Starting phenix.real_space_refine on Sat Feb 7 23:04:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q5c_72225/02_2026/9q5c_72225.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q5c_72225/02_2026/9q5c_72225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q5c_72225/02_2026/9q5c_72225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q5c_72225/02_2026/9q5c_72225.map" model { file = "/net/cci-nas-00/data/ceres_data/9q5c_72225/02_2026/9q5c_72225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q5c_72225/02_2026/9q5c_72225.cif" } resolution = 3.19 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 23718 2.51 5 N 6330 2.21 5 O 6840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37062 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6177 Classifications: {'peptide': 771} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 38, 'TRANS': 730} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 7.32, per 1000 atoms: 0.20 Number of scatterers: 37062 At special positions: 0 Unit cell: (179.82, 168.48, 99.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 6840 8.00 N 6330 7.00 C 23718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 351 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 351 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS D 351 " - pdb=" SG CYS D 420 " distance=2.03 Simple disulfide: pdb=" SG CYS E 351 " - pdb=" SG CYS E 420 " distance=2.03 Simple disulfide: pdb=" SG CYS F 351 " - pdb=" SG CYS F 420 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.7 seconds 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8424 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 54 sheets defined 25.4% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.531A pdb=" N TRP A 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 290 through 304 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 335 through 346 Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.419A pdb=" N GLU A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 417 Processing helix chain 'A' and resid 440 through 464 removed outlier: 4.087A pdb=" N ASN A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA A 449 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.610A pdb=" N GLN A 482 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 Processing helix chain 'A' and resid 529 through 541 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.728A pdb=" N CYS A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 592 Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.664A pdb=" N GLU A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.531A pdb=" N TRP B 54 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 290 through 304 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 363 through 372 removed outlier: 4.419A pdb=" N GLU B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 417 Processing helix chain 'B' and resid 440 through 464 removed outlier: 4.086A pdb=" N ASN B 446 " --> pdb=" O GLN B 442 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA B 449 " --> pdb=" O HIS B 445 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.609A pdb=" N GLN B 482 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 560 through 577 removed outlier: 3.729A pdb=" N CYS B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 592 Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.664A pdb=" N GLU B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 610 Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.531A pdb=" N TRP C 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 290 through 304 Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 335 through 346 Processing helix chain 'C' and resid 363 through 372 removed outlier: 4.420A pdb=" N GLU C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 417 Processing helix chain 'C' and resid 440 through 464 removed outlier: 4.087A pdb=" N ASN C 446 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA C 449 " --> pdb=" O HIS C 445 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.610A pdb=" N GLN C 482 " --> pdb=" O GLY C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 529 through 541 Processing helix chain 'C' and resid 555 through 559 Processing helix chain 'C' and resid 560 through 577 removed outlier: 3.729A pdb=" N CYS C 564 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 592 Processing helix chain 'C' and resid 598 through 603 removed outlier: 3.664A pdb=" N GLU C 602 " --> pdb=" O ALA C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'D' and resid 51 through 55 removed outlier: 3.531A pdb=" N TRP D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 290 through 304 Processing helix chain 'D' and resid 314 through 318 Processing helix chain 'D' and resid 335 through 346 Processing helix chain 'D' and resid 363 through 372 removed outlier: 4.419A pdb=" N GLU D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 417 Processing helix chain 'D' and resid 440 through 464 removed outlier: 4.086A pdb=" N ASN D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA D 449 " --> pdb=" O HIS D 445 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 483 removed outlier: 3.610A pdb=" N GLN D 482 " --> pdb=" O GLY D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 511 Processing helix chain 'D' and resid 529 through 541 Processing helix chain 'D' and resid 555 through 559 Processing helix chain 'D' and resid 560 through 577 removed outlier: 3.728A pdb=" N CYS D 564 " --> pdb=" O ASP D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 592 Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.664A pdb=" N GLU D 602 " --> pdb=" O ALA D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 610 Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.531A pdb=" N TRP E 54 " --> pdb=" O GLU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 267 Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 290 through 304 Processing helix chain 'E' and resid 314 through 318 Processing helix chain 'E' and resid 335 through 346 Processing helix chain 'E' and resid 363 through 372 removed outlier: 4.420A pdb=" N GLU E 367 " --> pdb=" O PRO E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 417 Processing helix chain 'E' and resid 440 through 464 removed outlier: 4.087A pdb=" N ASN E 446 " --> pdb=" O GLN E 442 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA E 449 " --> pdb=" O HIS E 445 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE E 450 " --> pdb=" O ASN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 483 removed outlier: 3.609A pdb=" N GLN E 482 " --> pdb=" O GLY E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 529 through 541 Processing helix chain 'E' and resid 555 through 559 Processing helix chain 'E' and resid 560 through 577 removed outlier: 3.728A pdb=" N CYS E 564 " --> pdb=" O ASP