Starting phenix.real_space_refine on Mon Jul 6 02:10:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ptr_13634/07_2026/7ptr_13634.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ptr_13634/07_2026/7ptr_13634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ptr_13634/07_2026/7ptr_13634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ptr_13634/07_2026/7ptr_13634.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ptr_13634/07_2026/7ptr_13634.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ptr_13634/07_2026/7ptr_13634.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ptr_13634/07_2026/7ptr_13634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ptr_13634/07_2026/7ptr_13634.cif" } resolution = 3.46 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 18 9.91 5 S 30 5.16 5 C 19014 2.51 5 N 4998 2.21 5 O 7644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31704 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5248 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 15, 'TRANS': 709} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' CA': 3, 'BGC': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 6.43, per 1000 atoms: 0.20 Number of scatterers: 31704 At special positions: 0 Unit cell: (205.7, 227.7, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 18 19.99 S 30 16.00 O 7644 8.00 N 4998 7.00 C 19014 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7752 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 72 sheets defined 14.1% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.605A pdb=" N GLU A 83 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL A 369 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.657A pdb=" N ASP A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 477' Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 606 through 618 removed outlier: 3.684A pdb=" N GLY A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 616 " --> pdb=" O GLY A 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 636 Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 641 " --> pdb=" O GLU A 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 637 through 641' Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU B 83 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY B 149 " --> pdb=" O SER B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL B 369 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 454 through 461 Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.656A pdb=" N ASP B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 473 through 477' Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 526 Processing helix chain 'B' and resid 606 through 618 removed outlier: 3.685A pdb=" N GLY B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 613 " --> pdb=" O ASP B 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 617 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 636 Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA B 640 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 641' Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU C 83 " --> pdb=" O GLY C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.762A pdb=" N GLY C 149 " --> pdb=" O SER C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL C 369 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 454 through 461 Processing helix chain 'C' and resid 473 through 477 removed outlier: 3.657A pdb=" N ASP C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 477' Processing helix chain 'C' and resid 489 through 496 removed outlier: 3.557A pdb=" N GLY C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 526 Processing helix chain 'C' and resid 606 through 618 removed outlier: 3.684A pdb=" N GLY C 612 " --> pdb=" O ASN C 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 613 " --> pdb=" O ASP C 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 616 " --> pdb=" O GLY C 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 617 " --> pdb=" O TYR C 613 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 636 Processing helix chain 'C' and resid 637 through 641 removed outlier: 3.738A pdb=" N ALA C 640 " --> pdb=" O ASP C 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 641 " --> pdb=" O GLU C 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 637 through 641' Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU D 83 " --> pdb=" O GLY D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY D 149 " --> pdb=" O SER D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL D 369 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 454 through 461 Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.656A pdb=" N ASP D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 473 through 477' Processing helix chain 'D' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY D 496 " --> pdb=" O GLU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 526 Processing helix chain 'D' and resid 606 through 618 removed outlier: 3.683A pdb=" N GLY D 612 " --> pdb=" O ASN D 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 613 " --> pdb=" O ASP D 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR D 616 " --> pdb=" O GLY D 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 617 " --> pdb=" O TYR D 613 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 636 Processing helix chain 'D' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA D 640 " --> pdb=" O ASP D 637 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 641 " --> pdb=" O GLU D 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 637 through 641' Processing helix chain 'E' and resid 38 