Starting phenix.real_space_refine on Thu Sep 18 04:56:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjy_38410/09_2025/8xjy_38410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjy_38410/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xjy_38410/09_2025/8xjy_38410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjy_38410/09_2025/8xjy_38410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xjy_38410/09_2025/8xjy_38410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjy_38410/09_2025/8xjy_38410.map" } resolution = 3.29 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.77, per 1000 atoms: 0.26 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: 1.25 Conformation dependent library (CDL) restraints added in 820.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.59 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: 2.48 Time building geometry restraints manager: 1.75 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: 1.630 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.100 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- 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 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: -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 ARG 0.025 0.001 ARG A 501 TYR 0.022 0.002 TYR B 540 PHE 0.031 0.003 PHE B 26 TRP 0.021 0.003 TRP B 27 HIS 0.009 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00691 (14540) covalent geometry : angle 1.10330 (19786) hydrogen bonds : bond 0.14700 ( 555) hydrogen bonds : angle 7.15995 ( 1575) *********************** 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 : 0.527 Fit side-chains REVERT: A 542 ARG cc_start: 0.4970 (mmt-90) cc_final: 0.4499 (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: 0.1359 time to fit residues: 41.3561 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 : 0.485 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS B 597 GLN B 671 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 961 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.187961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141481 restraints weight = 15932.688| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.66 r_work: 0.3503 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1434 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= 0.129 Angle : 0.632 12.251 19786 Z= 0.325 Chirality : 0.044 0.164 2257 Planarity : 0.006 0.069 2596 Dihedral : 6.151 55.659 2020 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.29 % Allowed : 8.51 % Favored : 90.20 % 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: -2.32 (0.18), residues: 1863 helix: -1.15 (0.17), residues: 766 sheet: -1.39 (0.34), residues: 234 loop : -1.87 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 645 TYR 0.015 0.001 TYR B 60 PHE 0.017 0.001 PHE B 26 TRP 0.009 0.001 TRP B 27 HIS 0.009 0.001 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00293 (14540) covalent geometry : angle 0.63152 (19786) hydrogen bonds : bond 0.04002 ( 555) hydrogen bonds : angle 5.32252 ( 1575) *********************** 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 164 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 136 HIS cc_start: 0.6030 (OUTLIER) cc_final: 0.5265 (t-170) REVERT: A 193 LEU cc_start: 0.8876 (mt) cc_final: 0.8550 (mt) REVERT: A 542 ARG cc_start: 0.5105 (mmt-90) cc_final: 0.4328 (ttm-80) REVERT: A 621 MET cc_start: 0.7760 (ptm) cc_final: 0.7534 (ptp) REVERT: A 727 MET cc_start: 0.6332 (ptp) cc_final: 0.5960 (ptm) REVERT: A 743 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.5048 (mmp-170) REVERT: A 831 ASP cc_start: 0.6926 (t0) cc_final: 0.6378 (t0) REVERT: B 137 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.5721 (m-80) REVERT: B 143 SER cc_start: 0.2036 (OUTLIER) cc_final: 0.1399 (t) REVERT: B 727 MET cc_start: 0.6516 (tmm) cc_final: 0.6313 (ttt) REVERT: B 745 ASN cc_start: 0.7283 (t0) cc_final: 0.6577 (m-40) outliers start: 19 outliers final: 10 residues processed: 153 average time/residue: 0.1195 time to fit residues: 27.2176 Evaluate side-chains 143 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS 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 662 MET Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 789 GLN 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 68 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 173 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 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 = 0.4284 r_free = 0.4284 target = 0.184967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137101 restraints weight = 16192.249| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.66 r_work: 0.3471 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14540 Z= 0.154 Angle : 0.615 10.792 19786 Z= 0.314 Chirality : 0.044 0.168 2257 Planarity : 0.006 0.053 2596 Dihedral : 5.810 52.870 