E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 592 Processing helix chain 'E' and resid 598 through 603 removed outlier: 3.665A pdb=" N GLU E 602 " --> pdb=" O ALA E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.531A pdb=" N TRP F 54 " --> pdb=" O GLU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 290 through 304 Processing helix chain 'F' and resid 314 through 318 Processing helix chain 'F' and resid 335 through 346 Processing helix chain 'F' and resid 363 through 372 removed outlier: 4.419A pdb=" N GLU F 367 " --> pdb=" O PRO F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 417 Processing helix chain 'F' and resid 440 through 464 removed outlier: 4.087A pdb=" N ASN F 446 " --> pdb=" O GLN F 442 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA F 449 " --> pdb=" O HIS F 445 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE F 450 " --> pdb=" O ASN F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 483 removed outlier: 3.609A pdb=" N GLN F 482 " --> pdb=" O GLY F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 529 through 541 Processing helix chain 'F' and resid 555 through 559 Processing helix chain 'F' and resid 560 through 577 removed outlier: 3.728A pdb=" N CYS F 564 " --> pdb=" O ASP F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 592 Processing helix chain 'F' and resid 598 through 603 removed outlier: 3.664A pdb=" N GLU F 602 " --> pdb=" O ALA F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 610 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 removed outlier: 3.913A pdb=" N VAL A 224 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 36 removed outlier: 5.389A pdb=" N VAL A 30 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA A 45 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 104 removed outlier: 4.307A pdb=" N ALA A 127 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 138 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG A 132 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 473 removed outlier: 6.543A pdb=" N LEU A 279 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N HIS A 312 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 281 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA7, first strand: chain 'A' and resid 633 through 638 Processing sheet with id=AA8, first strand: chain 'A' and resid 675 through 679 removed outlier: 5.480A pdb=" N GLU A 692 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR A 743 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 694 " --> pdb=" O THR A 743 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS A 745 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 696 " --> pdb=" O CYS A 745 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG A 747 " --> pdb=" O PHE A 696 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A 698 " --> pdb=" O ARG A 747 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP A 742 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 706 through 712 removed outlier: 6.718A pdb=" N THR A 707 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS A 723 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS A 709 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 721 " --> pdb=" O CYS A 709 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 711 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A 777 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.913A pdb=" N VAL B 224 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 36 removed outlier: 5.389A pdb=" N VAL B 30 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 45 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE B 72 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 100 through 104 removed outlier: 4.307A pdb=" N ALA B 127 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 138 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG B 132 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 472 through 473 removed outlier: 6.543A pdb=" N LEU B 279 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N HIS B 312 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 281 " --> pdb=" O HIS B 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AB6, first strand: chain 'B' and resid 596 through 597 Processing sheet with id=AB7, first strand: chain 'B' and resid 633 through 638 Processing sheet with id=AB8, first strand: chain 'B' and resid 675 through 679 removed outlier: 5.480A pdb=" N GLU B 692 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR B 743 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR B 694 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS B 745 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 696 " --> pdb=" O CYS B 745 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG B 747 " --> pdb=" O PHE B 696 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 698 " --> pdb=" O ARG B 747 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP B 742 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 706 through 712 removed outlier: 6.719A pdb=" N THR B 707 " --> pdb=" O LYS B 723 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS B 723 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS B 709 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 721 " --> pdb=" O CYS B 709 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 711 " --> pdb=" O ILE B 719 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 777 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 22 through 25 removed outlier: 3.912A pdb=" N VAL C 224 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 36 removed outlier: 5.390A pdb=" N VAL C 30 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA C 45 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE C 72 " --> pdb=" O PRO C 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 100 through 104 removed outlier: 4.306A pdb=" N ALA C 127 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR C 138 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG C 132 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 472 through 473 removed outlier: 6.543A pdb=" N LEU C 279 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N HIS C 312 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 281 " --> pdb=" O HIS C 312 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AC6, first strand: chain 'C' and resid 596 through 597 Processing sheet with id=AC7, first strand: chain 'C' and resid 633 through 638 Processing sheet with id=AC8, first strand: chain 'C' and resid 675 through 679 removed outlier: 5.480A pdb=" N GLU C 692 " --> pdb=" O GLY C 741 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR C 743 " --> pdb=" O GLU C 692 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR C 694 " --> pdb=" O THR C 743 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS C 745 