Starting phenix.real_space_refine on Wed Nov 19 20:55:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lvd_0990/11_2025/6lvd_0990.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lvd_0990/11_2025/6lvd_0990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lvd_0990/11_2025/6lvd_0990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lvd_0990/11_2025/6lvd_0990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lvd_0990/11_2025/6lvd_0990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lvd_0990/11_2025/6lvd_0990.map" } resolution = 3.2 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 17444 2.51 5 N 4836 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "H" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.10, per 1000 atoms: 0.22 Number of scatterers: 27628 At special positions: 0 Unit cell: (120.91, 155.15, 104.86, 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 5252 8.00 N 4836 7.00 C 17444 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 21.2% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.675A pdb=" N GLN A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 327' Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.656A pdb=" N TYR A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.652A pdb=" N LEU A 461 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 462 " --> pdb=" O MET A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 462' Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.356A 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: 3.883A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.633A pdb=" N ALA A 597 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 4.012A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 691 removed outlier: 3.831A pdb=" N LYS A 691 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.645A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 731 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.517A pdb=" N ILE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 41 Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.277A pdb=" N GLU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 72 through 78 removed outlier: 6.264A pdb=" N THR B 75 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.770A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.698A pdb=" N TYR C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.886A pdb=" N VAL C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 428 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 488 removed outlier: 4.376A 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: 4.127A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 537 removed outlier: 3.773A 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 605 removed outlier: 3.975A pdb=" N ILE C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 732 removed outlier: 4.341A pdb=" N GLY C 731 " --> pdb=" O ILE C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'D' and resid 19 through 41 Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.508A pdb=" N ALA D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 258 Processing helix chain 'E' and resid 323 through 327 removed outlier: 3.705A pdb=" N TYR E 327 " --> pdb=" O PRO E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 399 Processing helix chain 'E' and resid 422 through 431 removed outlier: 3.920A pdb=" N VAL E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 428 " --> pdb=" O ASN E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 488 removed outlier: 3.518A pdb=" N ASP E 478 " --> pdb=" O GLU E 474 " (cutoff:3.500A) removed outlier: 4.285A 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: 4.127A pdb=" N LEU E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 537 removed outlier: 3.769A 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 605 removed outlier: 3.971A pdb=" N ILE E 603 " --> pdb=" O ALA E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 754 Processing helix chain 'F' and resid 19 through 41 Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 111 through 130 removed outlier: 3.597A pdb=" N ALA F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 258 Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 323 through 327 removed outlier: 3.677A pdb=" N GLN G 326 " --> pdb=" O CYS G 323 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR G 327 " --> pdb=" O PRO G 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 323 through 327' Processing helix chain 'G' and resid 392 through 399 removed outlier: 3.672A pdb=" N TYR G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 431 Processing helix chain 'G' and resid 432 through 435 Processing helix chain 'G' and resid 458 through 462 removed outlier: 3.566A pdb=" N LEU G 461 " --> pdb=" O ILE G 458 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG G 462 " --> pdb=" O MET G 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 458 through 462' Processing helix chain 'G' and resid 473 through 488 removed outlier: 3.676A pdb=" N ALA G 477 " --> pdb=" O TRP G 473 " (cutoff:3.500A) removed outlier: 4.470A 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: 3.881A pdb=" N LEU G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 536 Processing helix chain 'G' and resid 593 through 597 removed outlier: 3.638A pdb=" N ALA G 597 " --> pdb=" O