Starting phenix.real_space_refine on Tue Dec 31 09:13:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwo_35775/12_2024/8iwo_35775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwo_35775/12_2024/8iwo_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_35775/12_2024/8iwo_35775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwo_35775/12_2024/8iwo_35775.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwo_35775/12_2024/8iwo_35775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwo_35775/12_2024/8iwo_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 16.95, per 1000 atoms: 1.12 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: 3.99 Conformation dependent library (CDL) restraints added in 1.7 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: 1.85 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: 5.28 Time building geometry restraints manager: 4.51 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: 0.00 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: 1.770 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: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.100 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.940 ------------------------------------------------------------------------------- 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= 0.448 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 *********************** 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 : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 311 average time/residue: 0.2967 time to fit residues: 132.6951 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 : 1.734 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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= 0.187 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 *********************** 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 : 1.744 Fit side-chains REVERT: A 323 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.5969 (m-70) REVERT: A 711 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7144 (mpp80) REVERT: B 95 HIS cc_start: 0.6434 (p90) cc_final: 0.6141 (p90) REVERT: B 323 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.5961 (m-70) outliers start: 51 outliers final: 21 residues processed: 268 average time/residue: 0.2679 time to fit residues: 107.6923 Evaluate side-chains 230 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 810 VAL 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 95 optimal weight: 0.1980 chunk 53 optimal weight: 0.0070 chunk 143 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 870 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2586 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= 0.172 Angle : 0.532 7.248 20902 Z= 0.277 Chirality : 0.039 0.218 2452 Planarity : 0.004 0.038 2594 Dihedral : 8.137 112.159 2140 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.70 % Allowed : 18.32 % 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: 1.23 (0.20), residues: 1896 helix: 1.80 (0.15), residues: 1246 sheet: 1.48 (0.54), residues: 72 loop : -1.52 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 985 HIS 0.004 0.001 HIS B 606 PHE 0.025 0.001 PHE B 195 TYR 0.010 0.001 TYR B 586 ARG 0.006 0.000 ARG B 711 *********************** 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 275 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 1.745 Fit side-chains REVERT: A 323 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.6127 (m-70) REVERT: A 547 MET cc_start: 0.7819 (tpp) cc_final: 0.7500 (tpp) REVERT: A 845 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7985 (mp) REVERT: B 323 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.6103 (m-70) outliers start: 44 outliers final: 25 residues processed: 257 average time/residue: 0.2793 time to fit residues: 108.3111 Evaluate side-chains 227 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 368 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 845 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 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 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 460 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 810 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.0060 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 0.1980 chunk 173 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15428 Z= 0.158 Angle : 0.528 7.746 20902 Z= 0.271 Chirality : 0.038 0.143 2452 Planarity : 0.004 0.038 2594 Dihedral : 7.660 94.696 2140 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.08 % Allowed : 19.42 % Favored : 78.49 % 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: 1.67 (0.20), residues: 1896 helix: 2.13 (0.15), residues: 1248 sheet: 1.58 (0.54), residues: 82 loop : -1.40 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 985 HIS 0.004 0.001 HIS A 319 PHE 0.015 0.001 PHE A 917 TYR 0.009 0.001 TYR A 129 ARG 0.006 0.000 ARG A 711 *********************** 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 258 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 1.715 Fit side-chains REVERT: A 323 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6040 (m-70) REVERT: A 547 MET cc_start: 0.7938 (tpp) cc_final: 0.7599 (tpp) REVERT: A 845 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8075 (mp) REVERT: B 323 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6084 (m-70) REVERT: B 547 MET cc_start: 0.7901 (tpp) cc_final: 0.7561 (tpp) outliers start: 34 outliers final: 22 residues processed: 242 