Starting phenix.real_space_refine on Sat May 17 05:38:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwo_35775/05_2025/8iwo_35775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwo_35775/05_2025/8iwo_35775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwo_35775/05_2025/8iwo_35775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwo_35775/05_2025/8iwo_35775.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwo_35775/05_2025/8iwo_35775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwo_35775/05_2025/8iwo_35775.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 9826 2.51 5 N 2516 2.21 5 O 2704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15118 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7516 Classifications: {'peptide': 956} Link IDs: {'PTRANS': 32, 'TRANS': 923} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 18.78, per 1000 atoms: 1.24 Number of scatterers: 15118 At special positions: 0 Unit cell: (107.06, 100.7, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 2 15.00 O 2704 8.00 N 2516 7.00 C 9826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.8 seconds 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3556 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 8 sheets defined 69.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 4.098A pdb=" N VAL A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 54 removed outlier: 3.658A pdb=" N THR A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.571A pdb=" N ILE A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 91 removed outlier: 4.003A pdb=" N LEU A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.180A pdb=" N GLU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 127 removed outlier: 3.775A pdb=" N ILE A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 161 through 191 removed outlier: 3.633A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 227 Processing helix chain 'A' and resid 232 through 254 removed outlier: 3.900A pdb=" N GLU A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 273 removed outlier: 3.708A pdb=" N THR A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 282 through 317 Processing helix chain 'A' and resid 324 through 353 removed outlier: 4.128A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 361 through 370 removed outlier: 4.121A pdb=" N LEU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 390 removed outlier: 3.784A pdb=" N LEU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 430 removed outlier: 3.661A pdb=" N SER A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 460 Processing helix chain 'A' and resid 471 through 477 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.840A pdb=" N LEU A 482 " --> pdb=" O ILE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 528 removed outlier: 3.730A pdb=" N ARG A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 547 Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.271A pdb=" N LEU A 561 " --> pdb=" O ASP A 557 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 removed outlier: 4.170A pdb=" N PHE A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 618 removed outlier: 3.664A pdb=" N THR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 593 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 634 Processing helix chain 'A' and resid 634 through 648 Processing helix chain 'A' and resid 650 through 679 removed outlier: 3.884A pdb=" N LYS A 677 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 678 " --> pdb=" O ASN A 674 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 703 Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.845A pdb=" N ASN A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 790 through 797 removed outlier: 3.505A pdb=" N VAL A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.927A pdb=" N ASP A 827 " --> pdb=" O LEU A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 847 removed outlier: 4.276A pdb=" N ILE A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 833 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 834 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 979 through 983 removed outlier: 3.828A pdb=" N LEU A 983 " --> pdb=" O SER A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1021 Processing helix chain 'B' and resid 8 through 29 removed outlier: 4.098A pdb=" N VAL B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 54 removed outlier: 3.659A pdb=" N THR B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.571A pdb=" N ILE B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 removed outlier: 4.003A pdb=" N LEU B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) Proline residue: B 82 - end of helix removed outlier: 4.180A pdb=" N GLU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 127 removed outlier: 3.775A pdb=" N ILE B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 149 through 157 Processing helix chain 'B' and resid 161 through 191 removed outlier: 3.634A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 227 Processing helix chain 'B' and resid 232 through 254 