues: 728 loop : -1.65 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 109 TYR 0.037 0.003 TYR A 245 PHE 0.039 0.003 PHE E 154 TRP 0.030 0.003 TRP G 331 HIS 0.011 0.003 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.01085 (28476) covalent geometry : angle 0.80418 (38692) hydrogen bonds : bond 0.05621 ( 880) hydrogen bonds : angle 5.50804 ( 2730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 0.864 Fit side-chains REVERT: A 150 ASP cc_start: 0.8376 (t0) cc_final: 0.8108 (t0) REVERT: A 294 TYR cc_start: 0.8120 (m-80) cc_final: 0.7508 (m-80) REVERT: A 406 HIS cc_start: 0.7833 (t70) cc_final: 0.7628 (t-170) REVERT: A 499 ASP cc_start: 0.8432 (m-30) cc_final: 0.8174 (m-30) REVERT: A 634 MET cc_start: 0.8868 (mmm) cc_final: 0.8311 (mmm) REVERT: B 17 ASP cc_start: 0.8748 (t0) cc_final: 0.8538 (t70) REVERT: B 116 MET cc_start: 0.8457 (mtt) cc_final: 0.8220 (mtm) REVERT: C 200 SER cc_start: 0.9014 (p) cc_final: 0.8741 (m) REVERT: C 698 MET cc_start: 0.7973 (mmt) cc_final: 0.7627 (mtt) REVERT: D 32 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8069 (mttm) REVERT: D 36 ASP cc_start: 0.7533 (m-30) cc_final: 0.7066 (m-30) REVERT: D 53 PHE cc_start: 0.9078 (m-80) cc_final: 0.8858 (m-80) REVERT: D 75 THR cc_start: 0.7856 (p) cc_final: 0.7625 (t) REVERT: E 200 SER cc_start: 0.9008 (p) cc_final: 0.8731 (m) REVERT: E 286 ASP cc_start: 0.8869 (p0) cc_final: 0.8646 (p0) REVERT: E 343 GLU cc_start: 0.8221 (tt0) cc_final: 0.7990 (tt0) REVERT: F 32 LYS cc_start: 0.8554 (mtmt) cc_final: 0.8064 (mttm) REVERT: F 36 ASP cc_start: 0.7541 (m-30) cc_final: 0.7069 (m-30) REVERT: F 53 PHE cc_start: 0.9081 (m-80) cc_final: 0.8841 (m-80) REVERT: F 75 THR cc_start: 0.7868 (p) cc_final: 0.7641 (t) REVERT: F 90 TYR cc_start: 0.8638 (m-80) cc_final: 0.8324 (m-80) REVERT: G 150 ASP cc_start: 0.8357 (t0) cc_final: 0.8094 (t0) REVERT: G 294 TYR cc_start: 0.8126 (m-80) cc_final: 0.7515 (m-80) REVERT: G 406 HIS cc_start: 0.7801 (t70) cc_final: 0.7591 (t-170) REVERT: G 499 ASP cc_start: 0.8454 (m-30) cc_final: 0.8199 (m-30) REVERT: G 634 MET cc_start: 0.8898 (mmm) cc_final: 0.8345 (mmm) REVERT: G 698 MET cc_start: 0.8564 (mmm) cc_final: 0.8161 (mtt) REVERT: H 17 ASP cc_start: 0.8753 (t0) cc_final: 0.8545 (t70) REVERT: H 116 MET cc_start: 0.8481 (mtt) cc_final: 0.8236 (mtm) outliers start: 54 outliers final: 37 residues processed: 315 average time/residue: 0.1670 time to fit residues: 85.7583 Evaluate side-chains 286 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 188 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 314 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 327 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 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 171 GLN A 417 HIS A 486 ASN C 403 GLN D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 14 ASN G 171 GLN G 417 HIS G 486 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.089961 restraints weight = 38024.265| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.65 r_work: 0.2851 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28476 Z= 0.109 Angle : 0.538 7.217 38692 Z= 0.290 Chirality : 0.045 0.189 3940 Planarity : 0.005 0.054 5132 Dihedral : 5.260 39.685 3878 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.15 % Allowed : 8.53 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3440 helix: 0.42 (0.20), residues: 636 sheet: -0.77 (0.20), residues: 696 loop : -1.41 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 588 TYR 0.013 0.001 TYR C 661 PHE 0.011 0.001 PHE H 120 TRP 0.017 0.001 TRP F 22 HIS 0.007 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00246 (28476) covalent geometry : angle 0.53816 (38692) hydrogen bonds : bond 0.03760 ( 880) hydrogen bonds : angle 4.81407 ( 2730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 