average time/residue: 0.2489 time to fit residues: 91.7456 Evaluate side-chains 221 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 28 LEU 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 810 VAL Chi-restraints excluded: chain A residue 845 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 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 680 LEU Chi-restraints excluded: chain B residue 810 VAL 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 152 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15428 Z= 0.188 Angle : 0.526 10.022 20902 Z= 0.272 Chirality : 0.039 0.129 2452 Planarity : 0.004 0.039 2594 Dihedral : 7.171 77.485 2140 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.57 % Allowed : 19.61 % Favored : 77.82 % 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: 1.91 (0.20), residues: 1896 helix: 2.33 (0.15), residues: 1238 sheet: 1.76 (0.56), residues: 72 loop : -1.22 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 985 HIS 0.004 0.001 HIS B 606 PHE 0.013 0.001 PHE B 228 TYR 0.010 0.001 TYR A 245 ARG 0.004 0.000 ARG B 433 *********************** 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 250 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 1.771 Fit side-chains REVERT: A 323 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.6053 (m-70) REVERT: A 547 MET cc_start: 0.8001 (tpp) cc_final: 0.7640 (tpp) REVERT: B 323 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.6113 (m-70) outliers start: 42 outliers final: 31 residues processed: 234 average time/residue: 0.2574 time to fit residues: 92.2706 Evaluate side-chains 224 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 142 LEU 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 460 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 810 VAL 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 34 VAL Chi-restraints excluded: chain B residue 142 LEU 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 368 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 810 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 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 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15428 Z= 0.162 Angle : 0.523 9.629 20902 Z= 0.271 Chirality : 0.038 0.173 2452 Planarity : 0.003 0.039 2594 Dihedral : 6.522 75.750 2140 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.08 % Allowed : 20.59 % 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: 2.05 (0.20), residues: 1896 helix: 2.47 (0.15), residues: 1230 sheet: 1.89 (0.57), residues: 72 loop : -1.23 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 985 HIS 0.004 0.001 HIS A 606 PHE 0.010 0.001 PHE A 320 TYR 0.009 0.001 TYR A 245 ARG 0.004 0.000 ARG B 433 *********************** 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 253 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 1.750 Fit side-chains REVERT: A 142 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7698 (tp) REVERT: A 323 HIS cc_start: 0.6594 (OUTLIER) cc_final: 0.6108 (m-70) REVERT: A 402 MET cc_start: 0.6711 (mmt) cc_final: 0.6286 (mmt) REVERT: B 323 HIS cc_start: 0.6705 (OUTLIER) cc_final: 0.6162 (m-70) REVERT: B 402 MET cc_start: 0.6729 (mmt) cc_final: 0.6341 (mmt) outliers start: 34 outliers final: 27 residues processed: 235 average time/residue: 0.2485 time to fit residues: 90.4051 Evaluate side-chains 241 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 142 LEU 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 368 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 810 VAL 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 34 VAL 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3482 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= 0.176 Angle : 0.513 7.501 20902 Z= 0.268 Chirality : 0.038 0.174 2452 Planarity : 0.003 0.038 2594 Dihedral : 6.406 74.507 2140 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.39 % Allowed : 20.53 % Favored : 77.08 % 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: 2.15 (0.20), residues: 1896 helix: 2.56 (0.15), residues: 1230 sheet: 1.95 (0.58), residues: 72 loop : -1.20 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 985 HIS 0.005 0.001 HIS B 288 PHE 0.013 0.001 PHE A 228 TYR 0.009 0.001 TYR A 245 ARG 0.002 0.000 ARG A 866 *********************** 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 247 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.715 Fit side-chains REVERT: A 323 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.6133 (m-70) REVERT: A 686 MET cc_start: 0.7103 (tpp) cc_final: 0.6815 (tpt) REVERT: B 323 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.6184 (m-70) outliers start: 39 outliers final: 30 residues processed: 226 average time/residue: 0.2906 time to fit residues: 100.5733 Evaluate side-chains 230 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 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 320 PHE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 863 ILE 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 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 92 MET 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 565 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.0020 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15428 Z= 0.214 Angle : 0.541 7.898 20902 Z= 0.282 Chirality : 0.039 0.181 2452 Planarity : 0.004 0.048 2594 Dihedral : 6.392 70.641 2140 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.33 % Allowed : 20.89 % Favored : 76.78 % 