removed outlier: 3.901A pdb=" N GLU B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 273 removed outlier: 3.707A pdb=" N THR B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 282 through 317 Processing helix chain 'B' and resid 324 through 353 removed outlier: 4.128A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 361 through 370 removed outlier: 4.122A pdb=" N LEU B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.784A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 430 removed outlier: 3.661A pdb=" N SER B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN B 423 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 460 Processing helix chain 'B' and resid 471 through 477 Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.840A pdb=" N LEU B 482 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 528 removed outlier: 3.730A pdb=" N ARG B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 547 Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.271A pdb=" N LEU B 561 " --> pdb=" O ASP B 557 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 removed outlier: 4.170A pdb=" N PHE B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 618 removed outlier: 3.664A pdb=" N THR B 588 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 593 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 634 Processing helix chain 'B' and resid 634 through 648 Processing helix chain 'B' and resid 650 through 679 removed outlier: 3.884A pdb=" N LYS B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 678 " --> pdb=" O ASN B 674 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 703 Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.845A pdb=" N ASN B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 790 through 797 removed outlier: 3.505A pdb=" N VAL B 794 " --> pdb=" O GLY B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 827 removed outlier: 3.927A pdb=" N ASP B 827 " --> pdb=" O LEU B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 847 removed outlier: 4.276A pdb=" N ILE B 832 " --> pdb=" O PRO B 828 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 833 " --> pdb=" O SER B 829 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU B 834 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 865 Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 979 through 983 removed outlier: 3.828A pdb=" N LEU B 983 " --> pdb=" O SER B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1021 Processing sheet with id=AA1, first strand: chain 'A' and resid 740 through 742 removed outlier: 3.620A pdb=" N ILE A 763 " --> pdb=" O HIS A 811 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE A 813 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL A 761 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE A 815 " --> pdb=" O TRP A 759 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TRP A 759 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 749 removed outlier: 7.010A pdb=" N MET A 804 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 868 through 872 removed outlier: 6.854A pdb=" N LEU A 945 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU A 888 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL A 947 " --> pdb=" O GLY A 886 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLY A 886 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 906 " --> pdb=" O TYR A 931 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AA5, first strand: chain 'B' and resid 740 through 742 removed outlier: 3.620A pdb=" N ILE B 763 " --> pdb=" O HIS B 811 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE B 813 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL B 761 " --> pdb=" O PHE B 813 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE B 815 " --> pdb=" O TRP B 759 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TRP B 759 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 747 through 749 removed outlier: 7.010A pdb=" N MET B 804 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 868 through 872 removed outlier: 6.855A pdb=" N LEU B 945 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU B 888 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL B 947 " --> pdb=" O GLY B 886 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLY B 886 " --> pdb=" O VAL B 947 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 906 " --> pdb=" O TYR B 931 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 877 through 878 962 hydrogen bonds defined for protein. 