Starting phenix.real_space_refine on Fri Jul 3 12:10:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9v_36116/07_2026/8j9v_36116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9v_36116/07_2026/8j9v_36116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j9v_36116/07_2026/8j9v_36116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9v_36116/07_2026/8j9v_36116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j9v_36116/07_2026/8j9v_36116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9v_36116/07_2026/8j9v_36116.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 8732 2.51 5 N 2396 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13918 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6307 Classifications: {'peptide': 778} Link IDs: {'PTRANS': 30, 'TRANS': 747} Chain: "B" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6307 Classifications: {'peptide': 778} Link IDs: {'PTRANS': 30, 'TRANS': 747} Chain: "C" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "E" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 338 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "F" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 338 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.98, per 1000 atoms: 0.21 Number of scatterers: 13918 At special positions: 0 Unit cell: (97.11, 126.99, 117.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 56 15.00 Mg 2 11.99 O 2676 8.00 N 2396 7.00 C 8732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 560.1 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 53.7% alpha, 10.9% beta 15 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.612A pdb=" N LYS A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 4.172A pdb=" N SER A 488 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 489 " --> pdb=" O THR A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 489' Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.656A pdb=" N ARG A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.874A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.556A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.621A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.842A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 730 Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 755 through 767 Processing helix chain 'A' and resid 797 through 800 Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 815 through 821 removed outlier: 3.826A pdb=" N LEU A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 944 through 953 Processing helix chain 'A' and resid 953 through 959 removed outlier: 3.575A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 991 removed outlier: 4.168A pdb=" N ARG A 985 " --> pdb=" O ASN A 981 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.614A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 5.186A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1081 through 1093 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1118 Processing helix chain 'A' and resid 1122 through 1128 removed outlier: 3.735A pdb=" N LEU A1128 " --> pdb=" O TYR A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1166 through 1186 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.591A pdb=" N LYS B 479 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 489 removed outlier: 4.190A pdb=" N SER B 488 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 489 " --> pdb=" O THR B 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 485 through 489' Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 528 removed outlier: 3.647A pdb=" N ARG B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.873A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.552A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.622A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.849A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 730 Processing helix chain 'B' and resid 738 through 750 Processing helix chain 'B' and resid 755 through 767 Processing helix chain 'B' and resid 797 through 800 Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 821 removed outlier: 3.852A pdb=" N LEU B 821 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 846 removed outlier: 3.595A pdb=" N ILE B 845 " --> pdb=" O PRO B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 877 Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 944 through 953 Processing helix chain 'B' and resid 953 through 959 removed outlier: 3.623A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 991 removed outlier: 4.168A pdb=" N ARG B 985 " --> pdb=" O ASN B 981 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.606A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 5.187A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 removed outlier: 3.593A pdb=" N TYR B1079 " --> pdb=" O LEU B1076 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1076 through 1079' Processing helix chain 'B' and resid 1081 through 1093 Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1118 Processing helix chain 'B' and resid 1122 through 1128 removed outlier: 3.717A pdb=" N LEU B1128 " --> pdb=" O TYR B1124 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1133 Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1186 Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 419 removed outlier: 3.584A pdb=" N MET A 467 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 577 through 581 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.780A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 853 Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.502A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 