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE C 696 " --> pdb=" O CYS C 745 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG C 747 " --> pdb=" O PHE C 696 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU C 698 " --> pdb=" O ARG C 747 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP C 742 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 706 through 712 removed outlier: 6.719A pdb=" N THR C 707 " --> pdb=" O LYS C 723 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS C 723 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS C 709 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR C 721 " --> pdb=" O CYS C 709 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 711 " --> pdb=" O ILE C 719 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 777 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 22 through 25 removed outlier: 3.913A pdb=" N VAL D 224 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 29 through 36 removed outlier: 5.390A pdb=" N VAL D 30 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA D 45 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 72 " --> pdb=" O PRO D 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 100 through 104 removed outlier: 4.307A pdb=" N ALA D 127 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR D 138 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG D 132 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 472 through 473 removed outlier: 6.544A pdb=" N LEU D 279 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N HIS D 312 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU D 281 " --> pdb=" O HIS D 312 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 357 through 358 Processing sheet with id=AD6, first strand: chain 'D' and resid 596 through 597 Processing sheet with id=AD7, first strand: chain 'D' and resid 633 through 638 Processing sheet with id=AD8, first strand: chain 'D' and resid 675 through 679 removed outlier: 5.481A pdb=" N GLU D 692 " --> pdb=" O GLY D 741 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR D 743 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR D 694 " --> pdb=" O THR D 743 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS D 745 " --> pdb=" O THR D 694 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE D 696 " --> pdb=" O CYS D 745 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG D 747 " --> pdb=" O PHE D 696 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU D 698 " --> pdb=" O ARG D 747 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP D 742 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 712 removed outlier: 6.720A pdb=" N THR D 707 " --> pdb=" O LYS D 723 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS D 723 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS D 709 " --> pdb=" O THR D 721 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR D 721 " --> pdb=" O CYS D 709 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL D 711 " --> pdb=" O ILE D 719 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR D 777 " --> pdb=" O GLU D 756 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 22 through 25 removed outlier: 3.913A pdb=" N VAL E 224 " --> pdb=" O THR E 189 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 29 through 36 removed outlier: 5.389A pdb=" N VAL E 30 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 45 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE E 72 " --> pdb=" O PRO E 68 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 100 through 104 removed outlier: 4.307A pdb=" N ALA E 127 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR E 138 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG E 132 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG E 136 " --> pdb=" O ARG E 132 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 472 through 473 removed outlier: 6.544A pdb=" N LEU E 279 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N HIS E 312 " --> pdb=" O LEU E 279 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU E 281 " --> pdb=" O HIS E 312 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 357 through 358 Processing sheet with id=AE6, first strand: chain 'E' and resid 596 through 597 Processing sheet with id=AE7, first strand: chain 'E' and resid 633 through 638 Processing sheet with id=AE8, first strand: chain 'E' and resid 675 through 679 removed outlier: 5.481A pdb=" N GLU E 692 " --> pdb=" O GLY E 741 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR E 743 " --> pdb=" O GLU E 692 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR E 694 " --> pdb=" O THR E 743 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS E 745 " --> pdb=" O THR E 694 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE E 696 " --> pdb=" O CYS E 745 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG E 747 " --> pdb=" O PHE E 696 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU E 698 " --> pdb=" O ARG E 747 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP E 742 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 706 through 712 removed outlier: 6.718A pdb=" N THR E 707 " --> pdb=" O LYS E 723 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS E 723 " --> pdb=" O THR E 707 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS E 709 " --> pdb=" O THR E 721 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR E 721 " --> pdb=" O CYS E 709 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL E 711 " --> pdb=" O ILE E 719 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 777 " --> pdb=" O GLU E 756 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 22 through 25 removed outlier: 3.913A pdb=" N VAL F 224 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 29 through 36 removed outlier: 5.390A pdb=" N VAL F 30 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA F 45 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE F 72 " --> pdb=" O PRO F 68 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 100 through 104 removed outlier: 4.307A pdb=" N ALA F 127 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR F 138 " --> pdb=" O PHE F 130 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG F 132 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 472 through 473 removed outlier: 6.543A pdb=" N LEU F 279 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N HIS F 312 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU F 281 " --> pdb=" O HIS F 312 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 357 through 358 Processing sheet with id=AF6, first strand: chain 'F' and resid 596 through 597 Processing sheet with id=AF7, first strand: chain 'F' and resid 633 through 638 Processing sheet with id=AF8, first strand: chain 'F' and resid 675 through 679 removed outlier: 5.480A pdb=" N GLU F 692 " --> pdb=" O GLY F 741 