Starting phenix.real_space_refine on Thu Jun 12 17:54:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjy_38410/06_2025/8xjy_38410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjy_38410/06_2025/8xjy_38410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjy_38410/06_2025/8xjy_38410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjy_38410/06_2025/8xjy_38410.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjy_38410/06_2025/8xjy_38410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjy_38410/06_2025/8xjy_38410.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9001 2.51 5 N 2477 2.21 5 O 2701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14239 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6607 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 41, 'TRANS': 831} Chain: "B" Number of atoms: 6614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6614 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 42, 'TRANS': 831} Chain: "C" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 509 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain breaks: 2 Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 509 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain breaks: 2 Time building chain proxies: 8.63, per 1000 atoms: 0.61 Number of scatterers: 14239 At special positions: 0 Unit cell: (118.437, 97.097, 198.462, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2701 8.00 N 2477 7.00 C 9001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.8 seconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3478 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 17 sheets defined 42.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 4.175A pdb=" N ASN A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.590A pdb=" N MET A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 49 " --> pdb=" O LEU A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 49' Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.320A pdb=" N PHE A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.608A pdb=" N LEU A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 106 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.526A pdb=" N MET A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.616A pdb=" N GLY A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 removed outlier: 3.764A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 320 through 333 removed outlier: 3.900A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.546A pdb=" N THR A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.608A pdb=" N PHE A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.526A pdb=" N ALA A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 removed outlier: 3.671A pdb=" N GLN A 549 " --> pdb=" O HIS A 545 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.528A pdb=" N ALA A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 572 through 578 removed outlier: 3.525A pdb=" N GLU A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 596 through 614 Processing helix chain 'A' and resid 626 through 635 removed outlier: 3.698A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 655 removed outlier: 3.797A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 676 removed outlier: 4.053A pdb=" N LEU A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.681A pdb=" N GLU A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 767 through 774 removed outlier: 4.288A pdb=" N TRP A 771 " --> pdb=" O THR A 767 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.848A pdb=" N GLN A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.578A pdb=" N ARG A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.517A pdb=" N PHE A 855 " --> pdb=" O LEU A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 removed outlier: 3.521A pdb=" N GLU B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 74 through 79 removed outlier: 4.274A pdb=" N PHE B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 89 through 107 Processing helix chain 'B' and resid 128 through 138 removed outlier: 5.288A pdb=" N MET B 134 " --> pdb=" O MET B 130 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 143 through 153 removed outlier: 4.070A pdb=" N GLN B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 287 through 301 Processing helix chain 'B' and resid 320 through 333 removed outlier: 4.011A pdb=" N VAL B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.786A pdb=" N THR B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 Processing helix chain 'B' and resid 455 through 470 Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.631A pdb=" N ALA B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 551 Processing helix chain 'B' and resid 551 through 569 removed outlier: 3.622A pdb=" N ALA B 555 " --> pdb=" O TRP B 551 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 Processing helix chain 'B' and resid 592 through 614 removed outlier: 3.826A pdb=" N GLN B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Proline residue: B 598 - end of helix Processing helix chain 'B' and resid 625 through 635 