Starting phenix.real_space_refine on Sat Aug 23 23:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwo_35775/08_2025/8iwo_35775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwo_35775/08_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_35775/08_2025/8iwo_35775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwo_35775/08_2025/8iwo_35775.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwo_35775/08_2025/8iwo_35775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwo_35775/08_2025/8iwo_35775.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.104 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.86, per 1000 atoms: 0.32 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: 0.91 Conformation dependent library (CDL) restraints added in 456.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.33 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: 1.84 Time building geometry restraints manager: 1.16 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: 0.02 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: 0.910 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A 645 TYR 0.009 0.001 TYR A 800 PHE 0.029 0.002 PHE A 814 TRP 0.026 0.001 TRP B 759 HIS 0.017 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00668 (15428) covalent geometry : angle 1.11021 (20902) hydrogen bonds : bond 0.17699 ( 962) hydrogen bonds : angle 7.35268 ( 2814) *********************** 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 : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 311 average time/residue: 0.1009 time to fit residues: 45.7955 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 : 0.400 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 418 ASN A 870 ASN A 897 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 394 HIS B 418 ASN B 673 GLN B 897 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.073704 restraints weight = 29705.198| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.35 r_work: 0.2747 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2063 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= 0.136 Angle : 0.571 7.533 20902 Z= 0.299 Chirality : 0.039 0.140 2452 Planarity : 0.004 0.043 2594 Dihedral : 8.764 126.579 2158 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.43 % Allowed : 16.12 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.19), residues: 1896 helix: 0.99 (0.15), residues: 1252 sheet: 1.17 (0.52), residues: 82 loop : -1.74 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 866 TYR 0.016 0.001 TYR A 586 PHE 0.011 0.001 PHE B 616 TRP 0.019 0.001 TRP B 985 HIS 0.006 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00307 (15428) covalent geometry : angle 0.57083 (20902) hydrogen bonds : bond 0.04293 ( 962) hydrogen bonds : angle 4.40304 ( 2814) *********************** 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 291 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 0.379 Fit side-chains REVERT: A 147 ASP cc_start: 0.8339 (t0) cc_final: 0.8103 (t0) REVERT: A 163 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8373 (ptmt) REVERT: A 323 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7308 (m-70) REVERT: A 685 GLU cc_start: 0.8518 (mp0) cc_final: 0.7860 (mp0) REVERT: A 706 LEU cc_start: 0.8684 (pt) cc_final: 0.8084 (mt) REVERT: A 711 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8652 (mpp80) REVERT: A 776 ARG cc_start: 0.9110 (tpp-160) cc_final: 0.8783 (mmm160) REVERT: A 847 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 849 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8950 (tpp) REVERT: B 95 HIS cc_start: 0.8308 (p90) cc_final: 0.8084 (p90) REVERT: B 147 ASP cc_start: 0.8372 (t0) cc_final: 0.8105 (t0) REVERT: B 163 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8414 (ptmt) REVERT: B 224 LEU cc_start: 0.9093 (mt) cc_final: 0.8854 (tt) REVERT: B 284 GLN cc_start: 0.8349 (tp40) cc_final: 0.8126 (tp-100) REVERT: B 323 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.7336 (m-70) REVERT: B 706 LEU cc_start: 0.8642 (pt) cc_final: 0.8063 (mt) REVERT: B 711 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8718 (mpp80) REVERT: B 776 ARG cc_start: 0.9117 (tpp-160) cc_final: 0.8792 (mmm160) REVERT: B 847 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8299 (tt) REVERT: B 849 MET cc_start: 0.9244 (tpp) cc_final: 0.8865 (tpp) outliers start: 56 outliers final: 24 residues processed: 268 average time/residue: 0.0954 time to fit residues: 38.5758 Evaluate side-chains 240 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 A residue 930 CYS Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 169 GLU 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 Chi-restraints