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR F 743 " --> pdb=" O GLU F 692 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR F 694 " --> pdb=" O THR F 743 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS F 745 " --> pdb=" O THR F 694 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE F 696 " --> pdb=" O CYS F 745 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG F 747 " --> pdb=" O PHE F 696 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU F 698 " --> pdb=" O ARG F 747 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP F 742 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 706 through 712 removed outlier: 6.718A pdb=" N THR F 707 " --> pdb=" O LYS F 723 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS F 723 " --> pdb=" O THR F 707 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS F 709 " --> pdb=" O THR F 721 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR F 721 " --> pdb=" O CYS F 709 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL F 711 " --> pdb=" O ILE F 719 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR F 777 " --> pdb=" O GLU F 756 " (cutoff:3.500A) 1530 hydrogen bonds defined for protein. 4140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.74 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12138 1.35 - 1.46: 9738 1.46 - 1.58: 16002 1.58 - 1.70: 0 1.70 - 1.82: 276 Bond restraints: 38154 Sorted by residual: bond pdb=" CA ILE F 429 " pdb=" CB ILE F 429 " ideal model delta sigma weight residual 1.537 1.526 0.011 1.29e-02 6.01e+03 6.99e-01 bond pdb=" CA ILE C 429 " pdb=" CB ILE C 429 " ideal model delta sigma weight residual 1.537 1.527 0.011 1.29e-02 6.01e+03 6.84e-01 bond pdb=" CA ILE D 429 " pdb=" CB ILE D 429 " ideal model delta sigma weight residual 1.537 1.527 0.010 1.29e-02 6.01e+03 6.50e-01 bond pdb=" CA ILE E 429 " pdb=" CB ILE E 429 " ideal model delta sigma weight residual 1.537 1.527 0.010 1.29e-02 6.01e+03 6.48e-01 bond pdb=" CA ILE B 429 " pdb=" CB ILE B 429 " ideal model delta sigma weight residual 1.537 1.527 0.010 1.29e-02 6.01e+03 6.42e-01 ... (remaining 38149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 50193 0.96 - 1.93: 1211 1.93 - 2.89: 210 2.89 - 3.85: 211 3.85 - 4.81: 21 Bond angle restraints: 51846 Sorted by residual: angle pdb=" N VAL B 28 " pdb=" CA VAL B 28 " pdb=" C VAL B 28 " ideal model delta sigma weight residual 113.71 110.19 3.52 9.50e-01 1.11e+00 1.37e+01 angle pdb=" N VAL A 28 " pdb=" CA VAL A 28 " pdb=" C VAL A 28 " ideal model delta sigma weight residual 113.71 110.21 3.50 9.50e-01 1.11e+00 1.35e+01 angle pdb=" N VAL F 28 " pdb=" CA VAL F 28 " pdb=" C VAL F 28 " ideal model delta sigma weight residual 113.71 110.23 3.48 9.50e-01 1.11e+00 1.34e+01 angle pdb=" N VAL C 28 " pdb=" CA VAL C 28 " pdb=" C VAL C 28 " ideal model delta sigma weight residual 113.71 110.24 3.47 9.50e-01 1.11e+00 1.34e+01 angle pdb=" N VAL E 28 " pdb=" CA VAL E 28 " pdb=" C VAL E 28 " ideal model delta sigma weight residual 113.71 110.24 3.47 9.50e-01 1.11e+00 1.33e+01 ... (remaining 51841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 19909 17.99 - 35.99: 1517 35.99 - 53.98: 474 53.98 - 71.98: 150 71.98 - 89.97: 72 Dihedral angle restraints: 22122 sinusoidal: 8892 harmonic: 13230 Sorted by residual: dihedral pdb=" CA CYS C 351 " pdb=" C CYS C 351 " pdb=" N VAL C 352 " pdb=" CA VAL C 352 " ideal model delta harmonic sigma weight residual 180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA CYS A 351 " pdb=" C CYS A 351 " pdb=" N VAL A 352 " pdb=" CA VAL A 352 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA CYS E 351 " pdb=" C CYS E 351 " pdb=" N VAL E 352 " pdb=" CA VAL E 352 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 22119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3075 0.027 - 0.053: 1496 0.053 - 0.080: 276 0.080 - 0.107: 279 0.107 - 0.133: 208 Chirality restraints: 5334 Sorted by residual: chirality pdb=" CA VAL B 669 " pdb=" N VAL B 669 " pdb=" C VAL B 669 " pdb=" CB VAL B 669 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL D 669 " pdb=" N VAL D 669 " pdb=" C VAL D 669 " pdb=" CB VAL D 669 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL A 669 " pdb=" N VAL A 669 " pdb=" C VAL A 669 " pdb=" CB VAL A 669 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 5331 not shown) Planarity restraints: 6780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 638 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO E 639 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 639 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 639 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 638 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO F 639 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 639 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 639 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 638 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO D 639 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 639 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 639 " -0.021 5.00e-02 4.00e+02 ... (remaining 6777 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 21533 3.03 - 3.50: 36624 3.50 - 3.96: 58165 3.96 - 4.43: 70111 4.43 - 4.90: 112686 Nonbonded interactions: 299119 Sorted by model distance: nonbonded pdb=" O ASP A 650 " pdb=" OD1 ASP A 650 " model vdw 2.561 3.040 nonbonded pdb=" O ASP C 650 " pdb=" OD1 ASP C 650 " model vdw 2.561 3.040 nonbonded pdb=" O ASP D 650 " pdb=" OD1 ASP D 650 " model vdw 2.562 3.040 nonbonded pdb=" O ASP E 650 " pdb=" OD1 ASP E 650 " model vdw 2.562 3.040 nonbonded pdb=" O ASP F 650 " pdb=" OD1 ASP F 650 " model vdw 2.562 3.040 ... (remaining 299114 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: 0.12 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.340 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 0.025 38160 Z= 0.079 Angle : 0.431 4.813 51858 Z= 0.226 Chirality : 0.042 0.133 5334 Planarity : 0.003 0.038 6780 Dihedral : 15.870 89.975 13680 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 0.92 % Allowed : 13.50 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.13), residues: 4614 helix: 3.76 (0.17), residues: 924 sheet: 0.62 (0.15), residues: 1362 loop : -0.78 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 268 TYR 0.013 0.001 TYR D 208 PHE 0.012 0.001 PHE B 238 TRP 0.010 0.001 TRP F 557 HIS 0.002 0.000 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00166 (38154) covalent geometry : angle 0.42894 (51846) SS BOND : bond 0.00279 ( 6) SS BOND : angle 3.00102 ( 12) hydrogen bonds : bond 0.13683 ( 1530) hydrogen bonds : angle 5.47867 ( 4140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.536 Fit side-chains REVERT: A 546 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7522 (tmm-80) REVERT: B 546 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7523 (tmm-80) REVERT: C 546 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7545 (tmm-80) REVERT: D 546 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7478 (tmm-80) REVERT: E 546 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7513 (tmm-80) REVERT: F 546 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7598 (tmm-80) outliers start: 36 outliers final: 18 residues processed: 149 average time/residue: 0.2444 time to fit residues: 60.9338 Evaluate side-chains 139 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 546 ARG Chi-restraints excluded: chain D residue 339 MET Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 483 PHE Chi-restraints excluded: chain E residue 546 ARG Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 483 PHE Chi-restraints excluded: chain F residue 546 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 10.0000 overall best weight: 7.