Starting phenix.real_space_refine on Fri Mar 6 15:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ptr_13634/03_2026/7ptr_13634.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ptr_13634/03_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_13634/03_2026/7ptr_13634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ptr_13634/03_2026/7ptr_13634.map" model { file = "/net/cci-nas-00/data/ceres_data/7ptr_13634/03_2026/7ptr_13634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ptr_13634/03_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-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 5.90, per 1000 atoms: 0.19 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: 2.93 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: 1.33 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: 8.28 Time building geometry restraints manager: 3.93 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: 18406 17.05 - 34.10: 639 34.10 - 51.15: 59 51.15 - 68.20: 18 68.20 - 85.25: 42 Dihedral angle restraints: 19164 sinusoidal: 6972 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 19161 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: 0.10 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: 5.900 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: 0.050 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.690 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 9.734 85.249 11412 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 covalent geometry : bond 0.00206 (31986) covalent geometry : angle 0.47164 (43740) hydrogen bonds : bond 0.14194 ( 1134) hydrogen bonds : angle 6.72882 ( 3240) Misc. bond : bond 0.00050 ( 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 : 1.141 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: 0.1807 time to fit residues: 74.5989 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 : 1.041 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 158 ASN C 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.072287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.057118 restraints weight = 136356.699| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.27 r_work: 0.3185 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32004 Z= 0.219 Angle : 0.559 6.619 43740 Z= 0.305 Chirality : 0.046 0.166 5382 Planarity : 0.003 0.045 5940 Dihedral : 4.348 19.042 4854 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.36 % Allowed : 4.79 % Favored : 94.85 % 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: -0.38 (0.13), residues: 4338 helix: 0.32 (0.30), residues: 348 sheet: -0.31 (0.13), residues: 1464 loop : -0.20 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 578 TYR 0.015 0.002 TYR B 157 PHE 0.013 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 covalent geometry : bond 0.00489 (31986) covalent geometry : angle 0.55935 (43740) hydrogen bonds : bond 0.03765 ( 1134) hydrogen bonds : angle 5.75331 ( 3240) Misc. bond : bond 0.00059 ( 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 127 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.6994 (m-30) cc_final: 0.6413 (m-30) REVERT: B 277 MET cc_start: 0.8344 (tpt) cc_final: 0.8098 (tpt) REVERT: B 355 ASP cc_start: 0.8296 (p0) cc_final: 0.8042 (p0) REVERT: B 455 ASP cc_start: 0.8492 (m-30) cc_final: 0.8087 (t0) REVERT: C 235 MET cc_start: 0.7657 (mtp) cc_final: 0.7410 (mtt) REVERT: C 455 ASP cc_start: 0.8426 (m-30) cc_final: 0.8085 (t0) REVERT: D 106 ASP cc_start: 0.6887 (m-30) cc_final: 0.6416 (m-30) REVERT: D 455 ASP cc_start: 0.8308 (m-30) cc_final: 0.7862 (t0) REVERT: E 277 MET cc_start: 0.8354 (tpt) cc_final: 0.8110 (tpt) REVERT: E 355 ASP cc_start: 0.8295 (p0) cc_final: 0.8043 (p0) REVERT: E 455 ASP cc_start: 0.8501 (m-30) cc_final: 0.8089 (t0) REVERT: F 455 ASP cc_start: 0.8419 (m-30) cc_final: 0.8074 (t0) outliers start: 13 outliers final: 3 residues processed: 127 average time/residue: 0.1694 time to fit residues: 36.5674 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 : 1.127 ------------------------------------------------------------------------------- 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: 9.9990 chunk 121 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 428 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 366 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 412 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN C 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.071074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.055829 restraints weight = 135812.396| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.26 r_work: 0.3157 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32004 Z= 0.226 Angle : 0.551 6.856 43740 Z= 0.300 Chirality : 0.046 0.183 5382 Planarity : 0.003 0.049 5940 Dihedral : 4.619 19.200 4854 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.62 % Allowed : 7.09 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.12), residues: 