2016 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.50 % Allowed : 11.91 % Favored : 86.59 % 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: -1.92 (0.19), residues: 1863 helix: -0.65 (0.18), residues: 767 sheet: -1.54 (0.33), residues: 246 loop : -1.69 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 645 TYR 0.010 0.001 TYR A 264 PHE 0.021 0.002 PHE B 26 TRP 0.014 0.001 TRP B 629 HIS 0.007 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00360 (14540) covalent geometry : angle 0.61487 (19786) hydrogen bonds : bond 0.03866 ( 555) hydrogen bonds : angle 5.01066 ( 1575) *********************** 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 157 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.376 Fit side-chains REVERT: A 84 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 193 LEU cc_start: 0.8881 (mt) cc_final: 0.8514 (mt) REVERT: A 232 PHE cc_start: 0.7811 (m-10) cc_final: 0.7562 (m-10) REVERT: A 542 ARG cc_start: 0.5230 (mmt-90) cc_final: 0.4430 (ttm-80) REVERT: A 554 TYR cc_start: 0.8098 (t80) cc_final: 0.7782 (t80) REVERT: A 727 MET cc_start: 0.6367 (ptp) cc_final: 0.5753 (ptm) REVERT: A 831 ASP cc_start: 0.7282 (t0) cc_final: 0.6568 (t0) REVERT: B 48 MET cc_start: 0.7710 (tmm) cc_final: 0.6872 (tmm) REVERT: B 130 MET cc_start: 0.6694 (mmt) cc_final: 0.6478 (mmt) REVERT: B 137 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.5667 (m-80) REVERT: B 638 PHE cc_start: 0.7176 (p90) cc_final: 0.6973 (p90) REVERT: D 964 GLU cc_start: 0.2899 (OUTLIER) cc_final: 0.1720 (pt0) outliers start: 22 outliers final: 14 residues processed: 148 average time/residue: 0.1293 time to fit residues: 28.1608 Evaluate side-chains 142 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 693 ILE 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 101 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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** D 961 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.182276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.135777 restraints weight = 16236.718| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.73 r_work: 0.3428 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14540 Z= 0.200 Angle : 0.639 9.881 19786 Z= 0.329 Chirality : 0.046 0.203 2257 Planarity : 0.006 0.054 2596 Dihedral : 5.663 59.116 2014 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.72 % Allowed : 13.82 % Favored : 83.46 % 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: -1.80 (0.19), residues: 1863 helix: -0.46 (0.18), residues: 761 sheet: -1.69 (0.33), residues: 241 loop : -1.65 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 83 TYR 0.014 0.002 TYR A 264 PHE 0.023 0.002 PHE B 26 TRP 0.022 0.002 TRP B 629 HIS 0.008 0.001 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00480 (14540) covalent geometry : angle 0.63885 (19786) hydrogen bonds : bond 0.03965 ( 555) hydrogen bonds : angle 4.99998 ( 1575) *********************** 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 176 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8950 (mt) cc_final: 0.8513 (mt) REVERT: A 232 PHE cc_start: 0.7855 (m-10) cc_final: 0.7655 (m-10) REVERT: A 430 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6172 (tp30) REVERT: A 542 ARG cc_start: 0.5324 (mmt-90) cc_final: 0.4203 (ttm-80) REVERT: A 640 LEU cc_start: 0.7104 (tp) cc_final: 0.6850 (tp) REVERT: A 727 MET cc_start: 0.6495 (ptp) cc_final: 0.5376 (ptm) REVERT: B 137 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6702 (p90) REVERT: B 745 ASN cc_start: 0.6987 (t0) cc_final: 0.6193 (m-40) REVERT: D 954 MET cc_start: 0.4895 (tmm) cc_final: 0.4492 (tmm) REVERT: D 957 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.5758 (ptp) REVERT: D 964 GLU cc_start: 0.2881 (OUTLIER) cc_final: 0.1624 (pt0) outliers start: 40 outliers final: 26 residues processed: 158 average time/residue: 0.1354 time to fit residues: 30.9576 Evaluate side-chains 156 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 222 ILE Chi-restraints excluded: chain B residue 347 VAL 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 663 LEU 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 772 ILE 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 165 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 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 = 0.4273 r_free = 0.4273 target = 0.183921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150180 restraints weight = 16170.163| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.68 r_work: 0.3485 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14540 Z= 0.145 Angle : 0.596 10.924 19786 Z= 0.302 Chirality : 0.043 0.255 2257 Planarity : 0.005 0.064 2596 Dihedral : 5.243 52.848 2012 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.97 % Allowed : 16.88 % Favored : 81.14 % 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: -1.53 (0.19), residues: 1863 helix: -0.19 (0.19), residues: 753 sheet: -1.52 (0.34), residues: 240 loop : -1.54 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.009 0.001 TYR A 605 PHE 0.019 0.001 PHE B 26 TRP 0.026 0.001 TRP B 629 HIS 0.007 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00342 (14540) covalent geometry : angle 0.59567 (19786) hydrogen bonds : bond 0.03589 ( 555) hydrogen bonds : angle 4.83414 ( 1575) *********************** 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 163 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8871 (mt) cc_final: 0.8498 (mt) REVERT: A 542 ARG cc_start: 0.5197 (mmt-90) cc_final: 0.4210 (ttm-80) REVERT: A 640 LEU cc_start: 0.7296 (tp) cc_final: 0.7094 (tp) REVERT: B 745 ASN cc_start: 0.7107 (t0) cc_final: 0.6166 (m-40) REVERT: D 954 MET cc_start: 0.4577 (tmm) cc_final: 0.4282 (tmm) REVERT: D 957 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.5955 (ptp) REVERT: D 964 GLU cc_start: 0.3191 (OUTLIER) cc_final: 0.1798 (pt0) outliers start: 29 outliers final: 19 residues processed: 153 average time/residue: 0.1313 time to fit residues: 29.5773 Evaluate side-chains 148 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 560 ARG 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 74 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 206 THR 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 797 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 9 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 chunk 149 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 733 GLN ** 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 = 0.4262 r_free = 0.4262 target = 0.182794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146810 restraints weight = 16257.633| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.78 r_work: 0.3451 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14540 Z= 0.169 Angle : 0.613 10.041 19786 Z= 0.311 Chirality : 0.044 0.252 2257 Planarity : 0.005 0.059 2596 Dihedral : 5.100 48.737 2010 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.65 % Allowed : 17.43 % Favored : 79.92 % 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: -1.47 (0.19), residues: 1863 helix: -0.13 (0.19), residues: 753 sheet: -1.42 (0.34), residues: 235 loop : -1.55 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.010 0.002 TYR A 264 PHE 0.021 0.002 PHE B 26 TRP 0.035 0.002 TRP B 629 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00404 (14540) covalent geometry : angle 0.61254 (19786) hydrogen bonds : bond 0.03670 ( 555) hydrogen bonds : angle 4.85023 ( 1575) *********************** 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 174 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8897 (mt) cc_final: 0.8491 (mt) REVERT: A 430 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6187 (tp30) REVERT: A 542 ARG cc_start: 0.5336 (mmt-90) cc_final: 0.4231 (ttm-80) REVERT: B 54 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6270 (t80) REVERT: B 745 ASN cc_start: 0.7231 (t0) cc_final: 0.6308 (m-40) REVERT: D 957 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.5996 (ptp) REVERT: D 964 GLU cc_start: 0.3239 (OUTLIER) cc_final: 0.1900 (pt0) outliers start: 39 outliers final: 26 residues processed: 160 average time/residue: 0.1233 time to fit residues: 29.3613 Evaluate side-chains 156 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 304 THR 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 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 180 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 347 VAL 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 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 182 optimal weight: 0.0870 chunk 84 optimal weight: 0.0170 chunk 109 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 99 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 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 = 0.4298 r_free = 0.4298 target = 0.186433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152356 restraints weight = 15997.903| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.69 r_work: 0.3529 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2691 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= 0.103 Angle : 0.571 12.988 19786 Z= 0.284 Chirality : 0.042 0.323 2257 Planarity : 0.005 0.063 2596 Dihedral : 4.733 44.177 2010 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.18 % Allowed : 18.38 % Favored : 79.44 % 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: -1.12 (0.19), residues: 1863 helix: 0.22 (0.19), residues: 754 sheet: -1.16 (0.34), residues: 240 loop : -1.44 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 645 TYR 0.008 0.001 TYR B 396 PHE 0.025 0.001 PHE B 781 TRP 0.032 0.001 TRP B 629 HIS 0.008 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00233 (14540) covalent