through 42 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU E 83 " --> pdb=" O GLY E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY E 149 " --> pdb=" O SER E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL E 369 " --> pdb=" O THR E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 452 No H-bonds generated for 'chain 'E' and resid 450 through 452' Processing helix chain 'E' and resid 454 through 461 Processing helix chain 'E' and resid 473 through 477 removed outlier: 3.656A pdb=" N ASP E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 473 through 477' Processing helix chain 'E' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 526 Processing helix chain 'E' and resid 606 through 618 removed outlier: 3.685A pdb=" N GLY E 612 " --> pdb=" O ASN E 608 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR E 613 " --> pdb=" O ASP E 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR E 616 " --> pdb=" O GLY E 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 617 " --> pdb=" O TYR E 613 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 636 Processing helix chain 'E' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA E 640 " --> pdb=" O ASP E 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 641 " --> pdb=" O GLU E 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 637 through 641' Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY F 149 " --> pdb=" O SER F 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 146 through 149' Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 366 through 370 removed outlier: 3.623A pdb=" N VAL F 369 " --> pdb=" O THR F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'F' and resid 454 through 461 Processing helix chain 'F' and resid 473 through 477 removed outlier: 3.657A pdb=" N ASP F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 473 through 477' Processing helix chain 'F' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 526 Processing helix chain 'F' and resid 606 through 618 removed outlier: 3.684A pdb=" N GLY F 612 " --> pdb=" O ASN F 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR F 616 " --> pdb=" O GLY F 612 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 617 " --> pdb=" O TYR F 613 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 636 Processing helix chain 'F' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA F 640 " --> pdb=" O ASP F 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 641 " --> pdb=" O GLU F 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 637 through 641' Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.197A pdb=" N VAL A 165 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.578A pdb=" N VAL A 254 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 375 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP A 355 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP A 278 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 271 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A 334 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR A 301 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 388 removed outlier: 5.855A pdb=" N VAL A 401 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 396 Processing sheet with id=AA8, first strand: chain 'A' and resid 393 through 396 Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 514 removed outlier: 4.273A pdb=" N GLY A 527 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 531 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 568 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY A 533 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP A 566 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 552 through 558 Processing sheet with id=AB2, first strand: chain 'A' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE A 659 " --> pdb=" O SER A 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER A 686 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL A 675 " --> pdb=" O VAL A 754 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY B 103 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 125 through 131 Processing sheet with id=AB6, first strand: chain 'B' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL B 165 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 246 through 249 Processing sheet with id=AB8, first strand: chain 'B' and resid 253 through 255 removed outlier: 3.579A pdb=" N VAL B 254 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 375 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP B 355 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP B 278 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 271 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU B 334 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR B 301 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 387 through 388 removed outlier: 5.854A pdb=" N VAL B 401 " --> pdb=" O ASP B 446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 393 through 396 Processing sheet with id=AC2, first strand: chain 'B' and resid 393 through 396 Processing sheet with id=AC3, first strand: chain 'B' and resid 513 through 514 removed outlier: 4.272A pdb=" N GLY B 527 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 531 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP B 568 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY B 533 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 566 " --> pdb=" O GLY B 533 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 552 through 558 Processing sheet with id=AC5, first strand: chain 'B' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE B 659 " --> pdb=" O SER B 686 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER B 686 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL B 675 " --> pdb=" O VAL B 754 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY C 103 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 125 through 131 Processing sheet with id=AC9, first strand: chain 'C' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL C 165 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 246 through 249 Processing sheet with id=AD2, first strand: chain 'C' and resid 253 through 255 removed outlier: 3.579A pdb=" N VAL C 254 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 375 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP C 355 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP C 278 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN C 271 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C 334 " --> pdb=" O THR C 301 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR C 301 " --> pdb=" O GLU C 334 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 387 through 388 removed outlier: 5.854A pdb=" N VAL C 401 " --> pdb=" O ASP C 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 393 through 396 Processing sheet with id=AD5, first strand: chain 'C' and resid 393 through 396 Processing sheet with id=AD6, first strand: chain 'C' and resid 513 through 514 removed outlier: 4.272A pdb=" N GLY C 527 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 531 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP C 568 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY C 533 " --> pdb=" O ASP C 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP C 566 " --> pdb=" O GLY C 533 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 552 through 558 Processing sheet with id=AD8, first strand: chain 'C' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE C 659 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER C 686 " --> pdb=" O ILE C 659 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL C 675 " --> pdb=" O VAL C 754 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY D 103 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 125 through 131 Processing sheet with id=AE3, first strand: chain 'D' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL D 165 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 246 through 249 Processing sheet with id=AE5, first strand: chain 'D' and resid 253 through 255 removed outlier: 3.579A pdb=" N VAL D 254 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 375 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP D 355 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP D 278 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN D 271 " --> pdb=" O ILE D 335 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU D 334 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR D 301 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 387 through 388 removed outlier: 5.855A pdb=" N VAL D 401 " --> pdb=" O ASP D 446 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 393 through 396 Processing sheet with id=AE8, first strand: chain 'D' and resid 393 through 396 Processing sheet with id=AE9, first strand: chain 'D' and resid 513 through 514 removed outlier: 4.273A pdb=" N GLY D 527 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE D 531 " --> pdb=" O ASP D 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP D 568 " --> pdb=" O ILE D 531 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY D 533 " --> pdb=" O ASP D 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP D 566 " --> pdb=" O GLY D 533 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 552 through 558 Processing sheet with id=AF2, first strand: chain 'D' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE D 659 " --> pdb=" O SER D 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER D 686 " --> pdb=" O ILE D 659 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 675 through 676 removed outlier: 5.750A pdb=" N VAL D 675 " --> pdb=" O VAL D 754 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY E 103 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 125 through 131 Processing sheet with id=AF6, first strand: chain 'E' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL E 165 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 246 through 249 Processing sheet with id=AF8, first strand: chain 'E' and resid 253 through 255 removed outlier: 3.578A pdb=" N VAL E 254 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E 375 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP E 355 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP E 278 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN E 271 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU E 334 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR E 301 " --> pdb=" O GLU E 334 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 387 through 388 removed outlier: 5.855A pdb=" N VAL E 401 " --> pdb=" O ASP E 446 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 393 through 396 Processing sheet with id=AG2, first strand: chain 'E' and resid 393 through 396 Processing sheet with id=AG3, first strand: chain 'E' and resid 513 through 514 removed outlier: 4.272A pdb=" N GLY E 527 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 531 " --> pdb=" O ASP E 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP E 568 " --> pdb=" O ILE E 531 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY E 533 " --> pdb=" O ASP E 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP E 566 " --> pdb=" O GLY E 533 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 552 through 558 Processing sheet with id=AG5, first strand: chain 'E' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE E 659 " --> pdb=" O SER E 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER E 686 " --> pdb=" O ILE E 659 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL E 675 " --> pdb=" O VAL E 754 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY F 103 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 125 through 131 Processing sheet with id=AG9, first strand: chain 'F' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL F 165 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 246 through 249 Processing sheet with id=AH2, first strand: chain 'F' and resid 253 through 255 removed outlier: 3.578A pdb=" N VAL F 254 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN F 375 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP F 355 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP F 278 " --> pdb=" O ASP F 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN F 271 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU F 334 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR F 301 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 387 through 388 removed outlier: 5.855A pdb=" N VAL F 401 " --> pdb=" O ASP F 446 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 393 through 396 Processing sheet with id=AH5, first strand: chain 'F' and resid 393 through 396 Processing sheet with id=AH6, first strand: chain 'F' and resid 513 through 514 removed outlier: 4.272A pdb=" N GLY F 527 " --> pdb=" O VAL F 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE F 531 " --> pdb=" O ASP F 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP F 568 " --> pdb=" O ILE F 531 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY F 533 " --> pdb=" O ASP F 566 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP F 566 " --> pdb=" O GLY F 533 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 552 through 558 Processing sheet with id=AH8, first strand: chain 'F' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE F 659 " --> pdb=" O SER F 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER F 686 " --> pdb=" O ILE F 659 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL F 675 " --> pdb=" O VAL F 754 " (cutoff:3.500A) 1242 hydrogen bonds defined for protein. 3240 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: 10.00 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11391 1.34 - 1.46: 4670 1.46 - 1.57: 15865 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 31986 Sorted by residual: bond pdb=" C5 BGC D 905 " pdb=" O5 BGC D 905 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C5 BGC E 904 " pdb=" O5 BGC E 904 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C5 BGC F 905 " pdb=" O5 BGC F 905 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 BGC C 905 " pdb=" O5 BGC C 905 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 BGC D 904 " pdb=" O5 BGC D 904 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.61e+00 ... (remaining 31981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 41608 0.95 - 1.91: 1702 1.91 - 2.86: 336 2.86 - 3.81: 73 3.81 - 4.77: 21 Bond angle restraints: 43740 Sorted by residual: angle pdb=" N TYR D 663 " pdb=" CA TYR D 663 " pdb=" C TYR D 663 " ideal model delta sigma weight residual 108.11 111.60 -3.49 1.29e+00 6.01e-01 7.33e+00 angle pdb=" N TYR C 663 " pdb=" CA TYR C 663 " pdb=" C TYR C 663 " ideal model delta sigma weight residual 108.11 111.59 -3.48 1.29e+00 6.01e-01 7.28e+00 angle pdb=" N TYR E 663 " pdb=" CA TYR E 663 " pdb=" C TYR E 663 " ideal model delta sigma weight residual 108.11 111.58 -3.47 1.29e+00 6.01e-01 7.24e+00 angle pdb=" N TYR A 663 " pdb=" CA TYR A 663 " pdb=" C TYR A 663 " ideal model delta sigma weight residual 108.11 111.57 -3.46 1.29e+00 6.01e-01 7.19e+00 angle pdb=" N TYR F 663 " pdb=" CA TYR F 663 " pdb=" C TYR F 663 " ideal model delta sigma weight residual 108.11 111.56 -3.45 1.29e+00 6.01e-01 7.14e+00 ... (remaining 43735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 18076 17.05 - 34.10: 627 34.10 - 51.15: 59 51.15 - 68.20: 18 68.20 - 85.25: 42 Dihedral angle restraints: 18822 sinusoidal: 6630 harmonic: 12192 Sorted by residual: dihedral pdb=" CB GLU E 756 " pdb=" CG GLU E 756 " pdb=" CD GLU E 756 " pdb=" OE1 GLU E 756 " ideal model delta sinusoidal sigma weight residual 0.00 -85.25 85.25 1 3.00e+01 1.11e-03 9.78e+00 dihedral pdb=" CB GLU F 756 " pdb=" CG GLU F 756 " pdb=" CD GLU F 756 " pdb=" OE1 GLU F 756 " ideal model delta sinusoidal sigma weight residual 0.00 -85.24 85.24 1 3.00e+01 1.11e-03 9.78e+00 dihedral pdb=" CB GLU D 756 " pdb=" CG GLU D 756 " pdb=" CD GLU D 756 " pdb=" OE1 GLU D 756 " ideal model delta sinusoidal sigma weight residual 0.00 -85.24 85.24 1 3.00e+01 1.11e-03 9.78e+00 ... (remaining 18819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3403 0.029 - 0.058: 1171 0.058 - 0.088: 351 0.088 - 0.117: 368 0.117 - 0.146: 89 Chirality restraints: 5382 Sorted by residual: chirality pdb=" CA ILE F 130 " pdb=" N ILE F 130 " pdb=" C ILE F 130 " pdb=" CB ILE F 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE C 130 " pdb=" N ILE C 130 " pdb=" C ILE C 130 " pdb=" CB ILE C 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE E 130 " pdb=" N ILE E 130 " pdb=" C ILE E 130 " pdb=" CB ILE E 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 5379 not shown) Planarity restraints: 5940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 171 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO F 172 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 172 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 172 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 171 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 172 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 172 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 172 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 171 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO D 172 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.025 5.00e-02 4.00e+02 ... (remaining 5937 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2986 2.74 - 3.28: 33061 3.28 - 3.82: 51115 3.82 - 4.36: 61041 4.36 - 4.90: 105420 Nonbonded interactions: 253623 Sorted by model distance: nonbonded pdb=" OG1 THR C 701 " pdb=" OG1 THR C 737 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR F 701 " pdb=" OG1 THR F 737 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR B 701 " pdb=" OG1 THR B 737 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR D 701 " pdb=" OG1 THR D 737 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR A 701 " pdb=" OG1 THR A 737 " model vdw 2.196 3.040 ... (remaining 253618 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.320 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.002 0.030 32004 Z= 0.109 Angle : 0.472 4.767 43740 Z= 0.267 Chirality : 0.043 0.146 5382 Planarity : 0.003 0.045 5940 Dihedral : 9.811 85.249 11070 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4338 helix: 0.50 (0.30), residues: 354 sheet: 0.21 (0.14), residues: 1314 loop : -0.20 (0.12), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 504 TYR 0.007 0.001 TYR D 663 PHE 0.005 0.001 PHE F 514 TRP 0.006 0.001 TRP F 716 HIS 0.002 0.001 HIS C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (31986) covalent geometry : angle 0.47164 / 0.27 (43740) hydrogen bonds : bond 0.14194 / 9.45 ( 1134) hydrogen bonds : angle 6.72882 / 4.58 ( 3240) Misc. bond : bond 0.00050 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ASP cc_start: 0.7750 (p0) cc_final: 0.7507 (p0) REVERT: B 455 ASP cc_start: 0.8302 (m-30) cc_final: 0.8039 (t0) REVERT: C 208 MET cc_start: 0.8279 (mmm) cc_final: 0.7937 (mmt) REVERT: C 249 LEU cc_start: 0.8675 (mt) cc_final: 0.8463 (mt) REVERT: C 455 ASP cc_start: 0.8155 (m-30) cc_final: 0.7867 (t0) REVERT: D 355 ASP cc_start: 0.7765 (p0) cc_final: 0.7523 (p0) REVERT: D 455 ASP cc_start: 0.8126 (m-30) cc_final: 0.7833 (t0) REVERT: E 455 ASP cc_start: 0.8324 (m-30) cc_final: 0.8056 (t0) REVERT: F 208 MET cc_start: 0.8265 (mmm) cc_final: 0.7902 (mmt) REVERT: F 249 LEU cc_start: 0.8683 (mt) cc_final: 0.8474 (mt) REVERT: F 455 ASP cc_start: 0.8157 (m-30) cc_final: 0.7864 (t0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2065 time to fit residues: 85.1277 Evaluate side-chains 102 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.2980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.072099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.056907 restraints weight = 136064.597| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.28 r_work: 0.3174 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 32004 Z= 0.221 Angle : 0.568 6.825 43740 Z= 0.309 Chirality : 0.046 0.174 5382 Planarity : 0.003 0.046 5940 Dihedral : 4.453 17.852 4512 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.36 % Allowed : 5.29 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4338 helix: 0.25 (0.31), residues: 348 sheet: -0.34 (0.13), residues: 1464 loop : -0.21 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 578 TYR 0.017 0.002 TYR E 157 PHE 0.014 0.002 PHE C 295 TRP 0.005 0.001 TRP E 722 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (31986) covalent geometry : angle 0.56767 / 0.31 (43740) hydrogen bonds : bond 0.03726 / 2.53 ( 1134) hydrogen bonds : angle 5.75033 / 3.92 ( 3240) Misc. bond : bond 0.00060 / 0.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.6989 (m-30) cc_final: 0.6415 (m-30) REVERT: B 355 ASP cc_start: 0.8293 (p0) cc_final: 0.8033 (p0) REVERT: B 455 ASP cc_start: 0.8485 (m-30) cc_final: 0.8066 (t0) REVERT: C 235 MET cc_start: 0.7660 (mtp) cc_final: 0.7440 (mtt) REVERT: C 455 ASP cc_start: 0.8418 (m-30) cc_final: 0.8076 (t0) REVERT: D 106 ASP cc_start: 0.6883 (m-30) cc_final: 0.6410 (m-30) REVERT: D 455 ASP cc_start: 0.8296 (m-30) cc_final: 0.7849 (t0) REVERT: E 355 ASP cc_start: 0.8294 (p0) cc_final: 0.8032 (p0) REVERT: E 455 ASP cc_start: 0.8493 (m-30) cc_final: 0.8082 (t0) REVERT: F 455 ASP cc_start: 0.8385 (m-30) cc_final: 0.8033 (t0) outliers start: 13 outliers final: 3 residues processed: 128 average time/residue: 0.1944 time to fit residues: 42.4797 Evaluate side-chains 105 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 180 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 321 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 428 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 366 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.070244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.054997 restraints weight = 136079.791| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 4.23 r_work: 0.3136 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 32004 Z= 0.283 Angle : 0.603 7.402 43740 Z= 0.328 Chirality : 0.047 0.198 5382 Planarity : 0.004 0.049 5940 Dihedral : 4.973 20.786 4512 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.84 % Allowed : 7.25 % Favored : 91.90 % 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: -0.87 (0.12), residues: 4338 helix: -0.40 (0.28), residues: 378 sheet: -0.50 (0.13), residues: 1422 loop : -0.57 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 55 TYR 0.017 0.002 TYR D 105 PHE 0.017 0.003 PHE D 295 TRP 0.006 0.001 TRP C 423 HIS 0.004 0.002 HIS C 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.28 (31986) covalent geometry : angle 0.60302 / 0.33 (43740) hydrogen bonds : bond 0.04090 / 2.78 ( 1134) hydrogen bonds : angle 5.64836 / 3.84 ( 3240) Misc. bond : bond 0.00096 / 0.