removed outlier: 3.929A pdb=" N TRP B 629 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 633 " --> pdb=" O TRP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 655 Processing helix chain 'B' and resid 668 through 674 Processing helix chain 'B' and resid 696 through 710 removed outlier: 3.573A pdb=" N GLU B 709 " --> pdb=" O GLN B 705 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 710 " --> pdb=" O ARG B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 728 through 734 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 769 through 774 Processing helix chain 'B' and resid 781 through 792 Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 828 through 830 No H-bonds generated for 'chain 'B' and resid 828 through 830' Processing helix chain 'B' and resid 831 through 847 removed outlier: 3.803A pdb=" N LEU B 837 " --> pdb=" O HIS B 833 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 845 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG B 846 " --> pdb=" O ALA B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.569A pdb=" N ALA B 856 " --> pdb=" O SER B 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 934 Processing helix chain 'C' and resid 952 through 962 Processing helix chain 'C' and resid 972 through 978 removed outlier: 4.024A pdb=" N ASP C 978 " --> pdb=" O ASP C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 994 Processing helix chain 'D' and resid 921 through 933 Processing helix chain 'D' and resid 952 through 964 Processing helix chain 'D' and resid 972 through 978 Processing helix chain 'D' and resid 980 through 994 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120 removed outlier: 6.167A pdb=" N GLY A 118 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLY A 203 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE A 120 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL A 205 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 247 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET A 13 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL A 249 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 265 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE A 267 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU A 430 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 269 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.531A pdb=" N LYS A 64 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.511A pdb=" N ILE A 873 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 374 through 375 Processing sheet with id=AA5, first strand: chain 'A' and resid 447 through 453 Processing sheet with id=AA6, first strand: chain 'A' and resid 618 through 620 removed outlier: 7.023A pdb=" N LEU A 529 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY A 530 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 799 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 532 " --> pdb=" O ILE A 799 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 714 through 716 removed outlier: 3.713A pdb=" N LYS A 715 " --> pdb=" O MET A 664 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TYR A 690 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL A 685 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 692 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 681 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 117 through 121 removed outlier: 3.560A pdb=" N GLY B 203 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 247 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET B 13 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 249 " --> pdb=" O ILE B 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.978A pdb=" N LYS B 64 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 73 removed outlier: 3.505A pdb=" N ILE B 873 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 269 through 273 Processing sheet with id=AB3, first strand: chain 'B' and resid 310 through 312 removed outlier: 6.289A pdb=" N CYS B 342 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 374 through 375 Processing sheet with id=AB5, first strand: chain 'B' and resid 447 through 453 Processing sheet with id=AB6, first strand: chain 'B' and resid 618 through 622 removed outlier: 7.389A pdb=" N LEU B 529 " --> pdb=" O THR B 619 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET B 621 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 531 " --> pdb=" O MET B 621 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY B 530 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE B 799 " --> pdb=" O GLY B 530 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 532 " --> pdb=" O ILE B 799 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 714 through 715 removed outlier: 3.752A pdb=" N LYS B 715 " --> pdb=" O MET B 664 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR B 690 " --> pdb=" O ASN B 686 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 686 " --> pdb=" O TYR B 690 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA B 694 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE B 682 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA B 683 " --> pdb=" O VAL B 779 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 752 through 753 removed outlier: 3.529A pdb=" N ALA B 758 " --> pdb=" O SER B 753 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2415 1.31 - 1.44: 3837 1.44 - 1.56: 8188 1.56 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 14540 Sorted by residual: bond pdb=" C PRO B 135 " pdb=" O PRO B 135 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" N GLY B 623 " pdb=" CA GLY B 623 " ideal model delta sigma weight residual 1.443 1.475 -0.031 8.60e-03 1.35e+04 1.34e+01 bond pdb=" N VAL A 205 " pdb=" CA VAL A 205 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.08e-02 8.57e+03 1.25e+01 bond pdb=" N LEU A 667 " pdb=" CA LEU A 667 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.04e-02 9.25e+03 1.13e+01 bond pdb=" N SER B 538 " pdb=" CA SER B 538 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.00e-02 1.00e+04 1.08e+01 ... (remaining 14535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18499 2.04 - 4.07: 1069 4.07 - 6.11: 145 6.11 - 8.15: 52 8.15 - 10.18: 21 Bond angle restraints: 19786 Sorted by residual: angle pdb=" N ASN A 132 " pdb=" CA ASN A 132 " pdb=" C ASN A 132 " ideal model delta sigma weight residual 114.31 105.50 8.81 1.29e+00 6.01e-01 4.67e+01 angle pdb=" C GLN D 963 " pdb=" N GLU D 964 " pdb=" CA GLU D 964 " ideal model delta sigma weight residual 122.65 112.47 10.18 1.66e+00 3.63e-01 3.76e+01 angle pdb=" N PRO A 209 " pdb=" CA PRO A 209 " pdb=" C PRO A 209 " ideal model delta sigma weight residual 110.70 117.68 -6.98 1.22e+00 6.72e-01 3.27e+01 angle pdb=" N ASP B 480 " pdb=" CA ASP B 480 " pdb=" C ASP B 480 " ideal model delta sigma weight residual 112.45 104.74 7.71 1.39e+00 5.18e-01 3.08e+01 angle pdb=" CA LEU B 481 " pdb=" C LEU B 481 " pdb=" O LEU B 481 " ideal model delta sigma weight residual 121.94 115.94 6.00 1.15e+00 7.56e-01 2.72e+01 ... (remaining 19781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 7485 16.09 - 32.18: 854 32.18 - 48.26: 211 48.26 - 64.35: 68 64.35 - 80.44: 20 Dihedral angle restraints: 8638 sinusoidal: 3245 harmonic: 5393 Sorted by residual: dihedral pdb=" CA PRO B 209 " pdb=" C PRO B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASN A 152 " pdb=" C ASN A 152 " pdb=" N ASP A 153 " pdb=" CA ASP A 153 " ideal model delta harmonic sigma weight residual -180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA PRO B 696 " pdb=" C PRO B 696 " pdb=" N THR B 697 " pdb=" CA THR B 697 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 8635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1996 0.101 - 0.203: 231 0.203 - 0.304: 23 0.304 - 0.405: 4 0.405 - 0.506: 3 Chirality restraints: 2257 Sorted by residual: chirality pdb=" CB ILE A 10 " pdb=" CA ILE A 10 " pdb=" CG1 ILE A 10 " pdb=" CG2 ILE A 10 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CB ILE B 119 " pdb=" CA ILE B 119 " pdb=" CG1 ILE B 119 " pdb=" CG2 ILE B 119 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 2254 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 746 " 0.079 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO B 747 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO B 747 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 747 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 402 " -0.051 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO B 403 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 403 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 403 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 304 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO A 305 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " 0.041 5.00e-02 4.00e+02 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3133 2.78 - 3.31: 12522 3.31 - 3.84: 23870 3.84 - 4.37: 28268 4.37 - 4.90: 48296 Nonbonded interactions: 116089 Sorted by model distance: nonbonded pdb=" O PRO B 305 " pdb=" OH TYR B 341 " model vdw 2.255 3.040 nonbonded pdb=" O THR B 176 " pdb=" OG1 THR B 180 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR A 282 " pdb=" OG1 THR B 159 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR B 40 " pdb=" OE2 GLU B 66 " model vdw 2.294 3.040 nonbonded pdb=" O PRO A 444 " pdb=" NH2 ARG A 478 " model vdw 2.309 3.120 ... (remaining 116084 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 7 through 879) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.100 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 0.074 14540 Z= 0.389 Angle : 1.103 10.183 19786 Z= 0.648 Chirality : 0.068 0.506 2257 Planarity : 0.009 0.119 2596 Dihedral : 15.724 80.438 5160 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.55 % Favored : 93.40 % Rotamer: Outliers : 3.47 % Allowed : 2.11 % Favored : 94.42 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.17), residues: 1863 helix: -2.31 (0.15), residues: 756 sheet: -1.79 (0.33), residues: 238 loop : -2.15 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 27 HIS 0.009 0.001 HIS A 92 PHE 0.031 0.003 PHE B 26 TYR 0.022 0.002 TYR B 540 ARG 0.025 0.001 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.14700 ( 555) hydrogen bonds : angle 7.15995 ( 1575) covalent geometry : bond 0.00691 (14540) covalent geometry : angle 1.10330 (19786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 1.454 Fit side-chains REVERT: A 542 ARG cc_start: 0.4970 (mmt-90) cc_final: 0.4501 (ttm-80) REVERT: A 727 MET cc_start: 0.5760 (ptp) cc_final: 0.5514 (ptm) REVERT: B 137 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5716 (m-80) REVERT: B 745 ASN cc_start: 0.7285 (t0) cc_final: 0.6541 (m-40) outliers start: 51 outliers final: 5 residues processed: 211 average time/residue: 0.2818 time to fit residues: 86.0123 Evaluate side-chains 142 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 137 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 168 optimal weight: 0.0970 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS B 136 HIS B 671 GLN D 961 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.184389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136568 restraints weight = 16108.428| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.62 r_work: 0.3470 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14540 Z= 0.193 Angle : 0.676 10.470 19786 Z= 0.351 Chirality : 0.046 0.189 2257 Planarity : 0.007 0.070 2596 Dihedral : 6.268 55.335 2020 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.43 % Allowed : 9.46 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.18), residues: 1863 helix: -1.21 (0.17), residues: 760 sheet: -1.70 (0.33), residues: 243 loop : -1.90 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 771 HIS 0.009 0.001 HIS B 575 PHE 0.023 0.002 PHE B 26 TYR 0.016 0.002 TYR B 60 ARG 0.004 0.001 ARG B 716 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 555) hydrogen bonds : angle 5.40694 ( 1575) covalent geometry : bond 0.00454 (14540) covalent geometry : angle 0.67591 (19786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.632 Fit side-chains REVERT: A 193 LEU cc_start: 0.8922 (mt) cc_final: 0.8555 (mt) REVERT: A 232 PHE cc_start: 0.7878 (m-10) cc_final: 0.7593 (m-10) REVERT: A 542 ARG cc_start: 0.5180 (mmt-90) cc_final: 0.4416 (ttm-80) REVERT: A 727 MET cc_start: 0.6332 (ptp) cc_final: 0.5554 (ptm) REVERT: A 729 GLN cc_start: 0.7465 (mp10) cc_final: 0.7206 (mp10) REVERT: A 743 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.4953 (mmp-170) REVERT: A 831 ASP cc_start: 0.7096 (t0) cc_final: 0.6482 (t0) REVERT: B 137 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: B 143 SER cc_start: 0.1876 (OUTLIER) cc_final: 0.1334 (t) outliers start: 21 outliers final: 10 residues processed: 157 average time/residue: 0.2745 time to fit residues: 64.5582 Evaluate side-chains 148 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 797 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 161 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 177 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.185771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149772 restraints weight = 16041.757| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.81 r_work: 0.3496 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14540 Z= 0.127 Angle : 0.596 12.754 19786 Z= 0.304 Chirality : 0.043 0.182 2257 Planarity : 0.006 0.064 2596 Dihedral : 5.667 53.802 2014 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.63 % Allowed : 12.53 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.19), residues: 1863 helix: -0.62 (0.18), residues: 767 sheet: -1.54 (0.33), residues: 242 loop : -1.71 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 629 HIS 0.008 0.001 HIS A 92 PHE 0.017 0.001 PHE B 26 TYR 0.007 0.001 TYR B 569 ARG 0.005 0.000 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 555) hydrogen bonds : angle 5.02486 ( 1575) covalent geometry : bond 0.00289 (14540) covalent geometry : angle 0.59605 (19786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.479 Fit side-chains REVERT: A 193 LEU cc_start: 0.8837 (mt) cc_final: 0.8492 (mt) REVERT: A 542 ARG cc_start: 0.5116 (mmt-90) cc_final: 0.4480 (ttm-80) REVERT: A 554 TYR cc_start: 0.7993 (t80) cc_final: 0.7696 (t80) REVERT: A 727 MET cc_start: 0.6300 (ptp) cc_final: 0.5764 (ptm) REVERT: A 831 ASP cc_start: 0.7235 (t0) cc_final: 0.6943 (t0) REVERT: B 48 MET cc_start: 0.7685 (tmm) cc_final: 0.6899 (tmm) REVERT: B 137 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: B 745 ASN cc_start: 0.7192 (t0) cc_final: 0.6404 (m-40) REVERT: D 964 GLU cc_start: 0.3149 (OUTLIER) cc_final: 0.1799 (pt0) outliers start: 24 outliers final: 16 residues processed: 149 average time/residue: 0.2598 time to fit residues: 57.7971 Evaluate side-chains 148 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain D residue 964 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 162 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN D 961 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.181746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3728 r_free = 0.3728 target = 0.132107 restraints weight = 16137.677| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.65 r_work: 0.3426 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14540 