geometry : angle 0.57118 (19786) hydrogen bonds : bond 0.03300 ( 555) hydrogen bonds : angle 4.66441 ( 1575) *********************** 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 166 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.5246 (mmt-90) cc_final: 0.4614 (tpp80) REVERT: B 130 MET cc_start: 0.6553 (mmt) cc_final: 0.5761 (mpp) REVERT: B 641 GLU cc_start: 0.8057 (mp0) cc_final: 0.7810 (mp0) REVERT: B 745 ASN cc_start: 0.7009 (t0) cc_final: 0.6092 (m-40) REVERT: B 789 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7604 (tm-30) REVERT: D 954 MET cc_start: 0.4034 (tmm) cc_final: 0.3583 (tmm) REVERT: D 957 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.5892 (ptp) REVERT: D 964 GLU cc_start: 0.3221 (OUTLIER) cc_final: 0.1831 (pt0) outliers start: 32 outliers final: 23 residues processed: 155 average time/residue: 0.1230 time to fit residues: 28.4862 Evaluate side-chains 153 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 304 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 560 ARG 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 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 727 MET Chi-restraints excluded: chain B residue 735 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 76 optimal weight: 5.9990 chunk 97 optimal weight: 0.0370 chunk 6 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 161 optimal weight: 0.1980 chunk 57 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.185406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.148662 restraints weight = 15964.863| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.82 r_work: 0.3484 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14540 Z= 0.119 Angle : 0.584 11.860 19786 Z= 0.291 Chirality : 0.043 0.241 2257 Planarity : 0.005 0.058 2596 Dihedral : 4.664 40.961 2010 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.04 % Allowed : 18.92 % Favored : 79.03 % 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: -1.03 (0.19), residues: 1863 helix: 0.29 (0.19), residues: 756 sheet: -1.08 (0.34), residues: 240 loop : -1.40 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 645 TYR 0.013 0.001 TYR B 60 PHE 0.017 0.001 PHE B 26 TRP 0.033 0.001 TRP B 629 HIS 0.007 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00280 (14540) covalent geometry : angle 0.58389 (19786) hydrogen bonds : bond 0.03334 ( 555) hydrogen bonds : angle 4.63312 ( 1575) *********************** 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 161 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7964 (mt) REVERT: A 542 ARG cc_start: 0.5410 (mmt-90) cc_final: 0.4584 (ttm-80) REVERT: A 727 MET cc_start: 0.6855 (ptp) cc_final: 0.6148 (ptm) REVERT: B 54 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6322 (t80) REVERT: B 130 MET cc_start: 0.6537 (mmt) cc_final: 0.5895 (mpp) REVERT: B 641 GLU cc_start: 0.8131 (mp0) cc_final: 0.7892 (mp0) REVERT: B 745 ASN cc_start: 0.7122 (t0) cc_final: 0.6208 (m-40) REVERT: B 789 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7629 (tm-30) REVERT: D 954 MET cc_start: 0.4132 (tmm) cc_final: 0.3630 (tmm) REVERT: D 957 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.5943 (ptp) REVERT: D 964 GLU cc_start: 0.3215 (OUTLIER) cc_final: 0.1801 (pt0) outliers start: 30 outliers final: 24 residues processed: 150 average time/residue: 0.1260 time to fit residues: 28.1095 Evaluate side-chains 153 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 509 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 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 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 642 ASP 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 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 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.184767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146151 restraints weight = 16117.238| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.86 r_work: 0.3447 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14540 Z= 0.135 Angle : 0.598 12.492 19786 Z= 0.298 Chirality : 0.043 0.211 2257 Planarity : 0.005 0.053 2596 Dihedral : 4.681 37.352 2010 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.31 % Allowed : 19.06 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.02 (0.19), residues: 1863 helix: 0.23 (0.19), residues: 761 sheet: -0.98 (0.35), residues: 238 loop : -1.37 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 645 TYR 0.008 0.001 TYR B 113 PHE 0.028 0.001 PHE B 781 TRP 0.043 0.001 TRP B 629 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00319 (14540) covalent geometry : angle 0.59758 (19786) hydrogen bonds : bond 0.03407 ( 555) hydrogen bonds : angle 4.69341 ( 1575) *********************** 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 162 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7981 (mt) REVERT: A 542 