ARG G 594 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 604 removed outlier: 3.999A pdb=" N ILE G 603 " --> pdb=" O ALA G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 688 through 691 removed outlier: 3.800A pdb=" N LYS G 691 " --> pdb=" O PRO G 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 688 through 691' Processing helix chain 'G' and resid 726 through 730 removed outlier: 3.807A pdb=" N TRP G 729 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 730 " --> pdb=" O ILE G 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 726 through 730' Processing helix chain 'G' and resid 740 through 754 removed outlier: 3.520A pdb=" N ILE G 754 " --> pdb=" O LEU G 750 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 15 Processing helix chain 'H' and resid 19 through 41 Processing helix chain 'H' and resid 42 through 51 removed outlier: 4.284A pdb=" N GLU H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 Processing helix chain 'H' and resid 72 through 78 removed outlier: 6.258A pdb=" N THR H 75 " --> pdb=" O MET H 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.776A pdb=" N ALA H 115 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.679A pdb=" N PHE A 346 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.015A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 360 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 36 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 64 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.345A pdb=" N LYS A 54 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 360 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 148 removed outlier: 3.515A pdb=" N GLY A 123 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 148 removed outlier: 3.515A pdb=" N GLY A 123 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.603A 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: 6.528A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 658 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE A 611 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR A 656 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N PHE A 613 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 13.620A pdb=" N GLY A 654 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.528A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.743A 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 'A' and resid 522 through 523 Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.579A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.990A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 54 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.990A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 64 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.989A pdb=" N SER C 122 " --> pdb=" O TRP C 116 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP C 116 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TRP C 124 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER C 114 " --> pdb=" O TRP C 124 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 126 " --> pdb=" O ILE C 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 202 removed outlier: 4.759A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 197 through 202 removed outlier: 4.759A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.290A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 12.441A pdb=" N PHE C 611 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 12.381A pdb=" N ARG C 660 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 11.796A pdb=" N PHE C 613 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N LEU C 658 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N HIS C 615 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR C 656 " --> pdb=" O HIS C 615 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.290A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AC2, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 522 through 523 Processing sheet with id=AC4, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.581A pdb=" N PHE E 346 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.993A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU E 38 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 54 " --> pdb=" O ILE E 42 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.993A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 64 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.985A pdb=" N SER E 122 " --> pdb=" O TRP E 116 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP E 116 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TRP E 124 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER E 114 " --> pdb=" O TRP E 124 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU E 126 " --> pdb=" O ILE E 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 197 through 202 removed outlier: 4.765A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 197 through 202 removed outlier: 4.765A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.262A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 12.471A pdb=" N PHE E 611 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 12.439A pdb=" N ARG E 660 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N PHE E 613 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N LEU E 658 " --> pdb=" O PHE E 613 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS E 615 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR E 656 " --> pdb=" O HIS E 615 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.262A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE E 611 " --> pdb=" O THR E 685 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 420 through 421 Processing sheet with id=AD4, first strand: chain 'E' and resid 451 through 453 Processing sheet with id=AD5, first strand: chain 'E' and resid 522 through 523 Processing sheet with id=AD6, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.676A pdb=" N PHE G 346 " --> pdb=" O PHE G 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 14 through 15 removed outlier: 5.067A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 360 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 33 through 36 removed outlier: 3.568A pdb=" N GLY G 64 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 145 through 148 removed outlier: 3.509A pdb=" N GLY G 123 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL G 239 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TRP G 101 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA G 241 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE G 99 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 145 through 148 removed outlier: 3.509A pdb=" N GLY G 123 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 330 " --> pdb=" O VAL G 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.543A pdb=" N ILE G 387 " --> pdb=" O ASP G 493 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA G 495 " --> pdb=" O ILE G 387 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL G 389 " --> pdb=" O ALA G 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL G 514 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 420 through 421 removed outlier: 3.515A pdb=" N TYR H 80 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 451 through 453 Processing sheet with id=AE5, first strand: chain 'G' and resid 522 through 523 Processing sheet with id=AE6, first strand: chain 'G' and resid 657 through 660 removed outlier: 6.697A pdb=" N LEU G 658 " --> pdb=" O SER G 609 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2697 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: 6.87 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8905 1.33 - 1.45: 5400 1.45 - 1.57: 13951 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28412 Sorted by residual: bond pdb=" CG1 ILE G 161 " pdb=" CD1 ILE G 161 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.60e+00 bond pdb=" CG1 ILE A 161 " pdb=" CD1 ILE A 161 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.57e+00 bond pdb=" C LEU C 461 " pdb=" N ARG C 462 " ideal model delta sigma weight residual 1.329 1.295 0.034 1.60e-02 3.91e+03 4.40e+00 bond pdb=" CG LEU C 330 " pdb=" CD1 LEU C 330 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.90e+00 bond pdb=" CG1 ILE G 244 " pdb=" CD1 ILE G 244 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.76e+00 ... (remaining 28407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 36300 1.77 - 3.53: 1923 3.53 - 5.30: 298 5.30 - 7.07: 57 7.07 - 8.84: 18 Bond angle restraints: 38596 Sorted by residual: angle pdb=" N GLY C 548 " pdb=" CA GLY C 548 " pdb=" C GLY C 548 " ideal model delta sigma weight residual 112.77 119.46 -6.69 1.28e+00 6.10e-01 2.73e+01 angle pdb=" C GLY A 655 " pdb=" N TYR A 656 " pdb=" CA TYR A 656 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C GLY E 655 " pdb=" N TYR E 656 " pdb=" CA TYR E 656 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C GLY C 655 " pdb=" N TYR C 656 " pdb=" CA TYR C 656 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" CA TYR C 522 " pdb=" CB TYR C 522 " pdb=" CG TYR C 522 " ideal model delta sigma weight residual 113.90 121.43 -7.53 1.80e+00 3.09e-01 1.75e+01 ... (remaining 38591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 15676 15.40 - 30.81: 735 30.81 - 46.21: 110 46.21 - 61.62: 9 61.62 - 77.02: 6 Dihedral angle restraints: 16536 sinusoidal: 6628 harmonic: 9908 Sorted by residual: dihedral pdb=" CA ASN G 547 " pdb=" C ASN G 547 " pdb=" N GLY G 548 " pdb=" CA GLY G 548 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ASN E 547 " pdb=" C ASN E 547 " pdb=" N GLY E 548 " pdb=" CA GLY E 548 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLY A 579 " pdb=" C GLY A 579 " pdb=" N GLU A 580 " pdb=" CA GLU A 580 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 16533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3441 0.092 - 0.184: 446 0.184 - 0.276: 21 0.276 - 0.368: 4 0.368 - 0.460: 4 Chirality restraints: 3916 Sorted by residual: 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 2.18 0.46 2.00e-01 2.50e+01 5.30e+00 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 2.19 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CB ILE C 283 " pdb=" CA ILE C 283 " pdb=" CG1 ILE C 283 " pdb=" CG2 ILE C 283 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 3913 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 331 " -0.021 2.00e-02 2.50e+03 1.99e-02 9.85e+00 pdb=" CG TRP A 331 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 331 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 331 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 