1.078 Fit side-chains REVERT: A 294 TYR cc_start: 0.8035 (m-80) cc_final: 0.7451 (m-80) REVERT: A 634 MET cc_start: 0.8733 (mmm) cc_final: 0.8221 (mmm) REVERT: C 200 SER cc_start: 0.8910 (p) cc_final: 0.8629 (m) REVERT: C 698 MET cc_start: 0.7774 (mmt) cc_final: 0.7530 (mtt) REVERT: D 32 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8030 (mttm) REVERT: D 36 ASP cc_start: 0.7448 (m-30) cc_final: 0.6985 (m-30) REVERT: D 53 PHE cc_start: 0.9114 (m-80) cc_final: 0.8726 (m-80) REVERT: E 69 ARG cc_start: 0.7796 (ptt180) cc_final: 0.7498 (ptt180) REVERT: E 200 SER cc_start: 0.8908 (p) cc_final: 0.8621 (m) REVERT: E 343 GLU cc_start: 0.8114 (tt0) cc_final: 0.7899 (tt0) REVERT: E 622 MET cc_start: 0.9252 (mmp) cc_final: 0.8893 (mmp) REVERT: F 32 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8028 (mttm) REVERT: F 36 ASP cc_start: 0.7443 (m-30) cc_final: 0.6979 (m-30) REVERT: F 53 PHE cc_start: 0.9118 (m-80) cc_final: 0.8717 (m-80) REVERT: F 125 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7708 (pt0) REVERT: G 294 TYR cc_start: 0.8036 (m-80) cc_final: 0.7447 (m-80) REVERT: G 634 MET cc_start: 0.8762 (mmm) cc_final: 0.8241 (mmm) REVERT: G 698 MET cc_start: 0.8422 (mmm) cc_final: 0.8169 (mtt) outliers start: 33 outliers final: 19 residues processed: 315 average time/residue: 0.1741 time to fit residues: 89.6389 Evaluate side-chains 278 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 249 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 327 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN C 465 HIS D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 488 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.087843 restraints weight = 38189.915| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.64 r_work: 0.2817 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 28476 Z= 0.166 Angle : 0.561 7.051 38692 Z= 0.298 Chirality : 0.046 0.206 3940 Planarity : 0.005 0.053 5132 Dihedral : 5.185 38.032 3878 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.22 % Allowed : 8.74 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3440 helix: 0.71 (0.21), residues: 636 sheet: -0.67 (0.20), residues: 708 loop : -1.32 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 71 TYR 0.017 0.001 TYR A 661 PHE 0.020 0.002 PHE H 53 TRP 0.015 0.001 TRP F 22 HIS 0.011 0.001 HIS G 417 Details of bonding type rmsd covalent geometry : bond 0.00392 (28476) covalent geometry : angle 0.56090 (38692) hydrogen bonds : bond 0.03868 ( 880) hydrogen bonds : angle 4.71192 ( 2730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 1.035 Fit side-chains REVERT: A 261 GLU cc_start: 0.8506 (tt0) cc_final: 0.8296 (mt-10) REVERT: A 294 TYR cc_start: 0.8028 (m-80) cc_final: 0.7432 (m-80) REVERT: C 200 SER cc_start: 0.8930 (p) cc_final: 0.8651 (m) REVERT: D 32 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8060 (mttm) REVERT: D 36 ASP cc_start: 0.7461 (m-30) cc_final: 0.7029 (m-30) REVERT: D 53 PHE cc_start: 0.9075 (m-80) cc_final: 0.8624 (m-80) REVERT: D 75 THR cc_start: 0.7865 (p) cc_final: 0.7599 (t) REVERT: E 69 ARG cc_start: 0.7847 (ptt180) cc_final: 0.7544 (ptt180) REVERT: E 200 SER cc_start: 0.8925 (p) cc_final: 0.8644 (m) REVERT: E 343 GLU cc_start: 0.8163 (tt0) cc_final: 0.7957 (tt0) REVERT: E 698 MET cc_start: 0.7802 (mmt) cc_final: 0.7392 (mtt) REVERT: F 32 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8057 (mttm) REVERT: F 36 ASP cc_start: 0.7452 (m-30) cc_final: 0.7019 (m-30) REVERT: F 53 PHE cc_start: 0.9080 (m-80) cc_final: 0.8581 (m-80) REVERT: F 75 THR cc_start: 0.7930 (p) cc_final: 0.7677 (t) REVERT: F 125 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7752 (pt0) REVERT: G 261 GLU cc_start: 0.8526 (tt0) cc_final: 0.8318 (mt-10) REVERT: G 294 TYR cc_start: 0.8031 (m-80) cc_final: 0.7439 (m-80) outliers