4338 helix: -0.07 (0.30), residues: 342 sheet: -0.40 (0.13), residues: 1434 loop : -0.42 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 504 TYR 0.014 0.002 TYR B 157 PHE 0.015 0.002 PHE C 295 TRP 0.005 0.001 TRP C 423 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00507 (31986) covalent geometry : angle 0.55109 (43740) hydrogen bonds : bond 0.03785 ( 1134) hydrogen bonds : angle 5.52693 ( 3240) Misc. bond : bond 0.00070 ( 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 131 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.149 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: 0.8208 (tpt) cc_final: 0.7990 (tpt) REVERT: B 355 ASP cc_start: 0.8366 (p0) cc_final: 0.8117 (p0) REVERT: B 455 ASP cc_start: 0.8539 (m-30) cc_final: 0.8070 (t0) REVERT: C 235 MET cc_start: 0.7673 (mtp) cc_final: 0.7402 (mtt) REVERT: C 455 ASP cc_start: 0.8427 (m-30) cc_final: 0.8194 (t0) REVERT: D 106 ASP cc_start: 0.6813 (m-30) cc_final: 0.6406 (m-30) REVERT: D 455 ASP cc_start: 0.8385 (m-30) cc_final: 0.7940 (t0) REVERT: E 355 ASP cc_start: 0.8361 (p0) cc_final: 0.8133 (p0) REVERT: E 455 ASP cc_start: 0.8517 (m-30) cc_final: 0.8035 (t0) REVERT: F 455 ASP cc_start: 0.8425 (m-30) cc_final: 0.8185 (t0) outliers start: 22 outliers final: 9 residues processed: 120 average time/residue: 0.1791 time to fit residues: 36.9257 Evaluate side-chains 102 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 28 optimal weight: 0.0470 chunk 416 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 76 optimal weight: 0.0170 chunk 341 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 172 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 387 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 overall best weight: 1.0918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.072882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.057867 restraints weight = 133454.629| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.25 r_work: 0.3211 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32004 Z= 0.099 Angle : 0.467 7.689 43740 Z= 0.254 Chirality : 0.044 0.186 5382 Planarity : 0.003 0.047 5940 Dihedral : 4.093 16.406 4854 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.53 % Allowed : 8.01 % Favored : 91.46 % 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: -0.40 (0.13), residues: 4338 helix: -0.08 (0.30), residues: 378 sheet: -0.07 (0.13), residues: 1368 loop : -0.33 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 504 TYR 0.014 0.001 TYR D 554 PHE 0.009 0.001 PHE B 514 TRP 0.006 0.001 TRP D 716 HIS 0.003 0.001 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.00216 (31986) covalent geometry : angle 0.46684 (43740) hydrogen bonds : bond 0.02918 ( 1134) hydrogen bonds : angle 5.19428 ( 3240) Misc. bond : bond 0.00032 ( 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 126 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 455 ASP cc_start: 0.8383 (m-30) cc_final: 0.8000 (t0) REVERT: B 578 ARG cc_start: 0.6885 (mmm160) cc_final: 0.6594 (mmm160) REVERT: C 235 MET cc_start: 0.7566 (mtp) cc_final: 0.7309 (mtt) REVERT: C 455 ASP cc_start: 0.8268 (m-30) cc_final: 0.7883 (t0) REVERT: D 455 ASP cc_start: 0.8258 (m-30) cc_final: 0.7838 (t0) REVERT: E 277 MET cc_start: 0.8118 (tpt) cc_final: 0.7908 (tpt) REVERT: E 455 ASP cc_start: 0.8389 (m-30) cc_final: 0.8003 (t0) REVERT: E 578 ARG cc_start: 0.6878 (mmm160) cc_final: 0.6594 (mmm160) REVERT: F 455 ASP cc_start: 0.8282 (m-30) cc_final: 0.7881 (t0) outliers start: 19 outliers final: 7 residues processed: 124 average time/residue: 0.1752 time to fit residues: 37.3713 Evaluate side-chains 104 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 681 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 313 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 398 optimal weight: 9.9990 chunk 427 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 368 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.071914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.056798 restraints weight = 133846.652| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 4.24 r_work: 0.3166 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1985 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= 0.153 Angle : 0.478 7.423 43740 Z= 0.260 Chirality : 0.044 0.157 5382 Planarity : 0.003 0.048 5940 Dihedral : 4.175 16.342 4854 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.78 % Allowed : 8.63 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4338 helix: -0.17 (0.29), residues: 378 sheet: -0.26 (0.13), residues: 1404 loop : -0.32 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 504 TYR 0.013 0.001 TYR D 554 PHE 0.009 0.001 PHE F 295 TRP 0.005 0.001 TRP D 716 HIS 0.002 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00345 (31986) covalent geometry : angle 0.47809 (43740) hydrogen bonds : bond 0.03163 ( 1134) hydrogen bonds : angle 5.16028 ( 3240) Misc. bond : bond 0.00044 ( 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 127 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8099 (tpt) cc_final: 0.7873 (tpt) REVERT: B 455 ASP cc_start: 0.8416 (m-30) cc_final: 0.8016 (t0) REVERT: C 235 MET cc_start: 0.7568 (mtp) cc_final: 0.7254 (mtt) REVERT: C 455 ASP cc_start: 0.8325 (m-30) cc_final: 0.7969 (t0) REVERT: D 455 ASP cc_start: 0.8305 (m-30) cc_final: 0.7870 (t0) REVERT: E 455 ASP cc_start: 0.8430 (m-30) cc_final: 0.8028 (t0) REVERT: F 455 ASP cc_start: 0.8317 (m-30) cc_final: 0.7958 (t0) outliers start: 28 outliers final: 16 residues processed: 120 average time/residue: 0.1744 time to fit residues: 35.7635 Evaluate side-chains 111 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 681 MET 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 681 MET Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 681 MET 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 356 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: 1.9990 chunk 391 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 414 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 283 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.071005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055824 restraints weight = 134539.511| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.25 r_work: 0.3159 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32004 Z= 0.208 Angle : 0.519 7.895 43740 Z= 0.282 Chirality : 0.045 0.163 5382 Planarity : 0.003 0.048 5940 Dihedral : 4.440 17.090 4854 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.26 % Allowed : 8.74 % Favored : 90.00 % 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: -0.66 (0.12), residues: 4338 helix: -0.24 (0.29), residues: 378 sheet: -0.39 (0.13), residues: 1404 loop : -0.41 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 578 TYR 0.012 0.002 TYR E 554 PHE 0.012 0.002 PHE A 295 TRP 0.004 0.001 TRP C 423 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00466 (31986) covalent geometry : angle 0.51917 (43740) hydrogen bonds : bond 0.03464 ( 1134) hydrogen bonds : angle 5.24237 ( 3240) Misc. bond : bond 0.00063 ( 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 138 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 93 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 277 MET cc_start: 0.8189 (tpt) cc_final: 0.7965 (tpt) REVERT: B 455 ASP cc_start: 0.8487 (m-30) cc_final: 0.8088 (t0) REVERT: C 106 ASP cc_start: 0.6874 (m-30) cc_final: 0.6084 (m-30) REVERT: C 235 MET cc_start: 0.7566 (mtp) cc_final: 0.7284 (mtt) REVERT: C 455 ASP cc_start: 0.8349 (m-30) cc_final: 0.7986 (t0) REVERT: D 87 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8441 (tt) REVERT: D 106 ASP cc_start: 0.6742 (m-30) cc_final: 0.6108 (m-30) REVERT: D 455 ASP cc_start: 0.8328 (m-30) cc_final: 0.7916 (t0) REVERT: E 277 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7907 (tpt) REVERT: E 455 ASP cc_start: 0.8503 (m-30) cc_final: 0.8099 (t0) REVERT: F 106 ASP cc_start: 0.6877 (m-30) cc_final: 0.6069 (m-30) REVERT: F 455 ASP cc_start: 0.8349 (m-30) cc_final: 0.7981 (t0) outliers start: 45 outliers final: 29 residues processed: 126 average time/residue: 0.1756 time to fit residues: 37.7952 Evaluate side-chains 120 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU 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 356 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 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 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 277 MET Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 356 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 Chi-restraints excluded: chain F residue 356 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: 0.0970 chunk 16 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 272 optimal weight: 0.4980 chunk 199 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 337 optimal weight: 7.9990 chunk 375 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.071902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.056716 restraints weight = 136949.877| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.37 r_work: 0.3161 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2172 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= 0.121 Angle : 0.468 6.853 43740 Z= 0.255 Chirality : 0.044 0.149 5382 Planarity : 0.003 0.047 5940 Dihedral : 4.162 16.538 4854 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.84 % Allowed : 9.61 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 4338 helix: -0.05 (0.30), residues: 378 sheet: -0.22 (0.14), residues: 1356 loop : -0.38 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 578 TYR 0.013 0.001 TYR D 554 PHE 0.007 0.001 PHE D 514 TRP 0.005 0.001 TRP D 716 HIS 0.002 0.001 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.00274 (31986) covalent geometry : angle 0.46772 (43740) hydrogen bonds : bond 0.02991 ( 1134) hydrogen bonds : angle 5.07604 ( 3240) Misc. bond : bond 0.00037 ( 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 128 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8123 (tpt) cc_final: 0.7894 (tpt) REVERT: B 455 ASP cc_start: 0.8445 (m-30) cc_final: 0.8037 (t0) REVERT: C 235 MET cc_start: 0.7549 (mtp) cc_final: 0.7284 (mtt) REVERT: C 455 ASP cc_start: 0.8302 (m-30) cc_final: 0.7951 (t0) REVERT: D 87 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8349 (tt) REVERT: D 106 ASP cc_start: 0.6927 (m-30) cc_final: 0.6299 (m-30) REVERT: D 455 ASP cc_start: 0.8315 (m-30) cc_final: 0.7895 (t0) REVERT: E 277 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7840 (tpt) REVERT: E 455 ASP cc_start: 0.8456 (m-30) cc_final: 0.8047 (t0) REVERT: F 455 ASP cc_start: 0.8321 (m-30) cc_final: 0.7963 (t0) outliers start: 30 outliers final: 19 residues processed: 119 average time/residue: 0.1760 time to fit residues: 35.1454 Evaluate side-chains 114 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP 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 87 LEU Chi-restraints excluded: chain B residue 298 ILE 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 681 MET Chi-restraints excluded: chain D residue 87 LEU 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 277 MET Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 681 MET 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: 0.0270 chunk 1 optimal weight: 3.9990 chunk 317 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 403 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 287 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 overall best weight: 2.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.067176 restraints weight = 98256.625| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.54 r_work: 0.3181 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2258 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= 0.147 Angle : 0.479 6.947 43740 Z= 0.261 Chirality : 0.044 0.154 5382 Planarity : 0.003 0.048 5940 Dihedral : 4.206 16.753 4854 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.98 % Allowed : 10.11 % Favored : 88.91 % 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: -0.54 (0.13), residues: 4338 helix: -0.07 (0.30), residues: 378 sheet: -0.30 (0.13), residues: 1404 loop : -0.34 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 578 TYR 0.014 0.001 TYR A 554 PHE 0.008 0.001 PHE F 545 TRP 0.004 0.001 TRP F 716 HIS 0.002 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00332 (31986) covalent geometry : angle 0.47855 (43740) hydrogen bonds : bond 0.03114 ( 1134) hydrogen bonds : angle 5.03891 ( 3240) Misc. bond : bond 0.00045 ( 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 134 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8069 (tpt) cc_final: 0.7835 (tpt) REVERT: B 455 ASP cc_start: 0.8430 (m-30) cc_final: 0.8023 (t0) REVERT: C 235 MET cc_start: 0.7580 (mtp) cc_final: 0.7311 (mtt) REVERT: C 455 ASP cc_start: 0.8313 (m-30) cc_final: 0.7962 (t0) REVERT: D 106 ASP cc_start: 0.6684 (m-30) cc_final: 0.6003 (m-30) REVERT: D 455 ASP cc_start: 0.8286 (m-30) cc_final: 0.7862 (t0) REVERT: E 277 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7793 (tpt) REVERT: E 455 ASP cc_start: 0.8444 (m-30) cc_final: 0.8036 (t0) REVERT: F 455 ASP cc_start: 0.8307 (m-30) cc_final: 0.7954 (t0) outliers start: 35 outliers final: 24 residues processed: 125 average time/residue: 0.1760 time to fit residues: 37.7686 Evaluate side-chains 115 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 681 MET Chi-restraints excluded: chain B residue 87 LEU 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 356 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 206 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 277 MET Chi-restraints excluded: chain E residue 298 ILE 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 681 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 0.7980 chunk 420 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 410 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 357 optimal weight: 6.9990 chunk 163 optimal weight: 0.0470 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.081824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.067042 restraints weight = 98118.742| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.56 r_work: 0.3172 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2330 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= 0.166 Angle : 0.492 7.144 43740 Z= 0.268 Chirality : 0.044 0.156 5382 Planarity : 0.003 0.048 5940 Dihedral : 4.299 17.049 4854 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.06 % Allowed : 10.50 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4338 helix: -0.09 (0.29), residues: 378 sheet: -0.57 (0.13), residues: 1506 loop : -0.27 (0.13), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 