331 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 331 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 331 " -0.007 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 " -0.019 2.00e-02 2.50e+03 1.87e-02 8.75e+00 pdb=" CG TRP G 331 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP G 331 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP G 331 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 331 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 331 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 331 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 331 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 331 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 656 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C TYR C 656 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR C 656 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU C 657 " -0.016 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4726 2.76 - 3.29: 23782 3.29 - 3.83: 46353 3.83 - 4.36: 57039 4.36 - 4.90: 99884 Nonbonded interactions: 231784 Sorted by model distance: nonbonded pdb=" O ILE E 552 " pdb=" OH TYR E 583 " model vdw 2.223 3.040 nonbonded pdb=" O ILE C 552 " pdb=" OH TYR C 583 " model vdw 2.227 3.040 nonbonded pdb=" O HIS G 615 " pdb=" OH TYR G 684 " model vdw 2.246 3.040 nonbonded pdb=" O HIS C 615 " pdb=" OH TYR C 684 " model vdw 2.246 3.040 nonbonded pdb=" O HIS A 615 " pdb=" OH TYR A 684 " model vdw 2.248 3.040 ... (remaining 231779 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.510 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.009 0.100 28412 Z= 0.390 Angle : 0.925 8.837 38596 Z= 0.519 Chirality : 0.061 0.460 3916 Planarity : 0.008 0.061 5116 Dihedral : 9.355 77.019 10248 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.31 % Allowed : 1.29 % Favored : 98.40 % 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: -3.48 (0.11), residues: 3424 helix: -2.37 (0.15), residues: 592 sheet: -1.93 (0.19), residues: 652 loop : -2.52 (0.10), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 109 TYR 0.045 0.004 TYR G 684 PHE 0.032 0.004 PHE A 332 TRP 0.052 0.004 TRP A 331 HIS 0.017 0.003 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00939 (28412) covalent geometry : angle 0.92513 (38596) hydrogen bonds : bond 0.22682 ( 817) hydrogen bonds : angle 9.04949 ( 2697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 476 time to evaluate : 1.005 Fit side-chains REVERT: B 51 ASN cc_start: 0.7958 (t0) cc_final: 0.7757 (t0) REVERT: B 112 GLU cc_start: 0.8370 (pt0) cc_final: 0.8041 (pm20) REVERT: C 65 GLN cc_start: 0.8246 (mt0) cc_final: 0.7997 (mt0) REVERT: C 425 ASP cc_start: 0.7864 (m-30) cc_final: 0.7597 (m-30) REVERT: C 474 GLU cc_start: 0.7730 (mp0) cc_final: 0.7472 (mp0) REVERT: C 642 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7881 (mtt180) REVERT: D 31 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7570 (mpp80) REVERT: D 110 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8232 (mmtm) REVERT: E 65 GLN cc_start: 0.8241 (mt0) cc_final: 0.7990 (mt0) REVERT: E 425 ASP cc_start: 0.7826 (m-30) cc_final: 0.7558 (m-30) REVERT: F 31 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7664 (mpp80) REVERT: F 110 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8221 (mmtm) REVERT: H 51 ASN cc_start: 0.8041 (t0) cc_final: 0.7826 (t0) REVERT: H 113 GLU cc_start: 0.8735 (mp0) cc_final: 0.8424 (mp0) outliers start: 9 outliers final: 2 residues processed: 485 average time/residue: 0.2157 time to fit residues: 158.1739 Evaluate side-chains 278 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain G residue 553 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 121 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN C 171 GLN C 403 GLN C 424 ASN C 699 ASN E 171 GLN E 322 HIS E 403 GLN E 424 ASN E 519 HIS E 699 ASN G 121 GLN G 403 GLN G 480 HIS H 68 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.087208 restraints weight = 41620.018| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.75 r_work: 0.2842 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28412 Z= 0.145 Angle : 0.578 6.939 38596 Z= 0.315 Chirality : 0.045 0.201 3916 Planarity : 0.005 0.046 5116 Dihedral : 5.556 51.308 3858 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.26 % Allowed : 4.50 % Favored : 94.25 % 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: -2.40 (0.12), residues: 3424 helix: -0.44 (0.19), residues: 604 sheet: -1.44 (0.20), residues: 608 loop : -2.08 (0.11), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 78 TYR 0.020 0.001 TYR C 661 PHE 0.015 0.002 PHE C 332 TRP 0.020 0.001 TRP B 22 HIS 0.005 0.001 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00329 (28412) covalent geometry : angle 0.57753 (38596) hydrogen bonds : bond 0.04694 ( 817) hydrogen bonds : angle 5.50362 ( 2697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 331 time to evaluate : 1.090 Fit side-chains REVERT: B 112 GLU cc_start: 0.8561 (pt0) cc_final: 0.7913 (pm20) REVERT: C 425 ASP cc_start: 0.8451 (m-30) cc_final: 0.8167 (m-30) REVERT: C 563 MET cc_start: 0.8825 (ttp) cc_final: 0.8204 (ttt) REVERT: D 37 ILE cc_start: 0.8313 (mt) cc_final: 0.8085 (mp) REVERT: D 110 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8333 (mmtm) REVERT: E 425 ASP cc_start: 