start: 35 outliers final: 29 residues processed: 309 average time/residue: 0.1726 time to fit residues: 86.9357 Evaluate side-chains 290 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 130 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 291 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 417 HIS ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 741 ASN F 14 ASN G 171 GLN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.084462 restraints weight = 38675.920| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.63 r_work: 0.2752 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 28476 Z= 0.352 Angle : 0.703 10.477 38692 Z= 0.372 Chirality : 0.052 0.230 3940 Planarity : 0.006 0.062 5132 Dihedral : 5.689 43.632 3878 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.02 % Allowed : 8.81 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3440 helix: 0.48 (0.20), residues: 644 sheet: -0.71 (0.20), residues: 716 loop : -1.41 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 109 TYR 0.027 0.002 TYR G 661 PHE 0.026 0.003 PHE B 53 TRP 0.018 0.002 TRP G 331 HIS 0.009 0.002 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00841 (28476) covalent geometry : angle 0.70302 (38692) hydrogen bonds : bond 0.04705 ( 880) hydrogen bonds : angle 5.03446 ( 2730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 0.762 Fit side-chains REVERT: A 294 TYR cc_start: 0.8100 (m-80) cc_final: 0.7516 (m-80) REVERT: A 634 MET cc_start: 0.8931 (mmm) cc_final: 0.8405 (mmm) REVERT: C 7 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8449 (mpp-170) REVERT: C 59 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8011 (mtpp) REVERT: C 200 SER cc_start: 0.8973 (p) cc_final: 0.8724 (m) REVERT: C 622 MET cc_start: 0.9273 (mmp) cc_final: 0.8914 (mmp) REVERT: C 698 MET cc_start: 0.8271 (mtt) cc_final: 0.7916 (mtt) REVERT: D 32 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8097 (mttm) REVERT: D 36 ASP cc_start: 0.7503 (m-30) cc_final: 0.7101 (m-30) REVERT: D 53 PHE cc_start: 0.9111 (m-80) cc_final: 0.8699 (m-80) REVERT: D 75 THR cc_start: 0.7896 (p) cc_final: 0.7643 (t) REVERT: E 69 ARG cc_start: 0.7841 (ptt180) cc_final: 0.7574 (ptt180) REVERT: E 200 SER cc_start: 0.8971 (p) cc_final: 0.8717 (m) REVERT: E 343 GLU cc_start: 0.8169 (tt0) cc_final: 0.7964 (tt0) REVERT: E 658 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8780 (mt) REVERT: E 698 MET cc_start: 0.7938 (mmt) cc_final: 0.7720 (mtt) REVERT: F 32 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8091 (mttm) REVERT: F 36 ASP cc_start: 0.7541 (m-30) cc_final: 0.7145 (m-30) REVERT: F 53 PHE cc_start: 0.9093 (m-80) cc_final: 0.8667 (m-80) REVERT: F 75 THR cc_start: 0.7908 (p) cc_final: 0.7637 (t) REVERT: G 294 TYR cc_start: 0.8099 (m-80) cc_final: 0.7500 (m-80) REVERT: G 634 MET cc_start: 0.8947 (mmm) cc_final: 0.8414 (mmm) outliers start: 58 outliers final: 40 residues processed: 306 average time/residue: 0.1734 time to fit residues: 86.1502 Evaluate side-chains 295 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 178 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 337 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 465 HIS F 14 ASN G 171 GLN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.087287 restraints weight = 38134.606| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.65 r_work: 0.2808 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28476 Z= 0.140 Angle : 0.563 9.341 38692 Z= 0.301 Chirality : 0.045 0.201 3940 Planarity : 0.005 0.053 5132 Dihedral : 5.260 41.617 3878 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.67 % Allowed : 9.33 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3440 helix: 0.81 (0.21), residues: 644 sheet: -0.59 (0.20), residues: 708 loop : -1.30 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.016 