578 TYR 0.014 0.002 TYR D 554 PHE 0.009 0.001 PHE A 295 TRP 0.004 0.001 TRP C 722 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00374 (31986) covalent geometry : angle 0.49231 (43740) hydrogen bonds : bond 0.03219 ( 1134) hydrogen bonds : angle 5.04930 ( 3240) Misc. bond : bond 0.00052 ( 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 132 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: B 277 MET cc_start: 0.8090 (tpt) cc_final: 0.7855 (tpt) REVERT: B 455 ASP cc_start: 0.8442 (m-30) cc_final: 0.8033 (t0) REVERT: C 235 MET cc_start: 0.7518 (mtp) cc_final: 0.7242 (mtt) REVERT: C 455 ASP cc_start: 0.8326 (m-30) cc_final: 0.7973 (t0) REVERT: D 106 ASP cc_start: 0.6618 (m-30) cc_final: 0.6012 (m-30) REVERT: D 455 ASP cc_start: 0.8283 (m-30) cc_final: 0.7885 (t0) REVERT: E 455 ASP cc_start: 0.8463 (m-30) cc_final: 0.8052 (t0) REVERT: F 455 ASP cc_start: 0.8315 (m-30) cc_final: 0.7959 (t0) outliers start: 38 outliers final: 27 residues processed: 122 average time/residue: 0.1644 time to fit residues: 34.3699 Evaluate side-chains 121 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 298 ILE 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 C residue 87 LEU 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 681 MET Chi-restraints excluded: chain D residue 206 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 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 681 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 55 optimal weight: 5.9990 chunk 268 optimal weight: 0.0870 chunk 231 optimal weight: 5.9990 chunk 342 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 412 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.079507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064648 restraints weight = 105538.164| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.58 r_work: 0.3148 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32004 Z= 0.211 Angle : 0.529 7.541 43740 Z= 0.287 Chirality : 0.045 0.161 5382 Planarity : 0.003 0.056 5940 Dihedral : 4.503 17.507 4854 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.95 % Allowed : 10.62 % Favored : 88.43 % 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 (0.13), residues: 4338 helix: -0.16 (0.29), residues: 378 sheet: -0.52 (0.13), residues: 1458 loop : -0.41 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 578 TYR 0.015 0.002 TYR A 554 PHE 0.011 0.002 PHE A 295 TRP 0.004 0.001 TRP D 722 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00475 (31986) covalent geometry : angle 0.52949 (43740) hydrogen bonds : bond 0.03442 ( 1134) hydrogen bonds : angle 5.12448 ( 3240) Misc. bond : bond 0.00067 ( 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 124 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 1.151 Fit side-chains REVERT: B 277 MET cc_start: 0.8119 (tpt) cc_final: 0.7892 (tpt) REVERT: B 455 ASP cc_start: 0.8473 (m-30) cc_final: 0.8056 (t0) REVERT: C 235 MET cc_start: 0.7560 (mtp) cc_final: 0.7295 (mtt) REVERT: C 455 ASP cc_start: 0.8366 (m-30) cc_final: 0.8005 (t0) REVERT: D 455 ASP cc_start: 0.8400 (m-30) cc_final: 0.8019 (t0) REVERT: E 455 ASP cc_start: 0.8486 (m-30) cc_final: 0.8067 (t0) REVERT: F 455 ASP cc_start: 0.8365 (m-30) cc_final: 0.8001 (t0) outliers start: 34 outliers final: 28 residues processed: 115 average time/residue: 0.1588 time to fit residues: 32.2151 Evaluate side-chains 114 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 298 ILE 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 C residue 87 LEU 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 681 MET 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 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 681 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 125 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 385 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.071389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056126 restraints weight = 136943.148| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.38 r_work: 0.3153 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32004 Z= 0.151 Angle : 0.496 7.505 43740 Z= 0.270 Chirality : 0.044 0.154 5382 Planarity : 0.003 0.057 5940 Dihedral : 4.355 18.147 4854 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.01 % Allowed : 10.59 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 4338 helix: -0.05 (0.30), residues: 378 sheet: -0.58 (0.13), residues: 1512 loop : -0.46 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 578 TYR 0.015 0.001 TYR A 554 PHE 0.008 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 covalent geometry : bond 0.00343 (31986) covalent geometry : angle 0.49620 (43740) hydrogen bonds : bond 0.03164 ( 1134) hydrogen bonds : angle 5.03218 ( 3240) Misc. bond : bond 0.00049 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6629.84 seconds wall clock time: 114 minutes 31.66 seconds (6871.66 seconds total)