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN B 481 GLN C 481 GLN D 481 GLN E 481 GLN F 481 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.050631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.038311 restraints weight = 125666.020| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 3.86 r_work: 0.2414 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 38160 Z= 0.263 Angle : 0.586 5.417 51858 Z= 0.310 Chirality : 0.047 0.149 5334 Planarity : 0.004 0.041 6780 Dihedral : 5.313 54.627 5100 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 1.84 % Allowed : 14.26 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.49 (0.13), residues: 4614 helix: 2.93 (0.17), residues: 954 sheet: 0.59 (0.15), residues: 1368 loop : -1.02 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 52 TYR 0.014 0.002 TYR F 208 PHE 0.015 0.002 PHE D 316 TRP 0.013 0.001 TRP E 126 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00611 (38154) covalent geometry : angle 0.58342 (51846) SS BOND : bond 0.00382 ( 6) SS BOND : angle 3.87340 ( 12) hydrogen bonds : bond 0.04691 ( 1530) hydrogen bonds : angle 4.88706 ( 4140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 114 time to evaluate : 1.487 Fit side-chains REVERT: A 126 TRP cc_start: 0.9336 (OUTLIER) cc_final: 0.8704 (t-100) REVERT: A 314 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8729 (t0) REVERT: B 126 TRP cc_start: 0.9337 (OUTLIER) cc_final: 0.8806 (t-100) REVERT: B 314 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8751 (t0) REVERT: C 126 TRP cc_start: 0.9349 (OUTLIER) cc_final: 0.8694 (t-100) REVERT: C 314 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8700 (t0) REVERT: D 126 TRP cc_start: 0.9337 (OUTLIER) cc_final: 0.8601 (t-100) REVERT: D 314 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8738 (t0) REVERT: E 126 TRP cc_start: 0.9326 (OUTLIER) cc_final: 0.8798 (t-100) REVERT: E 314 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8751 (t0) REVERT: F 126 TRP cc_start: 0.9330 (OUTLIER) cc_final: 0.8701 (t-100) REVERT: F 314 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8710 (t0) outliers start: 72 outliers final: 20 residues processed: 180 average time/residue: 0.1969 time to fit residues: 63.0206 Evaluate side-chains 142 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain C residue 126 TRP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 126 TRP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain E residue 126 TRP Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 711 VAL Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 711 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 425 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 chunk 306 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 449 optimal weight: 10.0000 chunk 406 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.2887 r_free = 0.2887 target = 0.049259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.036925 restraints weight = 127065.135| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 3.81 r_work: 0.2348 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 38160 Z= 0.270 Angle : 0.549 5.290 51858 Z= 0.292 Chirality : 0.046 0.180 5334 Planarity : 0.004 0.043 6780 Dihedral : 4.792 55.693 5046 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 1.76 % Allowed : 16.51 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.27 (0.13), residues: 4614 helix: 2.56 (0.17), residues: 984 sheet: 0.48 (0.15), residues: 1374 loop : -1.14 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 176 TYR 0.017 0.002 TYR F 208 PHE 0.012 0.001 PHE D 316 TRP 0.012 0.001 TRP F 317 HIS 0.006 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00625 (38154) covalent geometry : angle 0.54734 (51846) SS BOND : bond 0.00342 ( 6) SS BOND : angle 2.55872 ( 12) hydrogen bonds : bond 0.04845 ( 1530) hydrogen bonds : angle 4.88119 ( 4140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 108 time to evaluate : 1.481 Fit side-chains REVERT: A 314 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8746 (t0) REVERT: A 540 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8224 (mp) REVERT: B 314 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8769 (t0) REVERT: C 314 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8674 (t0) REVERT: C 540 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8239 (mp) REVERT: D 314 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8748 (t0) REVERT: D 540 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8229 (mp) REVERT: E 314 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8768 (t0) REVERT: F 314 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8672 (t0) REVERT: F 540 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8237 (mp) outliers start: 69 outliers final: 21 residues processed: 167 average time/residue: 0.1951 time to fit residues: 58.4697 Evaluate side-chains 139 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 540 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 183 optimal weight: 9.9990 chunk 380 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 405 optimal weight: 6.9990 chunk 437 optimal weight: 1.9990 chunk 375 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 = 0.2891 r_free = 0.2891 target = 0.049471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.037132 restraints weight = 126735.161| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 3.84 r_work: 0.2354 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 38160 Z= 0.214 Angle : 0.511 5.062 51858 Z= 0.271 Chirality : 0.044 0.152 5334 Planarity : 0.004 0.045 6780 Dihedral : 4.765 56.092 5046 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.51 % Favored : 95.36 % Rotamer: Outliers : 2.15 % Allowed : 16.82 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.20 (0.13), residues: 4614 helix: 2.52 (0.17), residues: 984 sheet: 0.46 (0.15), residues: 1374 loop : -1.21 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 