0.001 TYR G 661 PHE 0.014 0.002 PHE B 53 TRP 0.016 0.001 TRP D 22 HIS 0.019 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00322 (28476) covalent geometry : angle 0.56315 (38692) hydrogen bonds : bond 0.03884 ( 880) hydrogen bonds : angle 4.70523 ( 2730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 1.017 Fit side-chains REVERT: A 294 TYR cc_start: 0.8036 (m-80) cc_final: 0.7456 (m-80) REVERT: A 418 THR cc_start: 0.8056 (p) cc_final: 0.7831 (p) REVERT: A 634 MET cc_start: 0.8860 (mmm) cc_final: 0.8311 (mmm) REVERT: B 116 MET cc_start: 0.8358 (mmm) cc_final: 0.7645 (mmm) REVERT: C 59 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7946 (mtpp) REVERT: C 200 SER cc_start: 0.8930 (p) cc_final: 0.8699 (m) REVERT: C 622 MET cc_start: 0.9252 (mmp) cc_final: 0.8894 (mmp) REVERT: C 698 MET cc_start: 0.8203 (mtt) cc_final: 0.7900 (mtt) REVERT: D 32 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8085 (mttm) REVERT: D 36 ASP cc_start: 0.7470 (m-30) cc_final: 0.7072 (m-30) REVERT: D 53 PHE cc_start: 0.9133 (m-80) cc_final: 0.8720 (m-80) REVERT: D 75 THR cc_start: 0.7901 (p) cc_final: 0.7633 (t) REVERT: E 69 ARG cc_start: 0.7805 (ptt180) cc_final: 0.7486 (ptt180) REVERT: E 200 SER cc_start: 0.8922 (p) cc_final: 0.8691 (m) REVERT: E 343 GLU cc_start: 0.8139 (tt0) cc_final: 0.7927 (tt0) REVERT: E 698 MET cc_start: 0.7948 (mmt) cc_final: 0.7724 (mtt) REVERT: F 32 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8095 (mttm) REVERT: F 36 ASP cc_start: 0.7469 (m-30) cc_final: 0.7024 (m-30) REVERT: F 53 PHE cc_start: 0.9120 (m-80) cc_final: 0.8645 (m-80) REVERT: F 75 THR cc_start: 0.7900 (p) cc_final: 0.7622 (t) REVERT: G 294 TYR cc_start: 0.8042 (m-80) cc_final: 0.7457 (m-80) REVERT: G 634 MET cc_start: 0.8879 (mmm) cc_final: 0.8333 (mmm) outliers start: 48 outliers final: 38 residues processed: 309 average time/residue: 0.1716 time to fit residues: 86.3905 Evaluate side-chains 292 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 237 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** G 486 ASN ** 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 = 0.3252 r_free = 0.3252 target = 0.110555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.086752 restraints weight = 38224.099| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.65 r_work: 0.2797 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28476 Z= 0.184 Angle : 0.578 9.252 38692 Z= 0.307 Chirality : 0.047 0.207 3940 Planarity : 0.005 0.054 5132 Dihedral : 5.216 40.597 3878 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.74 % Allowed : 9.23 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3440 helix: 0.89 (0.21), residues: 644 sheet: -0.56 (0.19), residues: 720 loop : -1.24 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 306 TYR 0.018 0.001 TYR A 661 PHE 0.014 0.002 PHE G 187 TRP 0.016 0.001 TRP D 22 HIS 0.005 0.001 HIS G 465 Details of bonding type rmsd covalent geometry : bond 0.00438 (28476) covalent geometry : angle 0.57795 (38692) hydrogen bonds : bond 0.03945 ( 880) hydrogen bonds : angle 4.67508 ( 2730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 1.049 Fit side-chains REVERT: A 294 TYR cc_start: 0.8042 (m-80) cc_final: 0.7475 (m-80) REVERT: A 634 MET cc_start: 0.8885 (mmm) cc_final: 0.8286 (mmm) REVERT: A 698 MET cc_start: 0.8711 (mtp) cc_final: 0.8489 (mtt) REVERT: B 116 MET cc_start: 0.8276 (mmm) cc_final: 0.8022 (mmm) REVERT: C 59 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8046 (mtpp) REVERT: C 200 SER cc_start: 0.8939 (p) cc_final: 0.8703 (m) REVERT: C 698 MET cc_start: 0.8217 (mtt) cc_final: 0.7910 (mtt) REVERT: D 32 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8092 (mttm) REVERT: D 36 ASP cc_start: 0.7482 (m-30) cc_final: 0.7031 (m-30) REVERT: D 53 PHE cc_start: 0.9102 (m-80) cc_final: 0.8613 (m-80) REVERT: D 75 THR cc_start: 0.7879 (p) cc_final: 0.7609 (t) REVERT: E 69 ARG cc_start: 0.7825 (ptt180) cc_final: 0.7515 (ptt180) REVERT: E 200 SER cc_start: 0.8940 (p) cc_final: 0.8702 (m) REVERT: E 343 GLU cc_start: 0.8168 (tt0) cc_final: 0.7968 (tt0) REVERT: E 403 GLN cc_start: 0.8437 (mt0) cc_final: 0.8157 (mt0) REVERT: F 32 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8092 (mttm) REVERT: F 36 ASP cc_start: 0.7483 (m-30) cc_final: 0.7034 (m-30) REVERT: F 53 PHE cc_start: 0.9107 (m-80) cc_final: 0.8632 (m-80) REVERT: F 75 THR cc_start: 0.7897 (p) cc_final: 0.7615 (t) REVERT: G 294 TYR cc_start: 0.8069 (m-80) cc_final: 0.7490 (m-80) REVERT: G 634 MET cc_start: 0.8903 (mmm) cc_final: 0.8299 (mmm) REVERT: H 116 MET cc_start: 0.8484 (mmm) cc_final: 0.8096 (mmm) outliers start: 50 outliers final: 42 residues processed: 301 average time/residue: 0.1664 time to fit residues: 81.8920 Evaluate side-chains 295 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 339 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 251 optimal weight: 0.0970 chunk 133 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.087392 restraints weight = 38003.019| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.64 r_work: 0.2807 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28476 Z= 0.165 Angle : 0.565 11.158 38692 Z= 0.299 Chirality : 0.046 0.205 3940 Planarity : 0.005 0.053 5132 Dihedral : 5.127 39.969 3878 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.53 % Allowed : 9.51 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3440 helix: 0.97 (0.21), residues: 644 sheet: -0.54 (0.19), residues: 720 loop : -1.21 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 306 TYR 0.017 0.001 TYR G 661 PHE 0.013 0.002 PHE G 187 TRP 0.016 0.001 TRP F 22 HIS 0.005 0.001 HIS G 465 Details of bonding type rmsd covalent geometry : bond 0.00392 (28476) covalent geometry : angle 0.56476 (38692) hydrogen bonds : bond 0.03825 ( 880) hydrogen bonds : angle 4.61619 ( 2730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 0.872 Fit side-chains REVERT: A 294 TYR cc_start: 0.8041 (m-80) cc_final: 0.7460 (m-80) REVERT: A 634 MET cc_start: 0.8870 (mmm) cc_final: 0.8265 (mmm) REVERT: B 116 MET cc_start: 0.8232 (mmm) cc_final: 0.8031 (mmm) REVERT: C 59 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8057 (mtpp) REVERT: C 200 SER cc_start: 0.8910 (p) cc_final: 0.8678 (m) REVERT: C 698 MET cc_start: 0.8212 (mtt) cc_final: 0.7919 (mtt) REVERT: D 32 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8081 (mttm) REVERT: D 36 ASP cc_start: 0.7468 (m-30) cc_final: 0.7016 (m-30) REVERT: D 53 PHE cc_start: 0.9114 (m-80) cc_final: 0.8656 (m-80) REVERT: D 75 THR cc_start: 0.7880 (p) cc_final: 0.7608 (t) REVERT: E 69 ARG cc_start: 0.7825 (ptt180) cc_final: 0.7498 (ptt180) REVERT: E 200 SER cc_start: 0.8929 (p) cc_final: 0.8699 (m) REVERT: E 343 GLU cc_start: 0.8186 (tt0) cc_final: 0.7981 (tt0) REVERT: E 403 GLN cc_start: 0.8447 (mt0) cc_final: 0.8184 (mt0) REVERT: E 698 MET cc_start: 0.8134 (mtt) cc_final: 0.7867 (mtt) REVERT: F 32 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8085 (mttm) REVERT: F 36 ASP cc_start: 0.7466 (m-30) cc_final: 0.7015 (m-30) REVERT: F 53 PHE cc_start: 0.9089 (m-80) cc_final: 0.8586 (m-80) REVERT: F 75 THR cc_start: 0.7881 (p) cc_final: 0.7607 (t) REVERT: F 116 MET cc_start: 0.8042 (mtp) cc_final: 0.7666 (mtp) REVERT: G 294 TYR cc_start: 0.8074 (m-80) cc_final: 0.7490 (m-80) REVERT: G 634 MET cc_start: 0.8889 (mmm) cc_final: 0.8294 (mmm) REVERT: H 116 MET cc_start: 0.8397 (mmm) cc_final: 0.8049 (mmm) outliers start: 44 outliers final: 39 residues processed: 296 average time/residue: 0.1778 time to fit residues: 85.7911 Evaluate side-chains 294 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 