0.8413 (m-30) cc_final: 0.7958 (m-30) REVERT: F 37 ILE cc_start: 0.8446 (mt) cc_final: 0.8236 (mp) REVERT: F 80 TYR cc_start: 0.8137 (m-80) cc_final: 0.7852 (m-80) REVERT: F 110 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8348 (mmtm) outliers start: 36 outliers final: 22 residues processed: 351 average time/residue: 0.2016 time to fit residues: 108.7831 Evaluate side-chains 273 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 304 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 338 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 334 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.099272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.080735 restraints weight = 42645.120| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.87 r_work: 0.2729 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 28412 Z= 0.262 Angle : 0.619 6.273 38596 Z= 0.333 Chirality : 0.048 0.199 3916 Planarity : 0.005 0.048 5116 Dihedral : 5.495 52.667 3858 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.67 % Allowed : 6.28 % Favored : 92.05 % 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: -1.95 (0.13), residues: 3424 helix: 0.45 (0.20), residues: 604 sheet: -1.24 (0.20), residues: 608 loop : -1.91 (0.11), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 31 TYR 0.028 0.002 TYR C 661 PHE 0.015 0.002 PHE G 332 TRP 0.018 0.002 TRP G 101 HIS 0.009 0.002 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00626 (28412) covalent geometry : angle 0.61855 (38596) hydrogen bonds : bond 0.04772 ( 817) hydrogen bonds : angle 5.13090 ( 2697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 1.040 Fit side-chains REVERT: A 1 MET cc_start: 0.8213 (mtm) cc_final: 0.7906 (mtt) REVERT: B 112 GLU cc_start: 0.8564 (pt0) cc_final: 0.7958 (pm20) REVERT: C 59 LYS cc_start: 0.8589 (tptt) cc_final: 0.8373 (tptp) REVERT: C 425 ASP cc_start: 0.8543 (m-30) cc_final: 0.8217 (m-30) REVERT: D 37 ILE cc_start: 0.8346 (mt) cc_final: 0.8068 (mp) REVERT: D 110 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8369 (mmtm) REVERT: E 59 LYS cc_start: 0.8658 (tptt) cc_final: 0.8446 (tptp) REVERT: E 425 ASP cc_start: 0.8559 (m-30) cc_final: 0.8076 (m-30) REVERT: E 689 ASP cc_start: 0.7929 (m-30) cc_final: 0.7682 (m-30) REVERT: F 37 ILE cc_start: 0.8447 (mt) cc_final: 0.8164 (mp) REVERT: F 80 TYR cc_start: 0.8171 (m-80) cc_final: 0.7960 (m-80) REVERT: F 110 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8337 (mmtm) REVERT: G 628 GLU cc_start: 0.8402 (pm20) cc_final: 0.7960 (tp30) outliers start: 48 outliers final: 38 residues processed: 291 average time/residue: 0.2050 time to fit residues: 92.2261 Evaluate side-chains 282 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 230 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 273 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 321 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.081617 restraints weight = 42360.294| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.84 r_work: 0.2756 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28412 Z= 0.163 Angle : 0.540 5.965 38596 Z= 0.291 Chirality : 0.045 0.182 3916 Planarity : 0.005 0.051 5116 Dihedral : 5.150 53.898 3858 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.46 % Allowed : 6.94 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.13), residues: 3424 helix: 1.07 (0.21), residues: 608 sheet: -0.89 (0.21), residues: 576 loop : -1.73 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 31 TYR 0.020 0.001 TYR E 661 PHE 0.016 0.002 PHE G 611 TRP 0.017 0.001 TRP B 22 HIS 0.006 0.001 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00385 (28412) covalent geometry : angle 0.53986 (38596) hydrogen bonds : bond 0.03985 ( 817) hydrogen bonds : angle 4.70790 ( 2697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 1.072 Fit side-chains REVERT: A 1 MET cc_start: 0.8184 (mtm) cc_final: 0.7959 (mtt) REVERT: A 634 MET cc_start: 0.8514 (mmm) cc_final: 0.8203 (mmm) REVERT: B 112 GLU cc_start: 0.8488 (pt0) cc_final: 0.7884 (pm20) REVERT: C 35 ASP cc_start: 0.7875 (m-30) cc_final: 0.7659 (t70) REVERT: C 59 LYS cc_start: 0.8586 (tptt) cc_final: 0.8351 (tptp) REVERT: C 425 ASP cc_start: 0.8533 (m-30) cc_final: 0.8191 (m-30) REVERT: D 37 ILE cc_start: 0.8452 (mt) cc_final: 0.8241 (mt) REVERT: D 110 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8341 (mmtm) REVERT: E 35 ASP cc_start: 0.7863 (m-30) cc_final: 0.7643 (t70) REVERT: E 59 LYS cc_start: 0.8656 (tptt) cc_final: 0.8430 (tptp) REVERT: E 425 ASP cc_start: 0.8524 (m-30) cc_final: 0.8180 (m-30) REVERT: E 689 ASP cc_start: 0.7885 (m-30) cc_final: 0.7667 (m-30) REVERT: F 37 ILE cc_start: 0.8461 (mt) cc_final: 0.8260 (mt) REVERT: F 110 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8380 (mmtm) REVERT: G 628 GLU cc_start: 0.8420 (pm20) cc_final: 0.8003 (tp30) REVERT: G 634 MET cc_start: 0.8545 (mmm) cc_final: 0.8192 (mmm) outliers start: 42 outliers final: 37 residues processed: 282 average time/residue: 0.2060 time to fit residues: 91.0204 Evaluate side-chains 274 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 355 LYS Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 162 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 241 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 263 optimal weight: 0.0970 chunk 112 