Z= 0.202 Angle : 0.641 9.763 19786 Z= 0.331 Chirality : 0.046 0.258 2257 Planarity : 0.006 0.062 2596 Dihedral : 5.752 59.329 2014 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.65 % Allowed : 14.30 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1863 helix: -0.49 (0.18), residues: 766 sheet: -1.60 (0.34), residues: 232 loop : -1.70 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 629 HIS 0.006 0.001 HIS A 353 PHE 0.025 0.002 PHE B 638 TYR 0.015 0.002 TYR A 264 ARG 0.006 0.001 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 555) hydrogen bonds : angle 5.01999 ( 1575) covalent geometry : bond 0.00481 (14540) covalent geometry : angle 0.64060 (19786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8954 (mt) cc_final: 0.8517 (mt) REVERT: A 430 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6107 (tp30) REVERT: A 542 ARG cc_start: 0.5274 (mmt-90) cc_final: 0.4245 (ttm-80) REVERT: A 727 MET cc_start: 0.6476 (ptp) cc_final: 0.5466 (ptm) REVERT: A 729 GLN cc_start: 0.7355 (mp10) cc_final: 0.7095 (mp10) REVERT: A 735 LEU cc_start: 0.7912 (tp) cc_final: 0.7668 (tt) REVERT: A 831 ASP cc_start: 0.7572 (t0) cc_final: 0.6785 (t0) REVERT: B 137 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.5655 (m-80) REVERT: B 745 ASN cc_start: 0.7131 (t0) cc_final: 0.6126 (m-40) REVERT: D 954 MET cc_start: 0.4895 (tmm) cc_final: 0.4486 (tmm) REVERT: D 957 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.5681 (ptp) REVERT: D 964 GLU cc_start: 0.2895 (OUTLIER) cc_final: 0.1642 (pt0) outliers start: 39 outliers final: 24 residues processed: 161 average time/residue: 0.3132 time to fit residues: 75.3802 Evaluate side-chains 158 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain D residue 957 MET Chi-restraints excluded: chain D residue 964 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 70 optimal weight: 7.9990 chunk 98 optimal weight: 0.4980 chunk 159 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.183271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145123 restraints weight = 16212.282| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.94 r_work: 0.3422 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14540 Z= 0.156 Angle : 0.592 10.792 19786 Z= 0.302 Chirality : 0.044 0.258 2257 Planarity : 0.005 0.068 2596 Dihedral : 5.332 56.967 2012 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.11 % Allowed : 16.95 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1863 helix: -0.22 (0.19), residues: 763 sheet: -1.60 (0.33), residues: 241 loop : -1.60 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 629 HIS 0.008 0.001 HIS B 575 PHE 0.026 0.002 PHE B 638 TYR 0.009 0.001 TYR B 396 ARG 0.005 0.000 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 555) hydrogen bonds : angle 4.87372 ( 1575) covalent geometry : bond 0.00372 (14540) covalent geometry : angle 0.59243 (19786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8889 (mt) cc_final: 0.8496 (mt) REVERT: A 542 ARG cc_start: 0.5227 (mmt-90) cc_final: 0.4190 (ttm-80) REVERT: A 727 MET cc_start: 0.6509 (ptp) cc_final: 0.5486 (ptm) REVERT: A 831 ASP cc_start: 0.7629 (t0) cc_final: 0.7300 (t0) REVERT: B 137 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6588 (p90) REVERT: B 745 ASN cc_start: 0.7168 (t0) cc_final: 0.6252 (m-40) REVERT: D 954 MET cc_start: 0.4620 (tmm) cc_final: 0.4244 (tmm) REVERT: D 957 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.5857 (ptp) REVERT: D 964 GLU cc_start: 0.3110 (OUTLIER) cc_final: 0.1693 (pt0) outliers start: 31 outliers final: 24 residues processed: 161 average time/residue: 0.3856 time to fit residues: 96.4242 Evaluate side-chains 159 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain D residue 957 MET Chi-restraints excluded: chain D residue 964 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 0.0370 chunk 115 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 5 optimal weight: 0.1980 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN A 721 HIS B 164 HIS ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.185264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149666 restraints weight = 16213.728| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.81 r_work: 0.3485 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14540 Z= 0.109 Angle : 0.561 12.173 19786 Z= 0.281 Chirality : 0.042 0.254 2257 Planarity : 0.005 0.057 2596 Dihedral : 5.033 51.186 2012 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.31 % Allowed : 17.09 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1863 helix: 0.08 (0.19), residues: 763 sheet: -1.38 (0.34), residues: 240 loop : -1.52 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 629 HIS 0.007 0.001 HIS A 92 PHE 0.015 0.001 PHE B 26 TYR 0.008 0.001 TYR B 396 ARG 0.002 0.000 ARG B 716 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 555) hydrogen bonds : angle 4.68315 ( 1575) covalent geometry : bond 0.00253 (14540) covalent geometry : angle 0.56144 (19786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.5209 (mmt-90) cc_final: 0.4580 (tpp80) REVERT: A 831 ASP cc_start: 