287 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 263 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.084834 restraints weight = 38278.339| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.64 r_work: 0.2770 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 28476 Z= 0.282 Angle : 0.647 11.381 38692 Z= 0.341 Chirality : 0.050 0.216 3940 Planarity : 0.005 0.054 5132 Dihedral : 5.431 41.348 3878 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.60 % Allowed : 9.51 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3440 helix: 0.83 (0.21), residues: 644 sheet: -0.57 (0.19), residues: 720 loop : -1.25 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 109 TYR 0.024 0.002 TYR G 661 PHE 0.019 0.002 PHE G 187 TRP 0.014 0.002 TRP A 331 HIS 0.007 0.002 HIS G 582 Details of bonding type rmsd covalent geometry : bond 0.00675 (28476) covalent geometry : angle 0.64698 (38692) hydrogen bonds : bond 0.04324 ( 880) hydrogen bonds : angle 4.83272 ( 2730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 1.024 Fit side-chains REVERT: A 294 TYR cc_start: 0.8082 (m-80) cc_final: 0.7517 (m-80) REVERT: A 634 MET cc_start: 0.8910 (mmm) cc_final: 0.8295 (mmm) REVERT: B 116 MET cc_start: 0.8303 (mmm) cc_final: 0.7815 (mmm) REVERT: C 200 SER cc_start: 0.8924 (p) cc_final: 0.8695 (m) REVERT: C 622 MET cc_start: 0.9274 (mmp) cc_final: 0.8915 (mmp) REVERT: C 698 MET cc_start: 0.8306 (mtt) cc_final: 0.8018 (mtt) REVERT: D 32 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8155 (mttm) REVERT: D 36 ASP cc_start: 0.7489 (m-30) cc_final: 0.7083 (m-30) REVERT: D 75 THR cc_start: 0.7897 (p) cc_final: 0.7637 (t) REVERT: E 69 ARG cc_start: 0.7836 (ptt180) cc_final: 0.7579 (ptt180) REVERT: E 200 SER cc_start: 0.8924 (p) cc_final: 0.8688 (m) REVERT: E 403 GLN cc_start: 0.8451 (mt0) cc_final: 0.8140 (mt0) REVERT: F 32 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8161 (mttm) REVERT: F 36 ASP cc_start: 0.7523 (m-30) cc_final: 0.7119 (m-30) REVERT: F 75 THR cc_start: 0.7885 (p) cc_final: 0.7613 (t) REVERT: G 294 TYR cc_start: 0.8078 (m-80) cc_final: 0.7509 (m-80) REVERT: G 634 MET cc_start: 0.8920 (mmm) cc_final: 0.8302 (mmm) REVERT: H 116 MET cc_start: 0.8470 (mmm) cc_final: 0.8142 (mmm) outliers start: 46 outliers final: 39 residues processed: 295 average time/residue: 0.1665 time to fit residues: 80.4837 Evaluate side-chains 288 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 218 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 305 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 115 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 212 optimal weight: 0.0270 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 HIS C 488 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 HIS E 488 ASN G 171 GLN G 424 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.090249 restraints weight = 37762.702| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.65 r_work: 0.2853 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 28476 Z= 0.100 Angle : 0.525 10.357 38692 Z= 0.278 Chirality : 0.044 0.199 3940 Planarity : 0.004 0.053 5132 Dihedral : 4.865 37.820 3878 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.91 % Allowed : 10.38 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3440 helix: 1.13 (0.21), residues: 644 sheet: -0.61 (0.20), residues: 688 loop : -1.12 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.015 0.001 TYR E 661 PHE 0.011 0.001 PHE B 25 TRP 0.020 0.001 TRP D 22 HIS 0.006 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00225 (28476) covalent geometry : angle 0.52451 (38692) hydrogen bonds : bond 0.03427 ( 880) hydrogen bonds : angle 4.43646 ( 2730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5862.57 seconds wall clock time: 101 minutes 20.85 seconds (6080.85 seconds total)