2814 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: 4.97 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2398 1.30 - 1.43: 3942 1.43 - 1.56: 8960 1.56 - 1.69: 4 1.69 - 1.82: 124 Bond restraints: 15428 Sorted by residual: bond pdb=" C ASP A 731 " pdb=" O ASP A 731 " ideal model delta sigma weight residual 1.241 1.173 0.068 9.80e-03 1.04e+04 4.85e+01 bond pdb=" C ASP B 731 " pdb=" O ASP B 731 " ideal model delta sigma weight residual 1.241 1.173 0.068 9.80e-03 1.04e+04 4.81e+01 bond pdb=" C ASN B 418 " pdb=" O ASN B 418 " ideal model delta sigma weight residual 1.236 1.179 0.058 1.15e-02 7.56e+03 2.54e+01 bond pdb=" C ASN A 418 " pdb=" O ASN A 418 " ideal model delta sigma weight residual 1.236 1.179 0.058 1.15e-02 7.56e+03 2.52e+01 bond pdb=" C LEU A 119 " pdb=" O LEU A 119 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.26e+01 ... (remaining 15423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 19461 2.19 - 4.38: 1152 4.38 - 6.57: 248 6.57 - 8.76: 29 8.76 - 10.95: 12 Bond angle restraints: 20902 Sorted by residual: angle pdb=" N GLN A 575 " pdb=" CA GLN A 575 " pdb=" C GLN A 575 " ideal model delta sigma weight residual 111.36 101.41 9.95 1.09e+00 8.42e-01 8.33e+01 angle pdb=" N GLN B 575 " pdb=" CA GLN B 575 " pdb=" C GLN B 575 " ideal model delta sigma weight residual 111.36 101.45 9.91 1.09e+00 8.42e-01 8.27e+01 angle pdb=" N GLU B 831 " pdb=" CA GLU B 831 " pdb=" C GLU B 831 " ideal model delta sigma weight residual 113.12 103.58 9.54 1.25e+00 6.40e-01 5.83e+01 angle pdb=" N GLU A 831 " pdb=" CA GLU A 831 " pdb=" C GLU A 831 " ideal model delta sigma weight residual 113.12 103.58 9.54 1.25e+00 6.40e-01 5.83e+01 angle pdb=" CA LEU B 733 " pdb=" C LEU B 733 " pdb=" O LEU B 733 " ideal model delta sigma weight residual 120.82 113.48 7.34 1.05e+00 9.07e-01 4.89e+01 ... (remaining 20897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 8594 25.33 - 50.67: 534 50.67 - 76.00: 54 76.00 - 101.34: 12 101.34 - 126.67: 2 Dihedral angle restraints: 9196 sinusoidal: 3680 harmonic: 5516 Sorted by residual: dihedral pdb=" C GLN B 676 " pdb=" N GLN B 676 " pdb=" CA GLN B 676 " pdb=" CB GLN B 676 " ideal model delta harmonic sigma weight residual -122.60 -111.81 -10.79 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" C GLN A 676 " pdb=" N GLN A 676 " pdb=" CA GLN A 676 " pdb=" CB GLN A 676 " ideal model delta harmonic sigma weight residual -122.60 -111.83 -10.77 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C37 46E A1201 " pdb=" C38 46E A1201 " pdb=" C39 46E A1201 " pdb=" C3A 46E A1201 " ideal model delta sinusoidal sigma weight residual 178.43 -54.90 -126.67 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 9193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2099 0.075 - 0.149: 237 0.149 - 0.224: 81 0.224 - 0.299: 29 0.299 - 0.374: 6 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA ILE A 815 " pdb=" N ILE A 815 " pdb=" C ILE A 815 " pdb=" CB ILE A 815 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA ILE B 815 " pdb=" N ILE B 815 " pdb=" C ILE B 815 " pdb=" CB ILE B 815 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ILE B 805 " pdb=" N ILE B 805 " pdb=" C ILE B 805 " pdb=" CB ILE B 805 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 2449 not shown) Planarity restraints: 2594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 894 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C LYS B 894 " -0.076 2.00e-02 2.50e+03 pdb=" O LYS B 894 " 0.029 2.00e-02 2.50e+03 pdb=" N THR B 895 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 894 " 0.021 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C LYS A 894 " -0.076 2.00e-02 2.50e+03 pdb=" O LYS A 894 " 0.029 2.00e-02 2.50e+03 pdb=" N THR A 895 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 733 " 0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU A 733 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU A 733 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU A 734 " 0.026 2.00e-02 2.50e+03 ... (remaining 2591 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1766 2.75 - 3.28: 15084 3.28 - 3.82: 23909 3.82 - 4.36: 29248 4.36 - 4.90: 51687 Nonbonded interactions: 121694 Sorted by model distance: nonbonded pdb=" O LYS B 699 " pdb=" OD1 ASN B 703 " model vdw 2.207 3.040 nonbonded pdb=" O LYS A 699 " pdb=" OD1 ASN A 703 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP A 696 " pdb=" OG1 THR B 480 " model vdw 2.244 3.040 nonbonded pdb=" O SER A 282 " pdb=" OG SER A 282 " model vdw 2.260 3.040 nonbonded pdb=" O SER B 282 " pdb=" OG SER B 282 " model vdw 2.260 3.040 ... (remaining 121689 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 44.780 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.007 0.071 15428 Z= 0.496 Angle : 1.110 10.951 20902 Z= 0.813 Chirality : 0.063 0.374 2452 Planarity : 0.006 0.049 2594 Dihedral : 15.580 126.673 5640 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.53 % Allowed : 14.15 % Favored : 84.31 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 1896 helix: -0.59 (0.14), residues: 1220 sheet: 0.54 (0.48), residues: 92 loop : -2.35 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 759 HIS 0.017 0.001 HIS A 319 PHE 0.029 0.002 PHE A 814 TYR 0.009 0.001 TYR A 800 ARG 0.005 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.17699 ( 962) hydrogen bonds : angle 7.35268 ( 2814) covalent geometry : bond 0.00668 (15428) covalent geometry : angle 1.11021 (20902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 311 average time/residue: 0.2924 time to fit residues: 131.7159 Evaluate side-chains 213 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 761 