176 TYR 0.016 0.001 TYR D 208 PHE 0.011 0.001 PHE B 238 TRP 0.012 0.001 TRP F 317 HIS 0.003 0.001 HIS E 486 Details of bonding type rmsd covalent geometry : bond 0.00499 (38154) covalent geometry : angle 0.51100 (51846) SS BOND : bond 0.00102 ( 6) SS BOND : angle 1.32432 ( 12) hydrogen bonds : bond 0.04340 ( 1530) hydrogen bonds : angle 4.72491 ( 4140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 110 time to evaluate : 1.511 Fit side-chains REVERT: A 314 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8702 (t0) REVERT: A 707 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8436 (p) REVERT: B 314 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8733 (t0) REVERT: B 707 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8392 (p) REVERT: C 314 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8660 (t0) REVERT: C 707 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8308 (p) REVERT: D 314 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8708 (t0) REVERT: D 707 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8441 (p) REVERT: E 314 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8731 (t0) REVERT: E 707 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8382 (p) REVERT: F 314 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8674 (t0) REVERT: F 707 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8306 (p) outliers start: 84 outliers final: 39 residues processed: 186 average time/residue: 0.1716 time to fit residues: 57.5818 Evaluate side-chains 159 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 707 THR Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 707 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 600 MET Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 707 THR Chi-restraints excluded: chain F residue 711 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 138 optimal weight: 10.0000 chunk 436 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 340 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 287 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 chunk 329 optimal weight: 1.9990 chunk 445 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.2893 r_free = 0.2893 target = 0.049565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.037218 restraints weight = 125832.447| |-----------------------------------------------------------------------------| r_work (start): 0.2530 rms_B_bonded: 3.83 r_work: 0.2355 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 38160 Z= 0.203 Angle : 0.504 5.505 51858 Z= 0.267 Chirality : 0.044 0.162 5334 Planarity : 0.004 0.044 6780 Dihedral : 4.739 56.172 5046 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 2.25 % Allowed : 17.02 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.21 (0.13), residues: 4614 helix: 2.54 (0.17), residues: 984 sheet: 0.50 (0.15), residues: 1374 loop : -1.24 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.016 0.001 TYR D 208 PHE 0.011 0.001 PHE F 238 TRP 0.013 0.001 TRP E 317 HIS 0.003 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00472 (38154) covalent geometry : angle 0.50350 (51846) SS BOND : bond 0.00059 ( 6) SS BOND : angle 0.99411 ( 12) hydrogen bonds : bond 0.04224 ( 1530) hydrogen bonds : angle 4.66665 ( 4140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 108 time to evaluate : 1.297 Fit side-chains REVERT: A 314 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8692 (t0) REVERT: A 707 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8447 (p) REVERT: B 314 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8732 (t0) REVERT: B 707 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8403 (p) REVERT: C 128 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8451 (tt) REVERT: C 314 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8649 (t0) REVERT: C 707 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8318 (p) REVERT: D 128 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (tt) REVERT: D 314 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8679 (t0) REVERT: D 707 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8443 (p) REVERT: E 314 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8710 (t0) REVERT: E 707 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8397 (p) REVERT: F 314 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8659 (t70) REVERT: F 707 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8328 (p) outliers start: 88 outliers final: 38 residues processed: 189 average time/residue: 0.1817 time to fit residues: 61.6411 Evaluate side-chains 160 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 487 TRP Chi-restraints excluded: chain D residue 707 THR Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 707 THR Chi-restraints excluded: chain E residue 711 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 600 MET Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 707 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 304 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 336 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 266 optimal weight: 0.4980 chunk 398 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- 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 = 0.2907 r_free = 0.2907 target = 0.049876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.037698 restraints weight = 126181.102| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 3.65 r_work: 0.2384 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 38160 Z= 0.196 Angle : 0.529 7.050 51858 Z= 0.279 Chirality : 0.044 0.148 5334 Planarity : 0.004 0.043 6780 Dihedral : 4.770 56.632 5046 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 2.40 % Allowed : 16.49 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.23 (0.13), residues: 4614 helix: 2.55 (0.17), residues: 984 sheet: 0.56 (0.15), residues: 1374 loop : -1.26 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.015 0.001 TYR D 208 PHE 0.011 0.001 PHE F 238 TRP 0.012 0.001 TRP C 317 HIS 0.003 0.001 HIS E 312 Details of bonding type rmsd covalent geometry : bond 0.00454 (38154) covalent geometry : angle 0.52321 (51846) SS BOND : bond 0.00481 ( 6) SS BOND : angle 5.27822 ( 12) hydrogen bonds : bond 0.04156 ( 1530) hydrogen bonds : angle 4.62496 ( 4140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 108 time to evaluate : 1.785 Fit side-chains REVERT: A 128 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8376 (tt) REVERT: A 314 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8714 (t0) REVERT: A 707 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 314 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8742 (t0) REVERT: B 707 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8465 (p) REVERT: C 128 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8497 (tt) REVERT: C 314 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8684 (t70) REVERT: C 707 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8368 (p) REVERT: D 128 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8377 (tt) REVERT: D 314 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8718 (t0) REVERT: D 707 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8511 (p) REVERT: E 314 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8756 (t0) REVERT: E 707 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8463 (p) REVERT: F 128 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8487 (tt) REVERT: F 314 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8685 (t70) REVERT: F 707 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8381 (p) outliers start: 94 outliers final: 52 residues processed: 195 average time/residue: 0.2047 time to fit residues: 70.6606 Evaluate side-chains 176 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 108 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 487 TRP Chi-restraints excluded: chain D residue 707 THR Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 487 TRP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 707 THR Chi-restraints excluded: chain E residue 711 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 487 TRP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 600 MET Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 707 THR Chi-restraints excluded: chain F residue 711 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 165 optimal weight: 6.9990 chunk 443 optimal weight: 5.9990 chunk 435 optimal weight: 0.8980 chunk 312 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 283 optimal weight: 8.9990 chunk 444 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 518 HIS ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.051758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.039587 restraints weight = 123933.845| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 3.79 r_work: 0.2447 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 38160 Z= 0.094 Angle : 0.480 6.911 51858 Z= 0.251 Chirality : 0.042 0.167 5334 Planarity : 0.004 0.041 6780 Dihedral : 4.507 56.466 5046 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 1.84 % Allowed : 17.13 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.32 (0.13), residues: 4614 helix: 2.49 (0.17), residues: 1020 sheet: 0.70 (0.15), residues: 1374 loop : -1.26 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.015 0.001 TYR D 208 PHE 0.011 0.001 PHE B 238 TRP 0.014 0.001 TRP D 557 HIS 0.003 0.000 HIS D 486 Details of bonding type rmsd covalent geometry : bond 0.00209 (38154) covalent geometry : angle 0.47571 (51846) SS BOND : bond 0.00460 ( 6) SS BOND : angle 4.42219 ( 12) hydrogen bonds : bond 0.03353 ( 1530) hydrogen bonds : angle 4.41092 ( 4140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 116 time to evaluate : 1.439 Fit side-chains REVERT: A 128 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8348 (tt) REVERT: A 314 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8585 (t0) REVERT: B 314 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8607 (t0) REVERT: C 314 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8638 (t70) REVERT: D 128 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8344 (tt) REVERT: D 314 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8595 (t0) REVERT: E 314 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8647 (t0) REVERT: F 314 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8630 (t70) outliers start: 72 outliers final: 41 residues processed: 183 average time/residue: 0.1850 time to fit residues: 60.0061 Evaluate side-chains 160 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 487 TRP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 711 VAL Chi-restraints excluded: chain E residue 778 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 487 TRP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 778 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 136 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 281 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 443 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.2931 r_free = 0.2931 target = 0.050730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.038546 restraints weight = 125435.832| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 3.68 r_work: 0.2422 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 38160 Z= 0.169 Angle : 0.499 7.426 51858 Z= 0.260 Chirality : 0.044 0.145 5334 Planarity : 0.004 0.041 6780 Dihedral : 4.561 56.473 5046 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 1.66 % Allowed : 16.92 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.31 (0.13), residues: 4614 helix: 2.48 (0.17), residues: 1020 sheet: 0.66 (0.15), residues: 1368 loop : -1.23 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 176 TYR 0.015 0.001 TYR A 208 PHE 0.011 0.001 PHE E 238 TRP 0.013 0.001 TRP C 317 HIS 0.002 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00391 (38154) covalent geometry : angle 0.49435 (51846) SS BOND : bond 0.00262 ( 6) SS BOND : angle 4.25464 ( 12) hydrogen bonds : bond 0.03779 ( 1530) hydrogen bonds : angle 4.45764 ( 4140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 110 time to evaluate : 1.529 Fit side-chains REVERT: A 128 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8339 (tt) REVERT: A 314 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8682 (t0) REVERT: B 314 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8742 (t0) REVERT: C 314 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8727 (t70) REVERT: D 128 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8341 (tt) REVERT: D 314 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8703 (t0) REVERT: D 546 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8331 (mmm-85) REVERT: E 314 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8748 (t0) REVERT: F 314 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8725 (t70) outliers start: 65 outliers final: 50 residues processed: 172 average time/residue: 0.2089 time to fit residues: 63.0555 Evaluate side-chains 169 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 110 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 487 TRP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 711 VAL Chi-restraints excluded: chain E residue 778 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 487 TRP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 778 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 34 optimal weight: 10.0000 chunk 152 optimal weight: 0.0670 chunk 382 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 317 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 453 optimal weight: 20.0000 overall best weight: 6.0126 ------------------------------------------------------------------------------- 