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8270 (tpt) cc_final: 0.8027 (tpt) REVERT: B 455 ASP cc_start: 0.8495 (m-30) cc_final: 0.7999 (t0) REVERT: C 235 MET cc_start: 0.7600 (mtp) cc_final: 0.7337 (mtt) REVERT: C 455 ASP cc_start: 0.8432 (m-30) cc_final: 0.8187 (t0) REVERT: D 455 ASP cc_start: 0.8399 (m-30) cc_final: 0.8000 (t0) REVERT: E 277 MET cc_start: 0.8273 (tpt) cc_final: 0.8033 (tpt) REVERT: E 455 ASP cc_start: 0.8503 (m-30) cc_final: 0.8003 (t0) REVERT: F 455 ASP cc_start: 0.8432 (m-30) cc_final: 0.8176 (t0) outliers start: 30 outliers final: 13 residues processed: 118 average time/residue: 0.1923 time to fit residues: 38.6826 Evaluate side-chains 103 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 28 optimal weight: 5.9990 chunk 416 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 341 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.071713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.056579 restraints weight = 136183.065| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.31 r_work: 0.3184 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32004 Z= 0.126 Angle : 0.488 6.627 43740 Z= 0.266 Chirality : 0.045 0.232 5382 Planarity : 0.003 0.047 5940 Dihedral : 4.500 17.453 4512 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.62 % Allowed : 8.91 % Favored : 90.48 % 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: -0.72 (0.12), residues: 4338 helix: -0.17 (0.29), residues: 378 sheet: -0.39 (0.13), residues: 1392 loop : -0.50 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 578 TYR 0.014 0.001 TYR D 554 PHE 0.009 0.001 PHE E 514 TRP 0.005 0.001 TRP D 716 HIS 0.003 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (31986) covalent geometry : angle 0.48808 / 0.27 (43740) hydrogen bonds : bond 0.03203 / 2.18 ( 1134) hydrogen bonds : angle 5.34905 / 3.63 ( 3240) Misc. bond : bond 0.00044 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.6809 (m-30) cc_final: 0.6189 (m-30) REVERT: B 277 MET cc_start: 0.8224 (tpt) cc_final: 0.7965 (tpt) REVERT: B 455 ASP cc_start: 0.8461 (m-30) cc_final: 0.8060 (t0) REVERT: C 235 MET cc_start: 0.7467 (mtp) cc_final: 0.7202 (mtt) REVERT: C 455 ASP cc_start: 0.8370 (m-30) cc_final: 0.8039 (t0) REVERT: D 106 ASP cc_start: 0.6794 (m-30) cc_final: 0.6171 (m-30) REVERT: D 455 ASP cc_start: 0.8364 (m-30) cc_final: 0.7941 (t0) REVERT: E 277 MET cc_start: 0.8228 (tpt) cc_final: 0.8006 (tpt) REVERT: E 455 ASP cc_start: 0.8470 (m-30) cc_final: 0.8067 (t0) REVERT: F 235 MET cc_start: 0.6983 (mtt) cc_final: 0.6757 (mtt) REVERT: F 455 ASP cc_start: 0.8327 (m-30) cc_final: 0.7971 (t0) outliers start: 22 outliers final: 11 residues processed: 118 average time/residue: 0.1752 time to fit residues: 36.1258 Evaluate side-chains 94 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 313 optimal weight: 0.0570 chunk 229 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 427 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 368 optimal weight: 6.9990 chunk 282 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.071877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.056770 restraints weight = 134080.156| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.28 r_work: 0.3158 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32004 Z= 0.131 Angle : 0.478 8.002 43740 Z= 0.260 Chirality : 0.044 0.153 5382 Planarity : 0.003 0.048 5940 Dihedral : 4.358 16.787 4512 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.09 % Allowed : 8.57 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4338 helix: -0.14 (0.29), residues: 378 sheet: -0.31 (0.13), residues: 1404 loop : -0.39 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 578 TYR 0.013 0.001 TYR E 554 PHE 0.011 0.001 PHE E 514 TRP 0.005 0.001 TRP D 716 HIS 0.003 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (31986) covalent geometry : angle 0.47777 / 0.26 (43740) hydrogen bonds : bond 0.03111 / 2.11 ( 1134) hydrogen bonds : angle 5.22388 / 3.55 ( 3240) Misc. bond : bond 0.00044 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 106 ASP cc_start: 0.6829 (m-30) cc_final: 0.6205 (m-30) REVERT: B 277 MET cc_start: 0.8253 (tpt) cc_final: 0.8033 (tpt) REVERT: B 455 ASP cc_start: 0.8458 (m-30) cc_final: 0.8060 (t0) REVERT: C 235 MET cc_start: 0.7462 (mtp) cc_final: 0.7164 (mtt) REVERT: C 455 ASP cc_start: 0.8327 (m-30) cc_final: 0.7977 (t0) REVERT: D 87 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8363 (tt) REVERT: D 106 ASP cc_start: 0.6824 (m-30) cc_final: 0.6190 (m-30) REVERT: D 455 ASP cc_start: 0.8363 (m-30) cc_final: 0.7939 (t0) REVERT: E 277 MET cc_start: 0.8248 (tpt) cc_final: 0.8027 (tpt) REVERT: E 455 ASP cc_start: 0.8466 (m-30) cc_final: 0.8066 (t0) REVERT: F 455 ASP cc_start: 0.8328 (m-30) cc_final: 0.7965 (t0) outliers start: 39 outliers final: 25 residues processed: 123 average time/residue: 0.1697 time to fit residues: 36.8667 Evaluate side-chains 113 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 132 optimal weight: 0.6980 chunk 391 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 chunk 382 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 414 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.082034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067715 