excluded: chain B residue 930 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 298 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 870 ASN 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 = 0.101099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.073987 restraints weight = 30222.826| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.41 r_work: 0.2769 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2551 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= 0.119 Angle : 0.518 6.706 20902 Z= 0.271 Chirality : 0.039 0.222 2452 Planarity : 0.004 0.038 2594 Dihedral : 8.131 110.849 2140 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.00 % Allowed : 17.71 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.20), residues: 1896 helix: 1.79 (0.15), residues: 1248 sheet: 1.45 (0.54), residues: 72 loop : -1.45 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 866 TYR 0.010 0.001 TYR B 129 PHE 0.023 0.001 PHE B 195 TRP 0.016 0.001 TRP A 985 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00267 (15428) covalent geometry : angle 0.51816 (20902) hydrogen bonds : bond 0.03897 ( 962) hydrogen bonds : angle 4.07932 ( 2814) *********************** 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 267 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.356 Fit side-chains REVERT: A 147 ASP cc_start: 0.8391 (t0) cc_final: 0.8159 (t0) REVERT: A 163 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8359 (ptmt) REVERT: A 174 MET cc_start: 0.9112 (mpp) cc_final: 0.8878 (mpp) REVERT: A 284 GLN cc_start: 0.8364 (tp-100) cc_final: 0.7848 (tp-100) REVERT: A 323 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7423 (m-70) REVERT: A 541 ARG cc_start: 0.8951 (ttp-170) cc_final: 0.8672 (ttp-170) REVERT: A 685 GLU cc_start: 0.8594 (mp0) cc_final: 0.7932 (mp0) REVERT: A 706 LEU cc_start: 0.8657 (pt) cc_final: 0.8103 (mt) REVERT: A 711 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8648 (mpp80) REVERT: A 776 ARG cc_start: 0.9063 (tpp-160) cc_final: 0.8775 (mmm160) REVERT: B 147 ASP cc_start: 0.8403 (t0) cc_final: 0.8157 (t0) REVERT: B 163 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8373 (ptmt) REVERT: B 284 GLN cc_start: 0.8430 (tp40) cc_final: 0.8006 (tp-100) REVERT: B 323 HIS cc_start: 0.8451 (OUTLIER) cc_final: 0.7479 (m-70) REVERT: B 685 GLU cc_start: 0.8532 (mp0) cc_final: 0.8141 (mp0) REVERT: B 706 LEU cc_start: 0.8753 (pt) cc_final: 0.8171 (mt) REVERT: B 711 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8736 (mpp80) REVERT: B 776 ARG cc_start: 0.9084 (tpp-160) cc_final: 0.8563 (mmm-85) REVERT: B 847 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8382 (tt) REVERT: B 849 MET cc_start: 0.9195 (tpp) cc_final: 0.8880 (tpp) outliers start: 49 outliers final: 25 residues processed: 248 average time/residue: 0.0871 time to fit residues: 33.3314 Evaluate side-chains 228 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 163 LYS 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 368 VAL Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 810 VAL 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 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 163 LYS 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 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 868 THR Chi-restraints excluded: chain B residue 885 ILE 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 28 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 319 HIS ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 319 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.100828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.073855 restraints weight = 29863.149| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.38 r_work: 0.2766 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2909 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= 0.119 Angle : 0.529 10.394 20902 Z= 0.269 Chirality : 0.038 0.136 2452 Planarity : 0.004 0.039 2594 Dihedral : 7.648 91.366 2140 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.57 % Allowed : 18.57 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.20), residues: 1896 helix: 2.18 (0.15), residues: 1238 sheet: 1.57 (0.56), residues: 72 loop : -1.26 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 866 TYR 0.011 0.001 TYR B 129 PHE 0.012 0.001 PHE A 917 TRP 0.013 0.001 TRP A 985 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00269 (15428) covalent geometry : angle 0.52851 (20902) hydrogen bonds : bond 0.03770 ( 962) hydrogen bonds : angle 3.92297 ( 2814) *********************** 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 262 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.355 Fit side-chains REVERT: A 