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 523 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.083012 restraints weight = 42048.423| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.83 r_work: 0.2760 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 28412 Z= 0.150 Angle : 0.524 6.143 38596 Z= 0.281 Chirality : 0.045 0.178 3916 Planarity : 0.004 0.052 5116 Dihedral : 4.986 54.109 3858 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.64 % Allowed : 7.11 % Favored : 91.25 % 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: -1.27 (0.13), residues: 3424 helix: 1.44 (0.21), residues: 608 sheet: -0.76 (0.22), residues: 576 loop : -1.62 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 341 TYR 0.019 0.001 TYR C 661 PHE 0.012 0.002 PHE E 713 TRP 0.015 0.001 TRP B 22 HIS 0.005 0.001 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00355 (28412) covalent geometry : angle 0.52389 (38596) hydrogen bonds : bond 0.03824 ( 817) hydrogen bonds : angle 4.53500 ( 2697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 1.248 Fit side-chains REVERT: A 371 TYR cc_start: 0.8923 (m-80) cc_final: 0.8692 (m-80) REVERT: A 634 MET cc_start: 0.8500 (mmm) cc_final: 0.8198 (mmm) REVERT: A 721 MET cc_start: 0.8871 (tpt) cc_final: 0.8628 (tpt) REVERT: B 15 TYR cc_start: 0.8768 (m-80) cc_final: 0.8530 (m-80) REVERT: B 112 GLU cc_start: 0.8445 (pt0) cc_final: 0.7856 (pm20) REVERT: C 425 ASP cc_start: 0.8511 (m-30) cc_final: 0.8308 (m-30) REVERT: C 659 ASP cc_start: 0.8649 (m-30) cc_final: 0.8317 (m-30) REVERT: D 37 ILE cc_start: 0.8436 (mt) cc_final: 0.8210 (mt) REVERT: D 110 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8354 (mmtm) REVERT: E 59 LYS cc_start: 0.8706 (tptt) cc_final: 0.8453 (tptp) REVERT: E 425 ASP cc_start: 0.8522 (m-30) cc_final: 0.8313 (m-30) REVERT: F 37 ILE cc_start: 0.8434 (mt) cc_final: 0.8225 (mt) REVERT: F 110 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8384 (mmtm) REVERT: G 371 TYR cc_start: 0.8917 (m-80) cc_final: 0.8696 (m-80) REVERT: G 628 GLU cc_start: 0.8406 (pm20) cc_final: 0.8083 (tp30) REVERT: G 634 MET cc_start: 0.8526 (mmm) cc_final: 0.8177 (mmm) outliers start: 47 outliers final: 35 residues processed: 275 average time/residue: 0.2106 time to fit residues: 90.6625 Evaluate side-chains 270 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 355 LYS Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 331 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 333 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN C 171 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 523 GLN H 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.081930 restraints weight = 42117.466| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.74 r_work: 0.2713 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 28412 Z= 0.264 Angle : 0.602 6.112 38596 Z= 0.322 Chirality : 0.048 0.194 3916 Planarity : 0.005 0.053 5116 Dihedral : 5.247 51.479 3858 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.60 % Allowed : 7.50 % Favored : 90.90 % 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: -1.31 (0.13), residues: 3424 helix: 1.39 (0.21), residues: 608 sheet: -0.96 (0.20), residues: 616 loop : -1.59 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 123 TYR 0.025 0.002 TYR C 661 PHE 0.014 0.002 PHE A 154 TRP 0.018 0.002 TRP A 101 HIS 0.009 0.001 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00629 (28412) covalent geometry : angle 0.60211 (38596) hydrogen bonds : bond 0.04425 ( 817) hydrogen bonds : angle 4.73296 ( 2697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 1.219 Fit side-chains REVERT: A 474 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 634 MET cc_start: 0.8576 (mmm) cc_final: 0.8313 (mmm) REVERT: A 721 MET cc_start: 0.8994 (tpt) cc_final: 0.8790 (tpt) REVERT: B 112 GLU cc_start: 0.8447 (pt0) cc_final: 0.7861 (pm20) REVERT: C 549 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8322 (mtp) REVERT: D 110 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8379 (mmtm) REVERT: E 425 ASP cc_start: 0.8559 (m-30) cc_final: 0.8357 (m-30) REVERT: F 37 ILE cc_start: 0.8442 (mt) cc_final: 0.8192 (mp) REVERT: F 110 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8419 (mmtm) REVERT: G 371 TYR cc_start: 0.8941 (m-80) cc_final: 0.8713 (m-80) REVERT: G 628 GLU cc_start: 0.8371 (pm20) cc_final: 0.8106 (tp30) REVERT: G 634 MET cc_start: 0.8606 (mmm) cc_final: 0.8339 (mmm) outliers start: 46 outliers final: 36 residues processed: 278 average time/residue: 0.1990 time to fit residues: 87.2621 Evaluate side-chains 278 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 355 LYS Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 333 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 276 optimal weight: 0.4980 chunk 254 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 306 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN B 73 GLN C 171 GLN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 523 GLN H 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085975 restraints weight = 41479.161| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.74 r_work: 0.2868 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 28412 Z= 0.096 Angle : 0.492 6.433 38596 Z= 0.264 Chirality : 0.043 0.173 3916 Planarity : 0.004 0.054 5116 Dihedral : 4.769 