926 removed outlier: 6.436A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 931 " --> pdb=" O SER A 926 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 975 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 963 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS A 977 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AA9, first strand: chain 'B' and resid 418 through 419 removed outlier: 3.595A pdb=" N MET B 467 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 577 through 581 Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.786A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 849 through 853 Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913 removed outlier: 4.460A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.417A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 975 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 963 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS B 977 " --> pdb=" O GLU B 961 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1014 through 1016 600 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2250 1.32 - 1.44: 4172 1.44 - 1.56: 7746 1.56 - 1.69: 112 1.69 - 1.81: 88 Bond restraints: 14368 Sorted by residual: bond pdb=" CA LEU A 514 " pdb=" C LEU A 514 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.24e-02 6.50e+03 9.43e+00 bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.84e+00 bond pdb=" C3' DC F 10 " pdb=" C2' DC F 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.49e+00 bond pdb=" C3' DC F 15 " pdb=" C2' DC F 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.83e+00 bond pdb=" C3' DC D 15 " pdb=" C2' DC D 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.36e+00 ... (remaining 14363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 19152 1.75 - 3.50: 469 3.50 - 5.25: 46 5.25 - 7.01: 10 7.01 - 8.76: 7 Bond angle restraints: 19684 Sorted by residual: angle pdb=" N SER A 954 " pdb=" CA SER A 954 " pdb=" C SER A 954 " ideal model delta sigma weight residual 111.07 117.22 -6.15 1.07e+00 8.73e-01 3.31e+01 angle pdb=" N SER B 954 " pdb=" CA SER B 954 " pdb=" C SER B 954 " ideal model delta sigma weight residual 111.07 117.01 -5.94 1.07e+00 8.73e-01 3.08e+01 angle pdb=" N PRO A1105 " pdb=" CA PRO A1105 " pdb=" C PRO A1105 " ideal model delta sigma weight residual 113.57 107.52 6.05 1.31e+00 5.83e-01 2.13e+01 angle pdb=" C LEU A 514 " pdb=" N ASP A 515 " pdb=" CA ASP A 515 " ideal model delta sigma weight residual 122.87 115.94 6.93 1.61e+00 3.86e-01 1.85e+01 angle pdb=" C GLU B1106 " pdb=" CA GLU B1106 " pdb=" CB GLU B1106 " ideal model delta sigma weight residual 117.23 111.57 5.66 1.36e+00 5.41e-01 1.73e+01 ... (remaining 19679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 8290 35.72 - 71.44: 241 71.44 - 107.16: 5 107.16 - 142.88: 2 142.88 - 178.60: 2 Dihedral angle restraints: 8540 sinusoidal: 3978 harmonic: 4562 Sorted by residual: dihedral pdb=" C4' DA F 9 " pdb=" C3' DA F 9 " pdb=" O3' DA F 9 " pdb=" P DC F 10 " ideal model delta sinusoidal sigma weight residual -140.00 38.60 -178.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA D 9 " pdb=" C3' DA D 9 " pdb=" O3' DA D 9 " pdb=" P DC D 10 " ideal model delta sinusoidal sigma weight residual 220.00 41.50 178.50 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA SER A 853 " pdb=" C SER A 853 " pdb=" N GLU A 854 " pdb=" CA GLU A 854 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 8537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1618 0.047 - 0.094: 436 0.094 - 0.141: 95 0.141 - 0.188: 1 0.188 - 0.236: 4 Chirality restraints: 2154 Sorted by residual: chirality pdb=" C3' DA D 9 " pdb=" C4' DA D 9 " pdb=" O3' DA D 9 " pdb=" C2' DA D 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C3' DA F 9 " pdb=" C4' DA F 9 " pdb=" O3' DA F 9 " pdb=" C2' DA F 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C9 EVP F 101 " pdb=" C10 EVP F 101 " pdb=" C6 EVP F 101 " pdb=" C8 EVP F 101 " both_signs ideal model delta sigma weight residual False 2.49 2.71 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2151 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 512 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C LEU A 512 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU A 512 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY A 513 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1104 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C SER A1104 " 0.038 2.00e-02 2.50e+03 pdb=" O SER A1104 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO A1105 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 938 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.026 5.00e-02 4.00e+02 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 158 2.62 - 3.19: 12360 3.19 - 3.76: 22813 3.76 - 4.33: 31786 4.33 - 4.90: 50654 Nonbonded interactions: 117771 Sorted by model distance: nonbonded pdb=" OD2 ASP B 541 " pdb="MG MG B1201 " model vdw 2.053 2.170 nonbonded pdb=" OD2 ASP A 541 " pdb="MG MG A1201 " model vdw 2.053 2.170 nonbonded pdb=" OH TYR B 751 " pdb=" OP2 DG E 12 " model vdw 2.230 3.040 nonbonded pdb=" O PRO A 942 " pdb=" OG1 THR A 943 " model vdw 2.236 3.040 nonbonded pdb=" O PRO B 942 " pdb=" OG1 THR B 943 " model vdw 2.244 3.040 ... (remaining 117766 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.840 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 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 : 0.004 0.038 14368 Z= 0.274 Angle : 0.620 8.758 19684 Z= 0.410 Chirality : 0.044 0.236 2154 Planarity : 0.004 0.061 2290 Dihedral : 15.160 178.599 5616 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1552 helix: 1.25 (0.20), residues: 716 sheet: -0.02 (0.36), residues: 184 loop : -0.39 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1185 TYR 0.011 0.001 TYR B 698 PHE 0.011 0.001 PHE B1107 TRP 0.012 0.001 TRP B 560 HIS 0.003 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.27 (14368) covalent geometry : angle 0.62020 / 0.41 (19684) hydrogen bonds : bond 0.15790 / 10.74 ( 636) hydrogen bonds : angle 5.76756 / 4.07 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9042 (tp30) cc_final: 0.8744 (tp30) REVERT: B 1050 GLU cc_start: 0.9056 (tp30) cc_final: 0.8745 (tp30) outliers start: 0 outliers final: 1 residues processed: 57 average time/residue: 0.8281 time to fit residues: 50.5799 Evaluate side-chains 42 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1058 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN B 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.067033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.052073 restraints weight = 46108.775| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.12 r_work: 0.2895 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14368 Z= 0.150 Angle : 0.570 7.546 19684 Z= 0.315 Chirality : 0.042 0.351 2154 Planarity : 0.004 0.047 2290 Dihedral : 17.529 176.669 2504 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.37 % Allowed : 5.12 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1552 helix: 1.20 (0.20), residues: 734 sheet: -0.36 (0.33), residues: 208 loop : -0.07 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 718 TYR 0.013 0.001 TYR A 698 PHE 0.011 0.001 PHE A 990 TRP 0.008 0.001 TRP B 560 HIS 0.003 0.001 HIS B 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (14368) covalent geometry : angle 0.57012 / 0.32 (19684) hydrogen bonds : bond 0.04610 / 3.03 ( 636) hydrogen bonds : angle 4.81067 / 3.37 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9092 (tp30) cc_final: 0.8769 (tp30) REVERT: A 1060 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8214 (ttm) REVERT: B 929 ARG cc_start: 0.8763 (tpm170) cc_final: 0.8542 (tpm170) REVERT: B 1050 GLU cc_start: 0.9121 (tp30) cc_final: 0.8814 (tp30) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.7646 time to fit residues: 37.4752 Evaluate side-chains 43 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain B residue 493 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.0030 chunk 128 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1114 ASN B1114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049784 restraints weight = 46551.775| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.09 r_work: 0.2857 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14368 Z= 0.218 Angle : 0.595 8.313 19684 Z= 0.323 Chirality : 0.044 0.421 2154 Planarity : 0.004 0.049 2290 Dihedral : 17.377 178.050 2502 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.73 % Allowed : 6.95 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1552 helix: 1.23 (0.19), residues: 732 sheet: -0.54 (0.34), residues: 208 loop : 0.03 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 799 TYR 0.017 0.001 TYR A 698 PHE 0.015 0.001 PHE B1094 TRP 0.005 0.001 TRP B1170 HIS 0.004 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (14368) covalent geometry : angle 0.59522 / 0.32 (19684) hydrogen bonds : bond 0.04457 / 2.96 ( 636) hydrogen bonds : angle 4.68552 / 3.27 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9148 (tp30) cc_final: 0.8858 (tp30) REVERT: B 475 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.9070 (ttm) REVERT: B 514 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8583 (pp) REVERT: B 1050 GLU cc_start: 0.9134 (tp30) cc_final: 0.8834 (tp30) outliers start: 10 outliers final: 1 residues processed: 48 average time/residue: 0.6565 time to fit residues: 34.6397 Evaluate side-chains 44 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 27 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 143 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 690 HIS B 690 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.051163 restraints weight = 45733.362| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.07 r_work: 0.2899 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14368 Z= 0.127 Angle : 0.541 8.748 19684 Z= 0.297 Chirality : 0.042 0.362 2154 Planarity : 0.003 0.045 2290 Dihedral : 17.243 179.972 2502 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.95 % Allowed : 8.49 % Favored : 90.56 % 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 are not related in a simple way. whole: 0.73 (0.22), residues: 1552 helix: 1.25 (0.19), residues: 736 sheet: -0.18 (0.37), residues: 180 loop : -0.09 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 929 TYR 0.015 0.001 TYR A 698 PHE 0.009 0.001 PHE B 590 TRP 0.006 0.001 TRP B 560 HIS 0.003 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (14368) covalent geometry : angle 0.54085 / 0.30 (19684) hydrogen bonds : bond 0.03794 / 2.51 ( 636) hydrogen bonds : angle 4.53555 / 3.17 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9123 (tp30) cc_final: 0.8842 (tp30) REVERT: B 929 ARG cc_start: 0.8524 (tpm170) cc_final: 0.8244 (tpm170) REVERT: B 1050 GLU cc_start: 0.9121 (tp30) cc_final: 0.8833 (tp30) REVERT: B 1060 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8375 (ttm) REVERT: B 1173 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8710 (mt-10) outliers start: 13 outliers final: 5 residues processed: 54 average time/residue: 0.6153 time to fit residues: 36.6881 Evaluate side-chains 49 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 1060 MET Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 157 