ARG cc_start: 0.5399 (mmt-90) cc_final: 0.4546 (ttm-80) REVERT: A 716 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6736 (mtp85) REVERT: A 727 MET cc_start: 0.6903 (ptp) cc_final: 0.6125 (ptm) REVERT: B 54 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6403 (t80) REVERT: B 745 ASN cc_start: 0.7196 (t0) cc_final: 0.6238 (m-40) REVERT: B 789 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 954 MET cc_start: 0.4271 (tmm) cc_final: 0.3782 (tmm) REVERT: D 957 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.5943 (ptp) REVERT: D 964 GLU cc_start: 0.3231 (OUTLIER) cc_final: 0.1553 (pt0) outliers start: 34 outliers final: 26 residues processed: 153 average time/residue: 0.1279 time to fit residues: 29.0689 Evaluate side-chains 155 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 222 ILE 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 509 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 852 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 61 VAL 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 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 642 ASP 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 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 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 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 = 0.4279 r_free = 0.4279 target = 0.184527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146282 restraints weight = 16166.736| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.83 r_work: 0.3465 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14540 Z= 0.139 Angle : 0.593 11.224 19786 Z= 0.297 Chirality : 0.043 0.226 2257 Planarity : 0.005 0.053 2596 Dihedral : 4.585 20.771 2007 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.31 % Allowed : 18.86 % Favored : 78.83 % 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: -0.97 (0.19), residues: 1863 helix: 0.26 (0.19), residues: 754 sheet: -0.95 (0.35), residues: 238 loop : -1.32 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 645 TYR 0.008 0.001 TYR A 554 PHE 0.019 0.001 PHE B 26 TRP 0.048 0.001 TRP B 629 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00329 (14540) covalent geometry : angle 0.59348 (19786) hydrogen bonds : bond 0.03391 ( 555) hydrogen bonds : angle 4.68365 ( 1575) ********************** 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 162 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7967 (mt) REVERT: A 542 ARG cc_start: 0.5383 (mmt-90) cc_final: 0.4524 (ttm-80) REVERT: A 716 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.6706 (mtp85) REVERT: B 54 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6421 (t80) REVERT: B 130 MET cc_start: 0.6427 (mmt) cc_final: 0.5432 (ptt) REVERT: B 745 ASN cc_start: 0.7229 (t0) cc_final: 0.6337 (m-40) REVERT: D 954 MET cc_start: 0.4014 (tmm) cc_final: 0.3516 (tmm) REVERT: D 957 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.5963 (ptp) REVERT: D 964 GLU cc_start: 0.3240 (OUTLIER) cc_final: 0.1855 (pt0) outliers start: 34 outliers final: 28 residues processed: 152 average time/residue: 0.1341 time to fit residues: 29.8456 Evaluate side-chains 155 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 222 ILE 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 509 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 852 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 61 VAL 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 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 347 VAL 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 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 119 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 58 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN B 721 HIS ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.186079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152249 restraints weight = 16047.222| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.67 r_work: 0.3524 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14540 Z= 0.115 Angle : 0.585 12.593 19786 Z= 0.290 Chirality : 0.042 0.219 2257 Planarity : 0.005 0.050 2596 Dihedral : 4.476 20.238 2007 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.45 % Allowed : 18.99 % Favored : 78.56 % 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: -0.87 (0.20), residues: 1863 helix: 0.38 (0.19), residues: 760 sheet: -0.87 (0.35), residues: 238 loop : -1.32 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 645 TYR 0.011 0.001 TYR B 548 PHE 0.034 0.001 PHE B 781 TRP 0.046 0.001 TRP B 629 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00268 (14540) covalent geometry : angle 0.58538 (19786) hydrogen bonds : bond 0.03247 ( 555) hydrogen bonds : angle 4.58985 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.93 seconds wall clock time: 68 minutes 49.95 seconds (4129.95 seconds total)