147 ASP cc_start: 0.8380 (t0) cc_final: 0.8164 (t0) REVERT: A 284 GLN cc_start: 0.8407 (tp-100) cc_final: 0.7868 (tp-100) REVERT: A 323 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7428 (m-70) REVERT: A 541 ARG cc_start: 0.8977 (ttp-170) cc_final: 0.8639 (ttp-170) REVERT: A 547 MET cc_start: 0.9105 (tpp) cc_final: 0.8781 (tpp) REVERT: A 685 GLU cc_start: 0.8682 (mp0) cc_final: 0.8097 (mp0) REVERT: A 706 LEU cc_start: 0.8730 (pt) cc_final: 0.8186 (mt) REVERT: A 711 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8612 (mpp80) REVERT: A 776 ARG cc_start: 0.8960 (tpp-160) cc_final: 0.8674 (mmm160) REVERT: A 847 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8433 (tt) REVERT: A 849 MET cc_start: 0.9249 (tpp) cc_final: 0.8667 (tpp) REVERT: A 1024 MET cc_start: 0.8873 (mtp) cc_final: 0.8629 (mmm) REVERT: B 147 ASP cc_start: 0.8396 (t0) cc_final: 0.8159 (t0) REVERT: B 171 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8449 (tm-30) REVERT: B 284 GLN cc_start: 0.8532 (tp40) cc_final: 0.8080 (tp-100) REVERT: B 323 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7406 (m-70) REVERT: B 547 MET cc_start: 0.9072 (tpp) cc_final: 0.8770 (tpp) REVERT: B 685 GLU cc_start: 0.8623 (mp0) cc_final: 0.8054 (mp0) REVERT: B 686 MET cc_start: 0.8636 (tpp) cc_final: 0.8380 (tpt) REVERT: B 706 LEU cc_start: 0.8704 (pt) cc_final: 0.8182 (mt) REVERT: B 711 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8685 (mpp80) REVERT: B 776 ARG cc_start: 0.9043 (tpp-160) cc_final: 0.8764 (mmm160) REVERT: B 849 MET cc_start: 0.9198 (tpp) cc_final: 0.8849 (tpp) REVERT: B 850 MET cc_start: 0.8982 (mtp) cc_final: 0.8699 (ptm) outliers start: 42 outliers final: 25 residues processed: 250 average time/residue: 0.0867 time to fit residues: 33.1007 Evaluate side-chains 223 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 298 ASN 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 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 282 SER 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 174 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 298 ASN ** A 319 HIS ** 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 298 ASN ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.073959 restraints weight = 30249.139| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.44 r_work: 0.2770 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3100 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= 0.114 Angle : 0.517 9.113 20902 Z= 0.263 Chirality : 0.038 0.196 2452 Planarity : 0.003 0.039 2594 Dihedral : 7.234 78.744 2140 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.21 % Allowed : 19.24 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.20), residues: 1896 helix: 2.38 (0.15), residues: 1240 sheet: 1.75 (0.57), residues: 72 loop : -1.22 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 866 TYR 0.010 0.001 TYR B 129 PHE 0.010 0.001 PHE B 117 TRP 0.012 0.001 TRP A 985 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00257 (15428) covalent geometry : angle 0.51694 (20902) hydrogen bonds : bond 0.03695 ( 962) hydrogen bonds : angle 3.86081 ( 2814) *********************** 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 237 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.413 Fit side-chains REVERT: A 147 ASP cc_start: 0.8434 (t0) cc_final: 0.8189 (t0) REVERT: A 163 LYS cc_start: 0.8530 (ptmm) cc_final: 0.8326 (ptmm) REVERT: A 284 GLN cc_start: 0.8419 (tp-100) cc_final: 0.7890 (tp-100) REVERT: A 323 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7417 (m-70) REVERT: A 402 MET cc_start: 0.8156 (mmm) cc_final: 0.7816 (mmt) REVERT: A 541 ARG cc_start: 0.8976 (ttp-170) cc_final: 0.8749 (ttp-110) REVERT: A 685 GLU cc_start: 0.8790 (mp0) cc_final: 0.8245 (mp0) REVERT: A 686 MET cc_start: 0.8547 (tpp) cc_final: 0.8313 (tpt) REVERT: A 706 LEU cc_start: 0.8730 (pt) cc_final: 0.8254 (mt) REVERT: A 711 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8623 (mpp80) REVERT: A 776 ARG cc_start: 0.8950 (tpp-160) cc_final: 0.8684 (mmm160) REVERT: A 847 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8376 (tt) REVERT: A 849 MET cc_start: 0.9260 (tpp) cc_final: 0.8731 (tpp) REVERT: B 147 ASP cc_start: 0.8392 (t0) cc_final: 0.8188 (t0) REVERT: B 171 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 284 GLN cc_start: 0.8576 (tp40) cc_final: 0.8131 (tp-100) REVERT: B 323 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7431 (m-70) REVERT: B 402 MET cc_start: 0.8138 (mmm) cc_final: 0.7782 (mmt) REVERT: B 685 GLU cc_start: 0.8756 (mp0) cc_final: 0.8140 (mp0) REVERT: B 706 LEU cc_start: 0.8727 (pt) cc_final: 0.8297 (mt) REVERT: B 711 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8692 (mpp80) REVERT: B 776 ARG cc_start: 0.9005 (tpp-160) cc_final: 0.8558 (mmm-85) REVERT: B 847 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8343 (tt) REVERT: B 849 MET cc_start: 0.9198 (tpp) cc_final: 0.8888 (tpp) outliers start: 36 outliers final: 23 residues processed: 226 average time/residue: 0.0945 time to fit residues: 32.7658 Evaluate side-chains 222 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP 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 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 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 93 GLU 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 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 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 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 180 optimal weight: 0.0170 chunk 75 optimal weight: 0.0570 chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 298 ASN A 319 HIS A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 319 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.075932 restraints weight = 30097.785| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.40 r_work: 0.2810 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3364 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= 0.101 Angle : 0.502 9.130 20902 Z= 0.256 Chirality : 0.037 0.160 2452 Planarity : 0.003 0.038 2594 Dihedral : 6.467 82.816 2140 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.84 % Allowed : 19.85 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.20), residues: 1896 helix: 2.54 (0.15), residues: 1238 sheet: 1.94 (0.58), residues: 72 loop : -1.21 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.008 0.001 TYR A 245 PHE 0.013 0.001 PHE B 228 TRP 0.011 0.001 TRP A 985 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00220 (15428) covalent geometry : angle 0.50240 (20902) hydrogen bonds : bond 0.03381 ( 962) hydrogen bonds : angle 3.77631 ( 2814) *********************** 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 259 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.504 Fit side-chains REVERT: A 163 LYS cc_start: 0.8479 (ptmm) cc_final: 0.8269 (ptmm) REVERT: A 284 GLN cc_start: 0.8393 (tp-100) cc_final: 0.7882 (tp-100) REVERT: A 323 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7388 (m-70) REVERT: A 402 MET cc_start: 0.8104 (mmm) cc_final: 0.7695 (mmt) REVERT: A 541 ARG cc_start: 0.8962 (ttp-170) cc_final: 0.8601 (ttp-110) REVERT: A 685 GLU cc_start: 0.8796 (mp0) cc_final: 0.8212 (mp0) REVERT: A 706 LEU cc_start: 0.8727 (pt) cc_final: 0.8331 (mt) REVERT: A 709 MET cc_start: 0.8515 (mmm) cc_final: 0.8270 (mmm) REVERT: A 711 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8606 (mpp80) REVERT: A 776 ARG cc_start: 0.8930 (tpp-160) cc_final: 0.8688 (mmm160) REVERT: A 847 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 849 MET cc_start: 0.9223 (tpp) cc_final: 0.8642 (tpp) REVERT: B 171 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7994 (tm-30) REVERT: B 284 GLN cc_start: 0.8528 (tp40) cc_final: 0.8097 (tp-100) REVERT: B 292 MET cc_start: 0.8983 (tpp) cc_final: 0.8745 (tpp) REVERT: B 323 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7414 (m-70) REVERT: B 402 MET cc_start: 0.8099 (mmm) cc_final: 0.7702 (mmt) REVERT: B 540 MET cc_start: 0.9271 (mmt) cc_final: 0.9062 (mmm) REVERT: B 541 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8237 (tpp80) REVERT: B 685 GLU cc_start: 0.8755 (mp0) cc_final: 0.8390 (mp0) REVERT: B 706 LEU cc_start: 0.8751 (pt) cc_final: 0.8336 (mt) REVERT: B 709 MET cc_start: 0.8564 (mmm) cc_final: 0.8337 (mmm) REVERT: B 711 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8677 (mpp80) REVERT: B 776 ARG cc_start: 0.8958 (tpp-160) cc_final: 0.8649 (mmm160) REVERT: B 847 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8289 (tt) REVERT: B 849 MET cc_start: 0.9190 (tpp) cc_final: 0.8941 (tpp) outliers start: 30 outliers final: 19 residues processed: 250 average time/residue: 0.0947 time to fit residues: 36.1497 Evaluate side-chains 233 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 680 LEU 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 871 ILE Chi-restraints excluded: chain A residue 885 ILE 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 282 SER 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 460 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 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 68 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 167 optimal weight: 0.0270 chunk 82 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.100832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.073868 restraints weight = 