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.0040 chunk 144 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 394 HIS A 870 ASN A 897 ASN B 298 ASN B 394 HIS B 418 ASN B 673 GLN B 897 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076400 restraints weight = 29573.787| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.31 r_work: 0.2757 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15428 Z= 0.130 Angle : 0.566 7.644 20902 Z= 0.297 Chirality : 0.039 0.144 2452 Planarity : 0.004 0.043 2594 Dihedral : 8.761 127.076 2158 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.12 % Allowed : 16.79 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1896 helix: 0.98 (0.15), residues: 1252 sheet: 1.17 (0.53), residues: 82 loop : -1.76 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 985 HIS 0.006 0.001 HIS A 719 PHE 0.011 0.001 PHE B 616 TYR 0.015 0.001 TYR B 586 ARG 0.007 0.000 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 962) hydrogen bonds : angle 4.43315 ( 2814) covalent geometry : bond 0.00290 (15428) covalent geometry : angle 0.56580 (20902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 1.685 Fit side-chains REVERT: A 30 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8448 (tpp80) REVERT: A 147 ASP cc_start: 0.8317 (t0) cc_final: 0.8092 (t0) REVERT: A 163 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (ptmt) REVERT: A 323 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7314 (m-70) REVERT: A 685 GLU cc_start: 0.8454 (mp0) cc_final: 0.7813 (mp0) REVERT: A 706 LEU cc_start: 0.8650 (pt) cc_final: 0.8037 (mt) REVERT: A 711 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8646 (mpp80) REVERT: A 776 ARG cc_start: 0.9092 (tpp-160) cc_final: 0.8762 (mmm160) REVERT: A 847 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8259 (tt) REVERT: A 849 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8939 (tpp) REVERT: B 95 HIS cc_start: 0.8279 (p90) cc_final: 0.7239 (p90) REVERT: B 96 GLN cc_start: 0.9016 (mt0) cc_final: 0.8749 (mp10) REVERT: B 147 ASP cc_start: 0.8344 (t0) cc_final: 0.8074 (t0) REVERT: B 163 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (ptmt) REVERT: B 224 LEU cc_start: 0.9064 (mt) cc_final: 0.8830 (tt) REVERT: B 284 GLN cc_start: 0.8297 (tp40) cc_final: 0.8085 (tp-100) REVERT: B 323 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7316 (m-70) REVERT: B 706 LEU cc_start: 0.8601 (pt) cc_final: 0.8025 (mt) REVERT: B 711 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8743 (mpp80) REVERT: B 776 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.8779 (mmm160) REVERT: B 847 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8218 (tt) REVERT: B 849 MET cc_start: 0.9252 (tpp) cc_final: 0.8864 (tpp) outliers start: 51 outliers final: 21 residues processed: 268 average time/residue: 0.2589 time to fit residues: 104.0492 Evaluate side-chains 240 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 41 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 126 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.070954 restraints weight = 30350.848| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.43 r_work: 0.2712 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15428 Z= 0.174 Angle : 0.560 6.431 20902 Z= 0.293 Chirality : 0.040 0.220 2452 Planarity : 0.004 0.040 2594 Dihedral : 8.289 111.305 2140 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.55 % Allowed : 17.46 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1896 helix: 1.68 (0.15), residues: 1246 sheet: 1.43 (0.55), residues: 72 loop : -1.41 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 985 HIS 0.005 0.001 HIS B 606 PHE 0.023 0.001 PHE B 195 TYR 0.010 0.001 TYR A 129 ARG 0.005 0.000 ARG B 866 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 962) hydrogen bonds : angle 4.17232 ( 2814) covalent geometry : bond 0.00405 (15428) covalent geometry : angle 0.56010 (20902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 1.794 Fit side-chains REVERT: A 147 ASP cc_start: 0.8411 (t0) cc_final: 0.8166 (t0) REVERT: A 284 GLN cc_start: 0.8438 (tp-100) cc_final: 0.7922 (tp-100) REVERT: A 323 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7447 (m-70) REVERT: A 685 GLU cc_start: 0.8634 (mp0) cc_final: 0.7979 (mp0) REVERT: A 706 LEU cc_start: 0.8692 (pt) cc_final: 0.8128 (mt) REVERT: A 711 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8649 (mpp80) REVERT: A 776 ARG cc_start: 0.9129 (tpp-160) cc_final: 0.8791 (mmm160) REVERT: A 849 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8944 (tpp) REVERT: B 95 HIS cc_start: 0.8419 (p90) cc_final: 0.8191 (p90) REVERT: B 147 ASP cc_start: 0.8435 (t0) cc_final: 0.8165 (t0) REVERT: B 284 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8079 (tp-100) REVERT: B 323 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7446 (m-70) REVERT: B 541 ARG cc_start: 0.8645 (mtp180) cc_final: 0.8237 (mtp180) REVERT: B 685 GLU cc_start: 0.8615 (mp0) cc_final: 0.8040 (mp0) REVERT: B 706 LEU cc_start: 0.8712 (pt) cc_final: 0.8142 (mt) REVERT: B 776 ARG cc_start: 0.9139 (tpp-160) cc_final: 0.8808 (mmm160) REVERT: B 847 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8498 (tt) REVERT: B 849 MET cc_start: 0.9255 (tpp) cc_final: 0.8895 (tpp) outliers start: 58 outliers final: 34 residues processed: 244 average time/residue: 0.2519 time to fit residues: 93.6028 Evaluate side-chains 230 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.071001 restraints weight = 30188.149| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.41 r_work: 0.2713 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15428 Z= 0.160 Angle : 0.544 7.811 20902 Z= 0.283 Chirality : 0.039 0.139 2452 Planarity : 0.004 0.043 2594 Dihedral : 7.878 84.118 2140 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.88 % Allowed : 18.50 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1896 helix: 2.06 (0.15), residues: 1236 sheet: 1.64 (0.58), residues: 72 loop : -1.23 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 985 HIS 0.005 0.001 HIS B 606 PHE 0.011 0.001 PHE A 117 TYR 0.010 0.001 TYR B 245 ARG 0.004 0.000 ARG B 433 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 962) hydrogen bonds : angle 4.04625 ( 2814) covalent geometry : bond 0.00372 (15428) covalent geometry : angle 0.54356 (20902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 1.571 Fit side-chains REVERT: A 147 ASP cc_start: 0.8395 (t0) cc_final: 0.8195 (t0) REVERT: A 174 MET cc_start: 0.9007 (mmm) cc_final: 0.8757 (mpp) REVERT: A 284 GLN cc_start: 0.8483 (tp-100) cc_final: 0.7958 (tp-100) REVERT: A 323 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7379 (m-70) REVERT: A 685 GLU cc_start: 0.8670 (mp0) cc_final: 0.8085 (mp0) REVERT: A 686 MET cc_start: 0.8680 (tpp) cc_final: 0.8479 (tpt) REVERT: A 706 LEU cc_start: 0.8768 (pt) cc_final: 0.8214 (mt) REVERT: A 711 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8611 (mpp80) REVERT: A 776 ARG cc_start: 0.9070 (tpp-160) cc_final: 0.8786 (mmm160) REVERT: A 847 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8312 (tt) REVERT: B 147 ASP cc_start: 0.8384 (t0) cc_final: 0.8172 (t0) REVERT: B 174 MET cc_start: 0.9006 (mmm) cc_final: 0.8752 (mpp) REVERT: B 284 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8120 (tp-100) REVERT: B 323 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.7423 (m-70) REVERT: B 685 GLU cc_start: 0.8702 (mp0) cc_final: 0.8161 (mp0) REVERT: B 706 LEU cc_start: 0.8751 (pt) cc_final: 0.8251 (mt) REVERT: B 711 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8677 (mpp80) REVERT: B 776 ARG cc_start: 0.9073 (tpp-160) cc_final: 0.8785 (mmm160) REVERT: B 847 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 849 MET cc_start: 0.9264 (tpp) cc_final: 0.8891 (tpp) outliers start: 47 outliers final: 29 residues processed: 242 average time/residue: 0.2453 time to fit residues: 90.6089 Evaluate side-chains 232 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 134 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 175 optimal weight: 0.0970 chunk 50 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 319 HIS A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 319 HIS B 674 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.071827 restraints weight = 30230.540| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.38 r_work: 0.2727 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15428 Z= 0.140 Angle : 0.531 8.412 20902 Z= 0.274 Chirality : 0.039 0.135 2452 Planarity : 0.004 0.043 2594 Dihedral : 7.606 81.570 2140 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.76 % Allowed : 19.18 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.20), residues: 1896 helix: 2.23 (0.15), residues: 1238 sheet: 1.75 (0.58), residues: 72 loop : -1.16 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 985 HIS 0.004 0.001 HIS A 606 PHE 0.012 0.001 PHE B 117 TYR 0.010 0.001 TYR B 245 ARG 0.004 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 962) hydrogen bonds : angle 3.96133 ( 2814) covalent geometry : bond 0.00323 (15428) covalent geometry : angle 0.53055 (20902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.606 Fit side-chains REVERT: A 284 GLN cc_start: 0.8483 (tp-100) cc_final: 0.7943 (tp-100) REVERT: A 323 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7370 (m-70) REVERT: A 541 ARG cc_start: 0.8979 (ttp-170) cc_final: 0.8735 (ttp-170) REVERT: A 685 GLU cc_start: 0.8739 (mp0) cc_final: 0.8118 (mp0) REVERT: A 706 LEU cc_start: 0.8738 (pt) cc_final: 0.8386 (mt) REVERT: A 709 MET cc_start: 0.8538 (mmm) cc_final: 0.8299 (mmm) REVERT: A 711 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8636 (mpp80) REVERT: A 776 ARG cc_start: 0.9040 (tpp-160) cc_final: 0.8719 (mmm160) REVERT: A 847 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8469 (tt) REVERT: B 284 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8080 (tp-100) REVERT: B 323 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7423 (m-70) REVERT: B 402 MET cc_start: 0.8569 (mmt) cc_final: 0.8351 (mmt) REVERT: B 685 GLU cc_start: 0.8802 (mp0) cc_final: 0.8264 (mp0) REVERT: B 706 LEU cc_start: 0.8776 (pt) cc_final: 0.8380 (mt) REVERT: B 711 