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: 2.18 (0.20), residues: 1896 helix: 2.56 (0.15), residues: 1234 sheet: 1.96 (0.58), residues: 72 loop : -1.19 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 985 HIS 0.007 0.001 HIS A 288 PHE 0.012 0.001 PHE B 117 TYR 0.011 0.001 TYR A 245 ARG 0.012 0.000 ARG B 866 *********************** 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 230 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.707 Fit side-chains REVERT: A 323 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.6286 (m-70) REVERT: B 323 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6406 (m-70) REVERT: B 686 MET cc_start: 0.6990 (tpp) cc_final: 0.6764 (tpt) outliers start: 38 outliers final: 32 residues processed: 216 average time/residue: 0.2745 time to fit residues: 90.1377 Evaluate side-chains 225 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 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 460 LEU Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 863 ILE 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 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 92 MET 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 565 VAL Chi-restraints excluded: chain B residue 707 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.0970 chunk 170 optimal weight: 0.3980 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 673 GLN A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15428 Z= 0.163 Angle : 0.531 9.581 20902 Z= 0.275 Chirality : 0.038 0.179 2452 Planarity : 0.004 0.038 2594 Dihedral : 6.331 78.008 2140 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.08 % Allowed : 21.63 % 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: 2.28 (0.20), residues: 1896 helix: 2.64 (0.15), residues: 1238 sheet: 1.99 (0.57), residues: 72 loop : -1.17 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 985 HIS 0.006 0.001 HIS A 319 PHE 0.013 0.001 PHE A 228 TYR 0.009 0.001 TYR B 245 ARG 0.009 0.000 ARG A 866 *********************** 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 244 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 1.797 Fit side-chains REVERT: A 323 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.6241 (m-70) REVERT: B 323 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.6267 (m-70) REVERT: B 686 MET cc_start: 0.6979 (tpp) cc_final: 0.6733 (tpt) outliers start: 34 outliers final: 25 residues processed: 227 average time/residue: 0.2588 time to fit residues: 89.7125 Evaluate side-chains 223 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 28 LEU 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 708 LYS Chi-restraints excluded: chain A residue 810 VAL 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 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 92 MET 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 810 VAL Chi-restraints excluded: chain B residue 867 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 chunk 125 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3753 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= 0.187 Angle : 0.559 13.420 20902 Z= 0.285 Chirality : 0.039 0.191 2452 Planarity : 0.004 0.038 2594 Dihedral : 6.299 77.609 2140 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.02 % Allowed : 22.24 % 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: 2.37 (0.20), residues: 1896 helix: 2.74 (0.15), residues: 1230 sheet: 1.95 (0.57), residues: 72 loop : -1.14 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 985 HIS 0.006 0.001 HIS A 319 PHE 0.009 0.001 PHE A 320 TYR 0.010 0.001 TYR B 245 ARG 0.008 0.000 ARG B 866 ********************** 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 234 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.898 Fit side-chains REVERT: A 104 MET cc_start: 0.6934 (mtm) cc_final: 0.6674 (mtm) REVERT: A 323 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.6389 (m-70) REVERT: B 104 MET cc_start: 0.6932 (mtm) cc_final: 0.6687 (mtm) REVERT: B 323 HIS cc_start: 0.6826 (OUTLIER) cc_final: 0.6376 (m-70) REVERT: B 686 MET cc_start: 0.6980 (tpp) cc_final: 0.6727 (tpt) outliers start: 33 outliers final: 26 residues processed: 216 average time/residue: 0.2590 time to fit residues: 85.5650 Evaluate side-chains 222 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 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 810 VAL 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 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 92 MET 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 810 VAL Chi-restraints excluded: chain B residue 867 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 ASN A 937 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.071934 restraints weight = 30308.763| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.44 r_work: 0.2734 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15428 Z= 0.270 Angle : 0.621 17.996 20902 Z= 0.310 Chirality : 0.041 0.193 2452 Planarity : 0.004 0.053 2594 Dihedral : 6.463 68.666 2140 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.84 % Allowed : 22.73 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.20), residues: 1896 helix: 2.70 (0.15), residues: 1230 sheet: 1.57 (0.54), residues: 82 loop : -1.15 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 985 HIS 0.014 0.001 HIS A 319 PHE 0.013 0.001 PHE A 117 TYR 0.012 0.001 TYR A 245 ARG 0.006 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.31 seconds wall clock time: 56 minutes 0.17 seconds (3360.17 seconds total)