0.7609 (t0) cc_final: 0.7376 (t0) REVERT: B 137 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6557 (p90) REVERT: B 745 ASN cc_start: 0.7115 (t0) cc_final: 0.6219 (m-40) REVERT: B 789 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 954 MET cc_start: 0.4647 (tmm) cc_final: 0.4309 (tmm) REVERT: D 957 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6014 (ptp) REVERT: D 964 GLU cc_start: 0.3205 (OUTLIER) cc_final: 0.1819 (pt0) outliers start: 34 outliers final: 21 residues processed: 166 average time/residue: 0.2699 time to fit residues: 66.5243 Evaluate side-chains 158 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain D residue 957 MET Chi-restraints excluded: chain D residue 963 GLN Chi-restraints excluded: chain D residue 964 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 10 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 29 optimal weight: 0.0050 chunk 82 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.6314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149966 restraints weight = 16097.536| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.83 r_work: 0.3497 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14540 Z= 0.106 Angle : 0.566 12.697 19786 Z= 0.281 Chirality : 0.042 0.321 2257 Planarity : 0.005 0.050 2596 Dihedral : 4.829 49.368 2012 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.38 % Allowed : 17.84 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1863 helix: 0.31 (0.19), residues: 755 sheet: -1.13 (0.34), residues: 240 loop : -1.47 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 629 HIS 0.007 0.001 HIS A 92 PHE 0.022 0.001 PHE B 781 TYR 0.012 0.001 TYR B 60 ARG 0.004 0.000 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 555) hydrogen bonds : angle 4.57920 ( 1575) covalent geometry : bond 0.00243 (14540) covalent geometry : angle 0.56647 (19786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7870 (mt) REVERT: A 542 ARG cc_start: 0.5406 (mmt-90) cc_final: 0.4548 (ttm-80) REVERT: B 54 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6272 (t80) REVERT: B 130 MET cc_start: 0.6620 (mmt) cc_final: 0.5917 (mpp) REVERT: B 137 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.5914 (m-10) REVERT: B 641 GLU cc_start: 0.8150 (mp0) cc_final: 0.7926 (mp0) REVERT: B 745 ASN cc_start: 0.7108 (t0) cc_final: 0.6200 (m-40) REVERT: B 789 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7557 (tm-30) REVERT: D 957 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6050 (ptp) REVERT: D 964 GLU cc_start: 0.3216 (OUTLIER) cc_final: 0.1750 (pt0) outliers start: 35 outliers final: 25 residues processed: 163 average time/residue: 0.3474 time to fit residues: 85.8872 Evaluate side-chains 162 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain C residue 981 VAL Chi-restraints excluded: chain D residue 957 MET Chi-restraints excluded: chain D residue 963 GLN Chi-restraints excluded: chain D residue 964 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.186866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139037 restraints weight = 16074.352| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.63 r_work: 0.3509 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14540 Z= 0.104 Angle : 0.564 12.410 19786 Z= 0.279 Chirality : 0.042 0.238 2257 Planarity : 0.005 0.048 2596 Dihedral : 4.717 49.171 2012 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.45 % Allowed : 18.04 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1863 helix: 0.45 (0.19), residues: 748 sheet: -1.00 (0.34), residues: 240 loop : -1.38 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 629 HIS 0.007 0.001 HIS A 92 PHE 0.044 0.001 PHE B 781 TYR 0.008 0.001 TYR B 396 ARG 0.003 0.000 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 555) hydrogen bonds : angle 4.52456 ( 1575) covalent geometry : bond 0.00240 (14540) covalent geometry : angle 0.56435 (19786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7866 (mt) REVERT: A 542 ARG cc_start: 0.5418 (mmt-90) cc_final: 0.4445 (ttm-80) REVERT: B 54 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6394 (t80) REVERT: B 130 MET cc_start: 0.6648 (mmt) cc_final: 0.5332 (ptt) REVERT: B 137 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.5782 (m-10) REVERT: B 745 ASN cc_start: 0.6987 (t0) cc_final: 0.6070 (m-40) REVERT: B 789 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 976 MET cc_start: 0.1214 (tpp) cc_final: 0.0983 (tpp) REVERT: D 957 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.5853 (ptp) REVERT: D 964 GLU cc_start: 0.2918 (OUTLIER) cc_final: 0.1731 (pt0) outliers start: 36 outliers final: 26 residues processed: 160 average time/residue: 0.4214 time to fit residues: 103.2783 Evaluate side-chains 164 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 981 VAL Chi-restraints excluded: chain D residue 957 MET Chi-restraints excluded: chain D residue 963 GLN Chi-restraints excluded: chain D residue 964 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 28 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 114 optimal weight: 0.0020 chunk 22 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 