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8702 (mpp80) REVERT: B 776 ARG cc_start: 0.9058 (tpp-160) cc_final: 0.8613 (mmm-85) REVERT: B 847 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 849 MET cc_start: 0.9224 (tpp) cc_final: 0.8892 (tpp) REVERT: B 1024 MET cc_start: 0.8899 (mtp) cc_final: 0.8634 (mmm) outliers start: 45 outliers final: 29 residues processed: 232 average time/residue: 0.2538 time to fit residues: 89.6596 Evaluate side-chains 227 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 97 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.098500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.071641 restraints weight = 30295.166| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.40 r_work: 0.2722 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15428 Z= 0.144 Angle : 0.542 11.023 20902 Z= 0.279 Chirality : 0.039 0.170 2452 Planarity : 0.004 0.042 2594 Dihedral : 7.056 76.511 2140 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.76 % Allowed : 19.91 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.20), residues: 1896 helix: 2.34 (0.15), residues: 1236 sheet: 1.74 (0.58), residues: 72 loop : -1.15 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 985 HIS 0.005 0.001 HIS B 95 PHE 0.014 0.001 PHE B 117 TYR 0.010 0.001 TYR B 245 ARG 0.003 0.000 ARG B 866 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 962) hydrogen bonds : angle 3.91826 ( 2814) covalent geometry : bond 0.00334 (15428) covalent geometry : angle 0.54237 (20902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.932 Fit side-chains REVERT: A 232 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8443 (t0) REVERT: A 284 GLN cc_start: 0.8520 (tp-100) cc_final: 0.7971 (tp-100) REVERT: A 323 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7395 (m-70) REVERT: A 541 ARG cc_start: 0.8973 (ttp-170) cc_final: 0.8741 (ttp-110) REVERT: A 685 GLU cc_start: 0.8835 (mp0) cc_final: 0.8277 (mp0) REVERT: A 706 LEU cc_start: 0.8791 (pt) cc_final: 0.8444 (mt) REVERT: A 711 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8683 (mpp80) REVERT: A 776 ARG cc_start: 0.9049 (tpp-160) cc_final: 0.8752 (mmm160) REVERT: A 847 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8379 (tt) REVERT: B 284 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8073 (tp-100) REVERT: B 323 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.7436 (m-70) REVERT: B 541 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8324 (ttp-170) REVERT: B 685 GLU cc_start: 0.8865 (mp0) cc_final: 0.8337 (mp0) REVERT: B 706 LEU cc_start: 0.8768 (pt) cc_final: 0.8395 (mt) REVERT: B 709 MET cc_start: 0.8482 (mmm) cc_final: 0.8212 (mmm) REVERT: B 711 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8713 (mpp80) REVERT: B 776 ARG cc_start: 0.9054 (tpp-160) cc_final: 0.8765 (mmm160) REVERT: B 849 MET cc_start: 0.9249 (tpp) cc_final: 0.8882 (tpp) REVERT: B 1024 MET cc_start: 0.8930 (mtp) cc_final: 0.8721 (mmm) outliers start: 45 outliers final: 33 residues processed: 226 average time/residue: 0.2732 time to fit residues: 93.5334 Evaluate side-chains 232 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN B 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073198 restraints weight = 30584.757| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.43 r_work: 0.2757 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15428 Z= 0.115 Angle : 0.528 11.616 20902 Z= 0.271 Chirality : 0.038 0.168 2452 Planarity : 0.004 0.041 2594 Dihedral : 6.627 75.358 2140 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.27 % Allowed : 21.08 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.20), residues: 1896 helix: 2.48 (0.15), residues: 1234 sheet: 1.82 (0.57), residues: 72 loop : -1.14 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 985 HIS 0.006 0.001 HIS B 319 PHE 0.010 0.001 PHE B 117 TYR 0.009 0.001 TYR A 245 ARG 0.007 0.000 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 962) hydrogen bonds : angle 3.83505 ( 2814) covalent geometry : bond 0.00260 (15428) covalent geometry : angle 0.52817 (20902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.838 Fit side-chains REVERT: A 171 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 284 GLN cc_start: 0.8499 (tp-100) cc_final: 0.7991 (tp-100) REVERT: A 323 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7357 (m-70) REVERT: A 541 ARG cc_start: 0.8969 (ttp-170) cc_final: 0.8724 (ttp-110) REVERT: A 685 GLU cc_start: 0.8896 (mp0) cc_final: 0.8347 (mp0) REVERT: A 706 LEU cc_start: 0.8821 (pt) cc_final: 0.8528 (mt) REVERT: A 711 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8669 (mpp80) REVERT: A 776 ARG cc_start: 0.9024 (tpp-160) cc_final: 0.8750 (mmm160) REVERT: A 847 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8301 (tt) REVERT: A 866 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8648 (mtt-85) REVERT: B 74 ASP cc_start: 0.8888 (m-30) cc_final: 0.8554 (p0) REVERT: B 171 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 284 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8098 (tp-100) REVERT: B 323 