55.414 3858 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.19 % Allowed : 8.26 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3424 helix: 1.77 (0.21), residues: 608 sheet: -0.62 (0.21), residues: 644 loop : -1.40 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 31 TYR 0.018 0.001 TYR A 661 PHE 0.015 0.001 PHE H 25 TRP 0.020 0.001 TRP D 22 HIS 0.003 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00215 (28412) covalent geometry : angle 0.49212 (38596) hydrogen bonds : bond 0.03354 ( 817) hydrogen bonds : angle 4.29640 ( 2697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 1.119 Fit side-chains REVERT: A 235 TYR cc_start: 0.8963 (t80) cc_final: 0.8698 (t80) REVERT: A 474 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 634 MET cc_start: 0.8457 (mmm) cc_final: 0.8257 (mmm) REVERT: B 15 TYR cc_start: 0.8747 (m-80) cc_final: 0.8517 (m-80) REVERT: B 112 GLU cc_start: 0.8276 (pt0) cc_final: 0.7735 (pm20) REVERT: C 206 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7534 (mtpp) REVERT: C 425 ASP cc_start: 0.8463 (m-30) cc_final: 0.7846 (m-30) REVERT: D 110 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8452 (mmtm) REVERT: E 425 ASP cc_start: 0.8410 (m-30) cc_final: 0.8050 (m-30) REVERT: F 37 ILE cc_start: 0.8339 (mt) cc_final: 0.8114 (mt) REVERT: F 110 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8436 (mmtm) REVERT: G 371 TYR cc_start: 0.8877 (m-80) cc_final: 0.8629 (m-80) REVERT: G 628 GLU cc_start: 0.8348 (pm20) cc_final: 0.8080 (tp30) REVERT: G 634 MET cc_start: 0.8548 (mmm) cc_final: 0.8298 (mmm) REVERT: H 15 TYR cc_start: 0.8721 (m-80) cc_final: 0.8506 (m-80) REVERT: H 110 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8339 (ptmm) outliers start: 34 outliers final: 30 residues processed: 281 average time/residue: 0.2042 time to fit residues: 90.4006 Evaluate side-chains 270 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 10 CYS Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 355 LYS Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 289 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 330 optimal weight: 8.9990 chunk 14 optimal weight: 0.0170 chunk 7 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 overall best weight: 3.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN B 73 GLN C 171 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 748 ASN H 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.097607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.079423 restraints weight = 42726.628| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.84 r_work: 0.2773 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 28412 Z= 0.243 Angle : 0.576 6.973 38596 Z= 0.307 Chirality : 0.047 0.185 3916 Planarity : 0.005 0.049 5116 Dihedral : 5.011 52.021 3858 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.71 % Allowed : 8.54 % Favored : 89.75 % 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: -1.06 (0.14), residues: 3424 helix: 1.66 (0.21), residues: 608 sheet: -0.79 (0.21), residues: 616 loop : -1.44 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 592 TYR 0.023 0.002 TYR C 661 PHE 0.012 0.002 PHE E 94 TRP 0.016 0.001 TRP A 101 HIS 0.008 0.001 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00580 (28412) covalent geometry : angle 0.57554 (38596) hydrogen bonds : bond 0.04093 ( 817) hydrogen bonds : angle 4.55460 ( 2697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 1.133 Fit side-chains REVERT: A 474 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: A 657 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 699 ASN cc_start: 0.8973 (m110) cc_final: 0.8649 (m-40) REVERT: B 112 GLU cc_start: 0.8401 (pt0) cc_final: 0.7792 (pm20) REVERT: C 425 ASP cc_start: 0.8528 (m-30) cc_final: 0.8293 (m-30) REVERT: C 640 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7761 (mm-30) REVERT: E 640 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7768 (mm-30) REVERT: F 37 ILE cc_start: 0.8333 (mt) cc_final: 0.8066 (mp) REVERT: F 110 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8537 (mmtm) REVERT: G 371 TYR cc_start: 0.8921 (m-80) cc_final: 0.8662 (m-80) REVERT: G 628 GLU cc_start: 0.8390 (pm20) cc_final: 0.8081 (tp30) REVERT: G 634 MET cc_start: 0.8580 (mmm) cc_final: 0.8336 (mmm) REVERT: G 699 ASN cc_start: 0.8972 (m110) cc_final: 0.8651 (m-40) REVERT: H 110 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8338 (ptmm) outliers start: 49 outliers final: 43 residues processed: 274 average time/residue: 0.2002 time to fit residues: 86.2662 Evaluate side-chains 285 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 10 CYS Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 355 LYS Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 245 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 297 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 337 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 280 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN C 486 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 HIS H 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.082176 restraints weight = 42277.873| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.84 r_work: 0.2803 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28412 Z= 0.135 Angle : 0.518 6.920 38596 Z= 0.277 Chirality : 0.044 