30239.624| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.41 r_work: 0.2770 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15428 Z= 0.128 Angle : 0.524 8.581 20902 Z= 0.271 Chirality : 0.038 0.174 2452 Planarity : 0.003 0.048 2594 Dihedral : 6.354 75.456 2140 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.45 % Allowed : 19.67 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.20), residues: 1896 helix: 2.60 (0.15), residues: 1236 sheet: 1.95 (0.57), residues: 72 loop : -1.18 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 866 TYR 0.010 0.001 TYR A 245 PHE 0.013 0.001 PHE A 228 TRP 0.010 0.001 TRP B 985 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00295 (15428) covalent geometry : angle 0.52432 (20902) hydrogen bonds : bond 0.03730 ( 962) hydrogen bonds : angle 3.78759 ( 2814) *********************** 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 250 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 284 GLN cc_start: 0.8471 (tp-100) cc_final: 0.7924 (tp-100) REVERT: A 323 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7441 (m-70) REVERT: A 541 ARG cc_start: 0.8960 (ttp-170) cc_final: 0.8670 (ttp-110) REVERT: A 685 GLU cc_start: 0.8854 (mp0) cc_final: 0.8376 (mp0) REVERT: A 706 LEU cc_start: 0.8817 (pt) cc_final: 0.8433 (mt) REVERT: A 711 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8573 (mpp80) REVERT: A 776 ARG cc_start: 0.8974 (tpp-160) cc_final: 0.8713 (mmm160) REVERT: A 847 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 849 MET cc_start: 0.9272 (tpp) cc_final: 0.8673 (tpp) REVERT: B 171 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 284 GLN cc_start: 0.8604 (tp40) cc_final: 0.8143 (tp-100) REVERT: B 323 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7446 (m-70) REVERT: B 402 MET cc_start: 0.8160 (mmm) cc_final: 0.7791 (mmm) REVERT: B 540 MET cc_start: 0.9327 (mmt) cc_final: 0.9042 (mmm) REVERT: B 541 ARG cc_start: 0.8744 (mtp180) cc_final: 0.8282 (mtm-85) REVERT: B 685 GLU cc_start: 0.8929 (mp0) cc_final: 0.8454 (mp0) REVERT: B 706 LEU cc_start: 0.8685 (pt) cc_final: 0.8308 (mt) REVERT: B 711 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8621 (mpp80) REVERT: B 776 ARG cc_start: 0.8976 (tpp-160) cc_final: 0.8543 (mmm-85) REVERT: B 847 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8330 (tt) REVERT: B 849 MET cc_start: 0.9237 (tpp) cc_final: 0.8944 (tpp) outliers start: 40 outliers final: 22 residues processed: 239 average time/residue: 0.1003 time to fit residues: 36.4222 Evaluate side-chains 235 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 680 LEU 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 871 ILE Chi-restraints excluded: chain A residue 885 ILE 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 169 GLU 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 460 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 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 930 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.074993 restraints weight = 30383.205| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.42 r_work: 0.2791 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3559 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= 0.113 Angle : 0.520 8.614 20902 Z= 0.267 Chirality : 0.038 0.174 2452 Planarity : 0.003 0.039 2594 Dihedral : 6.291 79.273 2140 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.65 % Allowed : 20.83 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.20), residues: 1896 helix: 2.64 (0.15), residues: 1238 sheet: 2.01 (0.56), residues: 72 loop : -1.19 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 866 TYR 0.009 0.001 TYR A 245 PHE 0.010 0.001 PHE A 320 TRP 0.011 0.001 TRP B 985 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00256 (15428) covalent geometry : angle 0.52047 (20902) hydrogen bonds : bond 0.03536 ( 962) hydrogen bonds : angle 3.76336 ( 2814) *********************** 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 248 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.524 Fit side-chains REVERT: A 117 PHE cc_start: 0.9014 (m-80) cc_final: 0.8714 (m-80) REVERT: A 171 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 284 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7894 (tp-100) REVERT: A 323 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7450 (m-70) REVERT: A 541 ARG cc_start: 0.8959 (ttp-170) cc_final: 0.8677 (ttp-110) REVERT: A 682 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 685 GLU cc_start: 0.8833 (mp0) cc_final: 0.8417 (mp0) REVERT: A 706 LEU cc_start: 0.8771 (pt) cc_final: 0.8405 (mt) REVERT: A 711 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8582 (mpp80) REVERT: A 776 ARG cc_start: 