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7393 (m-70) REVERT: B 541 ARG cc_start: 0.8630 (mtp180) cc_final: 0.8361 (tpp80) REVERT: B 685 GLU cc_start: 0.8842 (mp0) cc_final: 0.8430 (mp0) REVERT: B 706 LEU cc_start: 0.8808 (pt) cc_final: 0.8468 (mt) REVERT: B 711 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8727 (mpp80) REVERT: B 776 ARG cc_start: 0.9033 (tpp-160) cc_final: 0.8769 (mmm160) REVERT: B 847 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8582 (tt) REVERT: B 849 MET cc_start: 0.9223 (tpp) cc_final: 0.8967 (tpp) outliers start: 37 outliers final: 23 residues processed: 243 average time/residue: 0.2435 time to fit residues: 89.8387 Evaluate side-chains 237 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 161 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 109 optimal weight: 0.0170 chunk 162 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.074069 restraints weight = 30301.000| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.42 r_work: 0.2779 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15428 Z= 0.112 Angle : 0.537 11.045 20902 Z= 0.273 Chirality : 0.038 0.173 2452 Planarity : 0.004 0.040 2594 Dihedral : 6.489 78.406 2140 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.14 % Allowed : 21.57 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.20), residues: 1896 helix: 2.57 (0.15), residues: 1234 sheet: 1.61 (0.53), residues: 82 loop : -1.21 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 985 HIS 0.011 0.001 HIS A 319 PHE 0.014 0.001 PHE A 228 TYR 0.009 0.001 TYR A 245 ARG 0.005 0.000 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 962) hydrogen bonds : angle 3.77116 ( 2814) covalent geometry : bond 0.00256 (15428) covalent geometry : angle 0.53727 (20902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 1.828 Fit side-chains REVERT: A 171 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8286 (tm-30) REVERT: A 284 GLN cc_start: 0.8463 (tp-100) cc_final: 0.7950 (tp-100) REVERT: A 323 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7372 (m-70) REVERT: A 541 ARG cc_start: 0.8965 (ttp-170) cc_final: 0.8703 (ttp-110) REVERT: A 685 GLU cc_start: 0.8878 (mp0) cc_final: 0.8455 (mp0) REVERT: A 706 LEU cc_start: 0.8832 (pt) cc_final: 0.8498 (mt) REVERT: A 711 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8669 (mpp80) REVERT: A 776 ARG cc_start: 0.9006 (tpp-160) cc_final: 0.8745 (mmm160) REVERT: A 847 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8221 (tt) REVERT: B 171 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 284 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8224 (tp-100) REVERT: B 323 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7412 (m-70) REVERT: B 402 MET cc_start: 0.8833 (mmm) cc_final: 0.8604 (mmp) REVERT: B 541 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8334 (tpp80) REVERT: B 685 GLU cc_start: 0.8883 (mp0) cc_final: 0.8458 (mp0) REVERT: B 706 LEU cc_start: 0.8725 (pt) cc_final: 0.8377 (mt) REVERT: B 711 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8685 (mpp80) REVERT: B 776 ARG cc_start: 0.8996 (tpp-160) cc_final: 0.8747 (mmm160) REVERT: B 847 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8511 (tt) REVERT: B 849 MET cc_start: 0.9229 (tpp) cc_final: 0.8959 (tpp) outliers start: 35 outliers final: 25 residues processed: 247 average time/residue: 0.2604 time to fit residues: 97.5681 Evaluate side-chains 247 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 145 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 177 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.073635 restraints weight = 30468.113| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.42 r_work: 0.2770 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15428 Z= 0.124 Angle : 0.549 9.556 20902 Z= 0.278 Chirality : 0.039 0.175 2452 Planarity : 0.004 0.040 2594 Dihedral : 6.452 77.652 2140 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.96 % Allowed : 22.30 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.20), residues: 1896 helix: 2.61 (0.15), residues: 1238 sheet: 1.59 (0.53), residues: 82 loop : -1.16 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 985 HIS 0.008 0.001 HIS A 319 PHE 0.011 0.001 PHE B 917 TYR 0.010 0.001 TYR A 245 ARG 0.008 0.000 ARG B 866 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 962) hydrogen bonds : angle 3.76354 ( 2814) covalent geometry : bond 0.00289 (15428) covalent geometry : angle 0.54857 (20902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 1.762 Fit side-chains REVERT: A 171 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 284 GLN cc_start: 0.8478 (tp-100) cc_final: 0.7915 (tp-100) REVERT: A 323 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7412 (m-70) REVERT: A 541 ARG cc_start: 0.8958 (ttp-170) cc_final: 0.8687 (ttp-110) REVERT: A 685 GLU cc_start: 0.8930 (mp0) cc_final: 0.8468 (mp0) REVERT: A 706 LEU cc_start: 0.8778 (pt) cc_final: 0.8464 (mt) REVERT: A 711 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8700 (mpp80) REVERT: A 776 ARG cc_start: 0.9040 (tpp-160) cc_final: 0.8791 (mmm160) REVERT: A 847 