0.173 3916 Planarity : 0.004 0.051 5116 Dihedral : 4.842 53.372 3858 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.46 % Allowed : 8.89 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3424 helix: 1.77 (0.21), residues: 612 sheet: -0.56 (0.22), residues: 568 loop : -1.32 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.018 0.001 TYR C 661 PHE 0.013 0.001 PHE B 25 TRP 0.017 0.001 TRP F 22 HIS 0.005 0.001 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00320 (28412) covalent geometry : angle 0.51781 (38596) hydrogen bonds : bond 0.03632 ( 817) hydrogen bonds : angle 4.37416 ( 2697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 1.002 Fit side-chains REVERT: A 474 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 699 ASN cc_start: 0.8954 (m110) cc_final: 0.8606 (m-40) REVERT: B 110 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8415 (ptmm) REVERT: B 112 GLU cc_start: 0.8309 (pt0) cc_final: 0.7762 (pm20) REVERT: C 425 ASP cc_start: 0.8495 (m-30) cc_final: 0.7864 (m-30) REVERT: C 640 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7754 (mm-30) REVERT: E 549 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8253 (mtp) REVERT: F 37 ILE cc_start: 0.8273 (mt) cc_final: 0.8070 (mt) REVERT: F 110 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8526 (mmtm) REVERT: G 371 TYR cc_start: 0.8903 (m-80) cc_final: 0.8671 (m-80) REVERT: G 628 GLU cc_start: 0.8306 (pm20) cc_final: 0.8035 (tp30) REVERT: G 699 ASN cc_start: 0.8939 (m110) cc_final: 0.8576 (m-40) REVERT: H 110 LYS cc_start: 0.8849 (mmtm) cc_final: 0.8375 (ptmm) outliers start: 42 outliers final: 39 residues processed: 275 average time/residue: 0.1992 time to fit residues: 86.6159 Evaluate side-chains 280 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 549 MET Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 10 CYS Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 322 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 323 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 296 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.100733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.083244 restraints weight = 42047.231| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.73 r_work: 0.2766 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28412 Z= 0.181 Angle : 0.543 6.934 38596 Z= 0.290 Chirality : 0.045 0.179 3916 Planarity : 0.004 0.050 5116 Dihedral : 4.905 52.065 3858 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.46 % Allowed : 9.00 % Favored : 89.54 % 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: -0.90 (0.14), residues: 3424 helix: 1.75 (0.21), residues: 612 sheet: -0.50 (0.22), residues: 536 loop : -1.36 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.020 0.001 TYR C 661 PHE 0.012 0.002 PHE C 713 TRP 0.014 0.001 TRP A 101 HIS 0.007 0.001 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00433 (28412) covalent geometry : angle 0.54339 (38596) hydrogen bonds : bond 0.03849 ( 817) hydrogen bonds : angle 4.44804 ( 2697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 0.891 Fit side-chains REVERT: A 474 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 15 TYR cc_start: 0.8772 (m-80) cc_final: 0.8521 (m-80) REVERT: B 110 LYS cc_start: 0.8818 (mmtm) cc_final: 0.8407 (ptmm) REVERT: B 112 GLU cc_start: 0.8249 (pt0) cc_final: 0.7722 (pm20) REVERT: C 425 ASP cc_start: 0.8498 (m-30) cc_final: 0.7860 (m-30) REVERT: C 640 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7733 (mm-30) REVERT: F 37 ILE cc_start: 0.8299 (mt) cc_final: 0.8095 (mt) REVERT: F 110 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8519 (mmtm) REVERT: G 371 TYR cc_start: 0.8887 (m-80) cc_final: 0.8626 (m-80) REVERT: G 628 GLU cc_start: 0.8304 (pm20) cc_final: 0.8030 (tp30) REVERT: H 15 TYR cc_start: 0.8783 (m-80) cc_final: 0.8558 (m-80) REVERT: H 110 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8374 (ptmm) outliers start: 42 outliers final: 39 residues processed: 271 average time/residue: 0.1917 time to fit residues: 82.6696 Evaluate side-chains 278 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 10 CYS Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 126 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 330 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.080610 restraints weight = 42396.846| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.93 r_work: 0.2781 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28412 Z= 0.139 Angle : 0.516 6.843 38596 Z= 0.276 Chirality : 0.044 0.175 3916 Planarity : 0.004 0.050 5116 Dihedral : 4.789 53.174 3858 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.50 % Allowed : 9.03 % Favored : 89.47 % 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: -0.76 (0.14), residues: 3424 helix: 1.85 (0.21), residues: 612 sheet: -0.51 (0.22), residues: 568 loop : -1.25 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.017 0.001 TYR C 661 PHE 0.013 0.001 PHE B 25 TRP 0.016 0.001 TRP F 22 HIS 0.005 0.001 HIS G 271 Details of bonding type rmsd covalent geometry : bond 0.00331 (28412) covalent geometry : angle 0.51635 (38596) hydrogen bonds : bond 0.03575 ( 817) hydrogen bonds : angle 4.32730 ( 2697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6265.44 seconds wall clock time: 108 minutes 17.27 seconds (6497.27 seconds total)