restraints weight = 93889.840| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.40 r_work: 0.3150 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 32004 Z= 0.255 Angle : 0.568 8.246 43740 Z= 0.308 Chirality : 0.046 0.168 5382 Planarity : 0.003 0.049 5940 Dihedral : 4.866 19.092 4512 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.37 % Allowed : 9.47 % Favored : 89.16 % 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: -1.01 (0.12), residues: 4338 helix: -0.39 (0.28), residues: 378 sheet: -0.72 (0.13), residues: 1476 loop : -0.59 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 578 TYR 0.015 0.002 TYR F 157 PHE 0.013 0.002 PHE D 295 TRP 0.005 0.001 TRP C 423 HIS 0.004 0.002 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (31986) covalent geometry : angle 0.56816 / 0.31 (43740) hydrogen bonds : bond 0.03772 / 2.55 ( 1134) hydrogen bonds : angle 5.38938 / 3.66 ( 3240) Misc. bond : bond 0.00086 / 0.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8400 (tt) REVERT: B 277 MET cc_start: 0.8164 (tpt) cc_final: 0.7939 (tpt) REVERT: B 455 ASP cc_start: 0.8487 (m-30) cc_final: 0.8080 (t0) REVERT: C 235 MET cc_start: 0.7575 (mtp) cc_final: 0.7348 (mtt) REVERT: C 455 ASP cc_start: 0.8360 (m-30) cc_final: 0.8104 (t0) REVERT: D 87 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8398 (tt) REVERT: D 455 ASP cc_start: 0.8398 (m-30) cc_final: 0.8009 (t0) REVERT: E 277 MET cc_start: 0.8149 (tpt) cc_final: 0.7922 (tpt) REVERT: E 455 ASP cc_start: 0.8501 (m-30) cc_final: 0.8091 (t0) REVERT: F 455 ASP cc_start: 0.8379 (m-30) cc_final: 0.8107 (t0) outliers start: 49 outliers final: 34 residues processed: 131 average time/residue: 0.1764 time to fit residues: 40.7627 Evaluate side-chains 121 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 324 optimal weight: 4.9990 chunk 272 optimal weight: 0.0070 chunk 199 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 337 optimal weight: 7.9990 chunk 375 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.071588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056434 restraints weight = 136964.197| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 4.35 r_work: 0.3173 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32004 Z= 0.120 Angle : 0.487 9.629 43740 Z= 0.264 Chirality : 0.044 0.279 5382 Planarity : 0.003 0.047 5940 Dihedral : 4.443 17.799 4512 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.29 % Allowed : 10.25 % Favored : 88.46 % 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: -0.74 (0.13), residues: 4338 helix: -0.12 (0.29), residues: 378 sheet: -0.50 (0.13), residues: 1398 loop : -0.47 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 578 TYR 0.013 0.001 TYR E 359 PHE 0.010 0.001 PHE B 514 TRP 0.005 0.001 TRP A 716 HIS 0.003 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (31986) covalent geometry : angle 0.48702 / 0.26 (43740) hydrogen bonds : bond 0.03074 / 2.08 ( 1134) hydrogen bonds : angle 5.16961 / 3.51 ( 3240) Misc. bond : bond 0.00044 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.6414 (mtt) cc_final: 0.6084 (mtt) REVERT: B 277 MET cc_start: 0.8206 (tpt) cc_final: 0.7980 (tpt) REVERT: B 455 ASP cc_start: 0.8456 (m-30) cc_final: 0.8068 (t0) REVERT: C 235 MET cc_start: 0.7389 (mtp) cc_final: 0.7129 (mtt) REVERT: C 455 ASP cc_start: 0.8356 (m-30) cc_final: 0.7995 (t0) REVERT: D 87 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8391 (tt) REVERT: D 235 MET cc_start: 0.6390 (mtt) cc_final: 0.6066 (mtt) REVERT: D 455 ASP cc_start: 0.8323 (m-30) cc_final: 0.7925 (t0) REVERT: E 455 ASP cc_start: 0.8468 (m-30) cc_final: 0.8074 (t0) REVERT: F 455 ASP cc_start: 0.8346 (m-30) cc_final: 0.7982 (t0) outliers start: 46 outliers final: 26 residues processed: 135 average time/residue: 0.1750 time to fit residues: 41.7980 Evaluate side-chains 113 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 630 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 317 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 403 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 287 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.081644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.067246 restraints weight = 95525.221| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.43 r_work: 0.3153 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32004 Z= 0.217 Angle : 0.541 8.578 43740 Z= 0.292 Chirality : 0.045 0.208 5382 Planarity : 0.003 0.049 5940 Dihedral : 4.678 21.085 4512 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.32 % Allowed : 10.39 % Favored : 88.29 % 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 (0.13), residues: 4338 helix: -0.27 (0.28), residues: 378 sheet: -0.58 (0.13), residues: 1428 loop : -0.54 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 578 TYR 0.012 0.002 TYR E 554 PHE 0.010 0.002 PHE D 295 TRP 0.005 0.001 TRP C 722 HIS 0.003 0.002 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (31986) covalent geometry : angle 0.54085 / 0.29 (43740) hydrogen bonds : bond 0.03515 / 2.38 ( 1134) hydrogen bonds : angle 5.29704 / 3.60 ( 3240) Misc. bond : bond 0.00067 / 0.