0.8980 (tpp-160) cc_final: 0.8727 (mmm160) REVERT: A 847 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 849 MET cc_start: 0.9236 (tpp) cc_final: 0.8652 (tpp) REVERT: B 171 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 284 GLN cc_start: 0.8587 (tp40) cc_final: 0.8108 (tp-100) REVERT: B 323 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7449 (m-70) REVERT: B 402 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8130 (mmm) REVERT: B 685 GLU cc_start: 0.8907 (mp0) cc_final: 0.8409 (mp0) REVERT: B 706 LEU cc_start: 0.8698 (pt) cc_final: 0.8307 (mt) REVERT: B 711 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8624 (mpp80) REVERT: B 776 ARG cc_start: 0.8948 (tpp-160) cc_final: 0.8532 (mmm-85) REVERT: B 847 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8305 (tt) REVERT: B 849 MET cc_start: 0.9231 (tpp) cc_final: 0.8957 (tpp) outliers start: 27 outliers final: 18 residues processed: 237 average time/residue: 0.1057 time to fit residues: 37.9679 Evaluate side-chains 235 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 871 ILE Chi-restraints excluded: chain A residue 885 ILE 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 402 MET Chi-restraints excluded: chain B residue 460 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 868 THR Chi-restraints excluded: chain B residue 871 ILE 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 68 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.102279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.075230 restraints weight = 30339.087| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.44 r_work: 0.2781 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15428 Z= 0.115 Angle : 0.534 8.621 20902 Z= 0.273 Chirality : 0.039 0.203 2452 Planarity : 0.003 0.038 2594 Dihedral : 6.281 81.139 2140 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.59 % Allowed : 21.69 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.20), residues: 1896 helix: 2.72 (0.15), residues: 1236 sheet: 1.98 (0.56), residues: 72 loop : -1.16 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 866 TYR 0.009 0.001 TYR B 245 PHE 0.011 0.001 PHE A 320 TRP 0.011 0.001 TRP B 985 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00265 (15428) covalent geometry : angle 0.53413 (20902) hydrogen bonds : bond 0.03572 ( 962) hydrogen bonds : angle 3.76027 ( 2814) *********************** 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 235 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.646 Fit side-chains REVERT: A 117 PHE cc_start: 0.8975 (m-80) cc_final: 0.8644 (m-10) REVERT: A 171 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8158 (tm-30) REVERT: A 284 GLN cc_start: 0.8470 (tp-100) cc_final: 0.7950 (tp-100) REVERT: A 323 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7526 (m-70) REVERT: A 402 MET cc_start: 0.8254 (mmm) cc_final: 0.7899 (mmm) REVERT: A 541 ARG cc_start: 0.8961 (ttp-170) cc_final: 0.8565 (ttp-110) REVERT: A 685 GLU cc_start: 0.8808 (mp0) cc_final: 0.8357 (mp0) REVERT: A 706 LEU cc_start: 0.8763 (pt) cc_final: 0.8432 (mt) REVERT: A 711 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8589 (mpp80) REVERT: A 776 ARG cc_start: 0.8995 (tpp-160) cc_final: 0.8740 (mmm160) REVERT: A 847 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 849 MET cc_start: 0.9257 (tpp) cc_final: 0.8700 (tpp) REVERT: B 117 PHE cc_start: 0.8998 (m-80) cc_final: 0.8719 (m-80) REVERT: B 171 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 284 GLN cc_start: 0.8614 (tp40) cc_final: 0.8126 (tp-100) REVERT: B 323 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7483 (m-70) REVERT: B 402 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7972 (mmt) REVERT: B 541 ARG cc_start: 0.8635 (ttp-170) cc_final: 0.8324 (tpp80) REVERT: B 685 GLU cc_start: 0.8942 (mp0) cc_final: 0.8421 (mp0) REVERT: B 706 LEU cc_start: 0.8674 (pt) cc_final: 0.8353 (mt) REVERT: B 711 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8629 (mpp80) REVERT: B 776 ARG cc_start: 0.8943 (tpp-160) cc_final: 0.8526 (mmm160) REVERT: B 847 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8305 (tt) REVERT: B 849 MET cc_start: 0.9241 (tpp) cc_final: 0.8968 (tpp) outliers start: 26 outliers final: 18 residues processed: 224 average time/residue: 0.1098 time to fit residues: 37.6554 Evaluate side-chains 230 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 871 ILE Chi-restraints excluded: chain A residue 885 ILE 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 402 MET Chi-restraints excluded: chain B residue 460 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 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 930 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.075635 