HIS ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.187661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152781 restraints weight = 15952.988| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.72 r_work: 0.3529 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14540 Z= 0.101 Angle : 0.557 12.619 19786 Z= 0.276 Chirality : 0.042 0.193 2257 Planarity : 0.005 0.048 2596 Dihedral : 4.578 48.989 2012 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.18 % Allowed : 18.31 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1863 helix: 0.47 (0.19), residues: 765 sheet: -0.85 (0.35), residues: 238 loop : -1.35 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP B 629 HIS 0.007 0.001 HIS A 92 PHE 0.015 0.001 PHE B 26 TYR 0.012 0.001 TYR B 548 ARG 0.006 0.000 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 555) hydrogen bonds : angle 4.45055 ( 1575) covalent geometry : bond 0.00231 (14540) covalent geometry : angle 0.55687 (19786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7811 (mt) REVERT: A 542 ARG cc_start: 0.5348 (mmt-90) cc_final: 0.4617 (tpp80) REVERT: A 727 MET cc_start: 0.6804 (ptp) cc_final: 0.6060 (ptm) REVERT: B 54 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6244 (t80) REVERT: B 130 MET cc_start: 0.6393 (mmt) cc_final: 0.5349 (ptt) REVERT: B 137 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.5748 (m-10) REVERT: B 745 ASN cc_start: 0.7273 (t0) cc_final: 0.6359 (m-40) REVERT: D 957 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6030 (ptp) REVERT: D 964 GLU cc_start: 0.3161 (OUTLIER) cc_final: 0.1793 (pt0) outliers start: 32 outliers final: 23 residues processed: 160 average time/residue: 0.2802 time to fit residues: 66.4581 Evaluate side-chains 161 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain D residue 957 MET Chi-restraints excluded: chain D residue 963 GLN Chi-restraints excluded: chain D residue 964 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN B 575 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.185591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.150669 restraints weight = 16048.186| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.72 r_work: 0.3511 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14540 Z= 0.133 Angle : 0.580 11.709 19786 Z= 0.292 Chirality : 0.042 0.189 2257 Planarity : 0.005 0.048 2596 Dihedral : 4.602 48.613 2009 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.11 % Allowed : 18.72 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1863 helix: 0.43 (0.19), residues: 755 sheet: -0.86 (0.35), residues: 238 loop : -1.33 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 629 HIS 0.006 0.001 HIS A 92 PHE 0.019 0.001 PHE B 26 TYR 0.020 0.001 TYR B 548 ARG 0.003 0.000 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 555) hydrogen bonds : angle 4.58662 ( 1575) covalent geometry : bond 0.00315 (14540) covalent geometry : angle 0.58035 (19786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7937 (mt) REVERT: A 542 ARG cc_start: 0.5385 (mmt-90) cc_final: 0.4693 (tpp80) REVERT: B 54 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6263 (t80) REVERT: B 130 MET cc_start: 0.6400 (mmt) cc_final: 0.5420 (ptt) REVERT: B 137 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.5935 (p90) REVERT: B 641 GLU cc_start: 0.8125 (mp0) cc_final: 0.7844 (mp0) REVERT: B 745 ASN cc_start: 0.7227 (t0) cc_final: 0.6364 (m-40) REVERT: D 957 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6035 (ptp) REVERT: D 964 GLU cc_start: 0.3190 (OUTLIER) cc_final: 0.1856 (pt0) outliers start: 31 outliers final: 24 residues processed: 152 average time/residue: 0.2535 time to fit residues: 58.5784 Evaluate side-chains 156 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain D residue 957 MET Chi-restraints excluded: chain D residue 963 GLN Chi-restraints excluded: chain D residue 964 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 75 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN B 575 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.184904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.137540 restraints weight = 16208.202| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.68 r_work: 0.3472 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14540 Z= 0.141 Angle : 0.592 11.335 19786 Z= 0.297 Chirality : 0.043 0.177 2257 Planarity : 0.005 0.048 2596 Dihedral : 4.661 48.699 2009 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.25 % Allowed : 19.06 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1863 helix: 0.34 (0.19), residues: 759 sheet: -0.87 (0.35), residues: 238 loop : -1.30 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 629 HIS 0.006 0.001 HIS A 92 PHE 0.024 0.002 PHE B 638 TYR 0.020 0.001 TYR B 548 ARG 0.003 0.000 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 555) hydrogen bonds : angle 4.63044 ( 1575) covalent geometry : bond 0.00335 (14540) covalent geometry : angle 0.59239 (19786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9352.14 seconds wall clock time: 164 minutes 40.60 seconds (9880.60 seconds total)