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 = 0.2902 r_free = 0.2902 target = 0.049686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.037520 restraints weight = 127222.024| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 3.67 r_work: 0.2373 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 38160 Z= 0.218 Angle : 0.535 9.054 51858 Z= 0.280 Chirality : 0.044 0.153 5334 Planarity : 0.004 0.041 6780 Dihedral : 4.718 56.507 5046 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 1.92 % Allowed : 16.56 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.24 (0.13), residues: 4614 helix: 2.43 (0.17), residues: 1020 sheet: 0.74 (0.15), residues: 1338 loop : -1.36 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 176 TYR 0.016 0.001 TYR F 208 PHE 0.011 0.001 PHE C 238 TRP 0.012 0.001 TRP C 317 HIS 0.003 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00506 (38154) covalent geometry : angle 0.53103 (51846) SS BOND : bond 0.00354 ( 6) SS BOND : angle 4.52653 ( 12) hydrogen bonds : bond 0.04243 ( 1530) hydrogen bonds : angle 4.57283 ( 4140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 108 time to evaluate : 1.436 Fit side-chains REVERT: A 128 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8353 (tt) REVERT: A 314 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8730 (t0) REVERT: A 546 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8325 (mmm-85) REVERT: B 314 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8777 (t0) REVERT: C 314 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8745 (t0) REVERT: D 128 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8352 (tt) REVERT: D 314 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8733 (t0) REVERT: E 314 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8765 (t0) REVERT: F 314 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8738 (t0) outliers start: 75 outliers final: 54 residues processed: 180 average time/residue: 0.1882 time to fit residues: 60.2452 Evaluate side-chains 171 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 108 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 487 TRP Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 487 TRP Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 711 VAL Chi-restraints excluded: chain E residue 778 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 487 TRP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 545 SER Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 778 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 400 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 397 optimal weight: 0.9980 chunk 124 optimal weight: 0.1980 chunk 266 optimal weight: 0.9990 chunk 337 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.040218 restraints weight = 124457.429| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.52 r_work: 0.2485 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 38160 Z= 0.087 Angle : 0.474 9.059 51858 Z= 0.247 Chirality : 0.043 0.156 5334 Planarity : 0.004 0.042 6780 Dihedral : 4.461 56.249 5046 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.80 % Rotamer: Outliers : 1.43 % Allowed : 16.95 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.39 (0.13), residues: 4614 helix: 2.54 (0.17), residues: 1020 sheet: 1.06 (0.16), residues: 1302 loop : -1.38 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 597 TYR 0.014 0.001 TYR F 208 PHE 0.011 0.001 PHE F 238 TRP 0.014 0.001 TRP A 557 HIS 0.002 0.000 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00190 (38154) covalent geometry : angle 0.47003 (51846) SS BOND : bond 0.00376 ( 6) SS BOND : angle 3.81432 ( 12) hydrogen bonds : bond 0.03271 ( 1530) hydrogen bonds : angle 4.35863 ( 4140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9228 Ramachandran restraints generated. 4614 Oldfield, 0 Emsley, 4614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 1.295 Fit side-chains REVERT: A 128 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 314 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8769 (t0) REVERT: B 314 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8763 (t0) REVERT: C 314 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8831 (t70) REVERT: D 128 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8555 (tt) REVERT: D 314 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8775 (t0) REVERT: D 546 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8511 (mmm-85) REVERT: E 314 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8764 (t0) REVERT: F 314 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8807 (t70) outliers start: 56 outliers final: 43 residues processed: 174 average time/residue: 0.2057 time to fit residues: 63.1769 Evaluate side-chains 166 residues out of total 3912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 487 TRP Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 487 TRP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 711 VAL Chi-restraints excluded: chain E residue 778 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 472 PHE Chi-restraints excluded: chain F residue 487 TRP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 778 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 323 optimal weight: 9.9990 chunk 307 optimal weight: 40.0000 chunk 127 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 398 optimal weight: 20.0000 chunk 418 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 452 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 overall best weight: 5.9590 ------------------------------------------------------------------------------- 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 = 0.2928 r_free = 0.2928 target = 0.050218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.038180 restraints weight = 126421.364| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 3.46 r_work: 0.2416 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 38160 Z= 0.211 Angle : 0.530 9.232 51858 Z= 0.275 Chirality : 0.044 0.147 5334 Planarity : 0.004 0.042 6780 Dihedral : 4.623 55.915 5046 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 1.61 % Allowed : 16.67 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.30 (0.13), residues: 4614 helix: 2.44 (0.17), residues: 1020 sheet: 0.96 (0.16), residues: 1302 loop : -1.38 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 176 TYR 0.017 0.001 TYR F 208 PHE 0.011 0.001 PHE F 238 TRP 0.012 0.001 TRP C 317 HIS 0.003 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00490 (38154) covalent geometry : angle 0.52543 (51846) SS BOND : bond 0.00312 ( 6) SS BOND : angle 4.34135 ( 12) hydrogen bonds : bond 0.04084 ( 1530) hydrogen bonds : angle 4.49789 ( 4140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6104.05 seconds wall clock time: 106 minutes 25.62 seconds (6385.62 seconds total)