restraints weight = 30510.790| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.46 r_work: 0.2807 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3762 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= 0.112 Angle : 0.532 9.983 20902 Z= 0.272 Chirality : 0.038 0.183 2452 Planarity : 0.003 0.038 2594 Dihedral : 6.256 83.925 2140 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.72 % Allowed : 21.69 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.20), residues: 1896 helix: 2.82 (0.15), residues: 1230 sheet: 2.00 (0.56), residues: 72 loop : -1.16 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 866 TYR 0.009 0.001 TYR A 245 PHE 0.010 0.001 PHE B 320 TRP 0.011 0.001 TRP B 985 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00259 (15428) covalent geometry : angle 0.53164 (20902) hydrogen bonds : bond 0.03478 ( 962) hydrogen bonds : angle 3.74253 ( 2814) ********************** 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 236 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.575 Fit side-chains REVERT: A 117 PHE cc_start: 0.8937 (m-80) cc_final: 0.8621 (m-10) REVERT: A 171 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 284 GLN cc_start: 0.8448 (tp-100) cc_final: 0.7929 (tp-100) REVERT: A 323 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7564 (m-70) REVERT: A 402 MET cc_start: 0.8240 (mmm) cc_final: 0.7858 (mmm) REVERT: A 541 ARG cc_start: 0.8962 (ttp-170) cc_final: 0.8557 (ttp-110) REVERT: A 685 GLU cc_start: 0.8820 (mp0) cc_final: 0.8468 (mp0) REVERT: A 706 LEU cc_start: 0.8790 (pt) cc_final: 0.8489 (mt) REVERT: A 711 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8603 (mpp80) REVERT: A 776 ARG cc_start: 0.9003 (tpp-160) cc_final: 0.8743 (mmm160) REVERT: A 847 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 849 MET cc_start: 0.9240 (tpp) cc_final: 0.8679 (tpp) REVERT: B 117 PHE cc_start: 0.8953 (m-80) cc_final: 0.8666 (m-10) REVERT: B 171 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 284 GLN cc_start: 0.8609 (tp40) cc_final: 0.8119 (tp-100) REVERT: B 323 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7489 (m-70) REVERT: B 402 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7924 (mmt) REVERT: B 477 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8884 (mtmm) REVERT: B 541 ARG cc_start: 0.8596 (ttp-170) cc_final: 0.8313 (tpp80) REVERT: B 685 GLU cc_start: 0.8940 (mp0) cc_final: 0.8462 (mp0) REVERT: B 706 LEU cc_start: 0.8682 (pt) cc_final: 0.8374 (mt) REVERT: B 711 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8660 (mpp80) REVERT: B 776 ARG cc_start: 0.8924 (tpp-160) cc_final: 0.8520 (mmm160) REVERT: B 847 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8263 (tt) REVERT: B 849 MET cc_start: 0.9246 (tpp) cc_final: 0.8967 (tpp) outliers start: 28 outliers final: 20 residues processed: 225 average time/residue: 0.1078 time to fit residues: 37.0826 Evaluate side-chains 232 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 482 LEU 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 871 ILE 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 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 460 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 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 930 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 175 optimal weight: 0.0970 chunk 125 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 188 optimal weight: 0.0670 chunk 162 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 169 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 674 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.104605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.077743 restraints weight = 30250.643| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.46 r_work: 0.2845 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15428 Z= 0.105 Angle : 0.529 10.088 20902 Z= 0.268 Chirality : 0.038 0.181 2452 Planarity : 0.003 0.038 2594 Dihedral : 6.202 89.149 2140 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.41 % Allowed : 21.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.20), residues: 1896 helix: 2.84 (0.15), residues: 1234 sheet: 2.12 (0.56), residues: 72 loop : -1.20 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 866 TYR 0.008 0.001 TYR A 245 PHE 0.013 0.001 PHE A 228 TRP 0.012 0.001 TRP B 985 HIS 0.004 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00237 (15428) covalent geometry : angle 0.52880 (20902) hydrogen bonds : bond 0.03210 ( 962) hydrogen bonds : angle 3.70497 ( 2814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.88 seconds wall clock time: 45 minutes 12.83 seconds (2712.83 seconds total)