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8479 (tt) REVERT: B 74 ASP cc_start: 0.8852 (m-30) cc_final: 0.8619 (p0) REVERT: B 171 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 284 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8073 (tp-100) REVERT: B 323 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7429 (m-70) REVERT: B 402 MET cc_start: 0.8864 (mmm) cc_final: 0.8636 (mmp) REVERT: B 541 ARG cc_start: 0.8666 (mtp180) cc_final: 0.8358 (tpp80) REVERT: B 685 GLU cc_start: 0.8909 (mp0) cc_final: 0.8467 (mp0) REVERT: B 706 LEU cc_start: 0.8683 (pt) cc_final: 0.8383 (mt) REVERT: B 776 ARG cc_start: 0.9005 (tpp-160) cc_final: 0.8761 (mmm160) REVERT: B 847 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8535 (tt) REVERT: B 849 MET cc_start: 0.9234 (tpp) cc_final: 0.8965 (tpp) outliers start: 32 outliers final: 24 residues processed: 233 average time/residue: 0.2739 time to fit residues: 95.9246 Evaluate side-chains 234 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 177 optimal weight: 0.4980 chunk 86 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.099756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.072537 restraints weight = 30505.660| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.42 r_work: 0.2747 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15428 Z= 0.143 Angle : 0.570 10.483 20902 Z= 0.288 Chirality : 0.039 0.184 2452 Planarity : 0.004 0.040 2594 Dihedral : 6.480 72.887 2140 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.96 % Allowed : 22.18 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1896 helix: 2.61 (0.15), residues: 1238 sheet: 1.59 (0.53), residues: 82 loop : -1.14 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 985 HIS 0.006 0.001 HIS A 319 PHE 0.013 0.001 PHE B 228 TYR 0.010 0.001 TYR A 245 ARG 0.008 0.000 ARG B 866 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 962) hydrogen bonds : angle 3.79969 ( 2814) covalent geometry : bond 0.00336 (15428) covalent geometry : angle 0.56989 (20902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.667 Fit side-chains REVERT: A 171 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 284 GLN cc_start: 0.8461 (tp-100) cc_final: 0.7953 (tp-100) REVERT: A 323 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7445 (m-70) REVERT: A 541 ARG cc_start: 0.8938 (ttp-170) cc_final: 0.8663 (ttp-110) REVERT: A 682 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 685 GLU cc_start: 0.8933 (mp0) cc_final: 0.8476 (mp0) REVERT: A 706 LEU cc_start: 0.8824 (pt) cc_final: 0.8535 (mt) REVERT: A 711 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8697 (mpp80) REVERT: A 776 ARG cc_start: 0.9067 (tpp-160) cc_final: 0.8761 (mmm160) REVERT: A 847 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 849 MET cc_start: 0.9110 (mmm) cc_final: 0.8643 (tpp) REVERT: B 74 ASP cc_start: 0.8864 (m-30) cc_final: 0.8622 (p0) REVERT: B 171 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 284 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8061 (tp-100) REVERT: B 323 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7491 (m-70) REVERT: B 402 MET cc_start: 0.8873 (mmm) cc_final: 0.8581 (mmp) REVERT: B 541 ARG cc_start: 0.8636 (mtp180) cc_final: 0.8325 (tpp80) REVERT: B 685 GLU cc_start: 0.8901 (mp0) cc_final: 0.8476 (mp0) REVERT: B 706 LEU cc_start: 0.8749 (pt) cc_final: 0.8497 (mt) REVERT: B 776 ARG cc_start: 0.9030 (tpp-160) cc_final: 0.8779 (mmm160) REVERT: B 847 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8564 (tt) REVERT: B 849 MET cc_start: 0.9252 (tpp) cc_final: 0.8951 (tpp) REVERT: B 866 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8586 (mtt-85) outliers start: 32 outliers final: 26 residues processed: 215 average time/residue: 0.2603 time to fit residues: 84.2951 Evaluate side-chains 224 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 67 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 141 optimal weight: 0.1980 chunk 126 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN B 674 ASN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.074305 restraints weight = 30533.506| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.45 r_work: 0.2785 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15428 Z= 0.116 Angle : 0.551 10.446 20902 Z= 0.277 Chirality : 0.038 0.180 2452 Planarity : 0.004 0.040 2594 Dihedral : 6.414 79.008 2140 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.84 % Allowed : 22.06 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.20), residues: 1896 helix: 2.68 (0.15), residues: 1238 sheet: 1.66 (0.53), residues: 82 loop : -1.16 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 985 HIS 0.005 0.001 HIS B 606 PHE 0.011 0.001 PHE B 917 TYR 0.009 0.001 TYR A 245 ARG 0.008 0.000 ARG B 866 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 962) hydrogen bonds : angle 3.73893 ( 2814) covalent geometry : bond 0.00269 (15428) covalent geometry : angle 0.55093 (20902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6422.38 seconds wall clock time: 112 minutes 38.43 seconds (6758.43 seconds total)