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 90 time to evaluate : 1.180 Fit side-chains REVERT: B 106 ASP cc_start: 0.6792 (m-30) cc_final: 0.6591 (m-30) REVERT: B 277 MET cc_start: 0.8134 (tpt) cc_final: 0.7913 (tpt) REVERT: B 455 ASP cc_start: 0.8419 (m-30) cc_final: 0.8006 (t0) REVERT: C 235 MET cc_start: 0.7523 (mtp) cc_final: 0.7274 (mtt) REVERT: C 455 ASP cc_start: 0.8353 (m-30) cc_final: 0.7981 (t0) REVERT: D 455 ASP cc_start: 0.8380 (m-30) cc_final: 0.7980 (t0) REVERT: E 106 ASP cc_start: 0.6808 (m-30) cc_final: 0.6607 (m-30) REVERT: E 455 ASP cc_start: 0.8428 (m-30) cc_final: 0.8012 (t0) REVERT: F 455 ASP cc_start: 0.8340 (m-30) cc_final: 0.7966 (t0) outliers start: 47 outliers final: 37 residues processed: 126 average time/residue: 0.1806 time to fit residues: 39.5750 Evaluate side-chains 116 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 6.9990 chunk 420 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 410 optimal weight: 9.9990 chunk 284 optimal weight: 0.3980 chunk 166 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 357 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.079543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064817 restraints weight = 106157.020| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.43 r_work: 0.3164 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32004 Z= 0.151 Angle : 0.508 8.128 43740 Z= 0.275 Chirality : 0.044 0.209 5382 Planarity : 0.003 0.047 5940 Dihedral : 4.535 20.335 4512 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.20 % Allowed : 10.81 % Favored : 87.98 % 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: -0.89 (0.13), residues: 4338 helix: -0.10 (0.29), residues: 378 sheet: -0.75 (0.12), residues: 1632 loop : -0.42 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 578 TYR 0.014 0.001 TYR A 554 PHE 0.007 0.001 PHE A 295 TRP 0.005 0.001 TRP C 722 HIS 0.002 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (31986) covalent geometry : angle 0.50754 / 0.27 (43740) hydrogen bonds : bond 0.03224 / 2.18 ( 1134) hydrogen bonds : angle 5.18780 / 3.52 ( 3240) Misc. bond : bond 0.00053 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 1.232 Fit side-chains REVERT: B 277 MET cc_start: 0.8157 (tpt) cc_final: 0.7937 (tpt) REVERT: B 455 ASP cc_start: 0.8451 (m-30) cc_final: 0.8049 (t0) REVERT: C 235 MET cc_start: 0.7404 (mtp) cc_final: 0.7142 (mtt) REVERT: C 455 ASP cc_start: 0.8366 (m-30) cc_final: 0.8004 (t0) REVERT: D 455 ASP cc_start: 0.8340 (m-30) cc_final: 0.7940 (t0) REVERT: E 455 ASP cc_start: 0.8461 (m-30) cc_final: 0.8060 (t0) REVERT: F 455 ASP cc_start: 0.8353 (m-30) cc_final: 0.7987 (t0) outliers start: 43 outliers final: 38 residues processed: 119 average time/residue: 0.1660 time to fit residues: 35.3505 Evaluate side-chains 119 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 55 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 342 optimal weight: 9.9990 chunk 63 optimal weight: 0.0570 chunk 175 optimal weight: 4.9990 chunk 412 optimal weight: 0.9990 chunk 193 optimal weight: 20.0000 chunk 225 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.079515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064760 restraints weight = 104402.897| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.43 r_work: 0.3149 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32004 Z= 0.199 Angle : 0.533 7.303 43740 Z= 0.289 Chirality : 0.045 0.204 5382 Planarity : 0.003 0.049 5940 Dihedral : 4.661 22.082 4512 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.29 % Allowed : 10.87 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4338 helix: -0.18 (0.29), residues: 378 sheet: -0.70 (0.12), residues: 1548 loop : -0.56 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 578 TYR 0.014 0.002 TYR D 554 PHE 0.009 0.002 PHE A 295 TRP 0.004 0.001 TRP C 722 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (31986) covalent geometry : angle 0.53338 / 0.29 (43740) hydrogen bonds : bond 0.03429 / 2.32 ( 1134) hydrogen bonds : angle 5.22735 / 3.56 ( 3240) Misc. bond : bond 0.00066 / 0.04 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 1.234 Fit side-chains REVERT: B 277 MET cc_start: 0.8110 (tpt) cc_final: 0.7895 (tpt) REVERT: B 455 ASP cc_start: 0.8412 (m-30) cc_final: 0.8007 (t0) REVERT: C 235 MET cc_start: 0.7539 (mtp) cc_final: 0.7306 (mtt) REVERT: C 455 ASP cc_start: 0.8327 (m-30) cc_final: 0.7958 (t0) REVERT: D 455 ASP cc_start: 0.8361 (m-30) cc_final: 0.7968 (t0) REVERT: E 106 ASP cc_start: 0.6957 (m-30) cc_final: 0.6726 (m-30) REVERT: E 455 ASP cc_start: 0.8394 (m-30) cc_final: 0.7978 (t0) REVERT: F 455 ASP cc_start: 0.8324 (m-30) cc_final: 0.7953 (t0) outliers start: 46 outliers final: 38 residues processed: 121 average time/residue: 0.1627 time to fit residues: 36.1310 Evaluate side-chains 117 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 125 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 385 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.079472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064668 restraints weight = 107629.160| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.58 r_work: 0.3163 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32004 Z= 0.143 Angle : 0.505 7.791 43740 Z= 0.274 Chirality : 0.044 0.203 5382 Planarity : 0.003 0.050 5940 Dihedral : 4.497 20.827 4512 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.29 % Allowed : 10.95 % Favored : 87.76 % 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: -0.88 (0.13), residues: 4338 helix: -0.05 (0.29), residues: 378 sheet: -0.60 (0.12), residues: 1536 loop : -0.56 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 578 TYR 0.014 0.001 TYR D 554 PHE 0.007 0.001 PHE F 545 TRP 0.005 0.001 TRP E 722 HIS 0.002 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (31986) covalent geometry : angle 0.50516 / 0.27 (43740) hydrogen bonds : bond 0.03154 / 2.13 ( 1134) hydrogen bonds : angle 5.12124 / 3.48 ( 3240) Misc. bond : bond 0.00053 / 0.03 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7257.34 seconds wall clock time: 125 minutes 17.69 seconds (7517.69 seconds total)