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.065146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050437 restraints weight = 46239.642| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.03 r_work: 0.2845 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14368 Z= 0.179 Angle : 0.564 9.336 19684 Z= 0.305 Chirality : 0.043 0.401 2154 Planarity : 0.004 0.047 2290 Dihedral : 17.185 177.811 2502 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.17 % Allowed : 9.37 % Favored : 89.46 % 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 are not related in a simple way. whole: 0.72 (0.22), residues: 1552 helix: 1.25 (0.19), residues: 734 sheet: -0.55 (0.34), residues: 208 loop : 0.05 (0.28), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 863 TYR 0.016 0.001 TYR A 698 PHE 0.012 0.001 PHE B1094 TRP 0.005 0.001 TRP B1170 HIS 0.003 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (14368) covalent geometry : angle 0.56379 / 0.31 (19684) hydrogen bonds : bond 0.03968 / 2.64 ( 636) hydrogen bonds : angle 4.50737 / 3.15 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9149 (tp30) cc_final: 0.8865 (tp30) REVERT: B 514 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8614 (pp) REVERT: B 929 ARG cc_start: 0.8626 (tpm170) cc_final: 0.8323 (tpm170) REVERT: B 1050 GLU cc_start: 0.9167 (tp30) cc_final: 0.8863 (tp30) REVERT: B 1173 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8719 (mt-10) outliers start: 16 outliers final: 7 residues processed: 55 average time/residue: 0.6258 time to fit residues: 38.2200 Evaluate side-chains 51 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 89 optimal weight: 4.9990 chunk 52 optimal weight: 0.0000 chunk 146 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.050259 restraints weight = 45709.347| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.09 r_work: 0.2881 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14368 Z= 0.146 Angle : 0.543 9.432 19684 Z= 0.294 Chirality : 0.042 0.372 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.133 179.322 2502 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.95 % Allowed : 10.47 % Favored : 88.58 % 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 are not related in a simple way. whole: 0.73 (0.22), residues: 1552 helix: 1.27 (0.19), residues: 734 sheet: -0.47 (0.34), residues: 208 loop : 0.02 (0.28), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 863 TYR 0.015 0.001 TYR A 698 PHE 0.009 0.001 PHE B1094 TRP 0.004 0.001 TRP B1170 HIS 0.003 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (14368) covalent geometry : angle 0.54282 / 0.29 (19684) hydrogen bonds : bond 0.03717 / 2.46 ( 636) hydrogen bonds : angle 4.43876 / 3.10 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9144 (tp30) cc_final: 0.8862 (tp30) REVERT: B 929 ARG cc_start: 0.8660 (tpm170) cc_final: 0.8371 (tpm170) REVERT: B 934 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9300 (pp) REVERT: B 1050 GLU cc_start: 0.9170 (tp30) cc_final: 0.8862 (tp30) REVERT: B 1173 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8724 (mt-10) outliers start: 13 outliers final: 9 residues processed: 54 average time/residue: 0.6321 time to fit residues: 37.4365 Evaluate side-chains 52 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 117 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.050201 restraints weight = 45756.054| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.09 r_work: 0.2845 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14368 Z= 0.159 Angle : 0.550 10.051 19684 Z= 0.295 Chirality : 0.042 0.383 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.102 177.950 2502 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.24 % Allowed : 10.61 % Favored : 88.14 % 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 are not related in a simple way. whole: 0.73 (0.22), residues: 1552 helix: 1.28 (0.19), residues: 734 sheet: -0.59 (0.34), residues: 212 loop : 0.06 (0.28), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 863 TYR 0.015 0.001 TYR A 698 PHE 0.009 0.001 PHE A1094 TRP 0.004 0.001 TRP B1170 HIS 0.003 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (14368) covalent geometry : angle 0.54955 / 0.30 (19684) hydrogen bonds : bond 0.03724 / 2.47 ( 636) hydrogen bonds : angle 4.40194 / 3.07 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 934 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9275 (pp) REVERT: A 1050 GLU cc_start: 0.9132 (tp30) cc_final: 0.8845 (tp30) REVERT: A 1173 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8694 (mt-10) REVERT: B 929 ARG cc_start: 0.8704 (tpm170) cc_final: 0.8444 (tpm170) REVERT: B 934 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9297 (pp) REVERT: B 1050 GLU cc_start: 0.9164 (tp30) cc_final: 0.8900 (tp30) REVERT: B 1173 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8707 (mt-10) outliers start: 17 outliers final: 9 residues processed: 57 average time/residue: 0.6241 time to fit residues: 39.3151 Evaluate side-chains 55 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 95 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.050905 restraints weight = 45469.705| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.08 r_work: 0.2893 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14368 Z= 0.131 Angle : 0.539 10.464 19684 Z= 0.289 Chirality : 0.041 0.363 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.069 178.743 2502 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.24 % Allowed : 10.98 % Favored : 87.77 % 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 are not related in a simple way. whole: 0.78 (0.22), residues: 1552 helix: 1.30 (0.19), residues: 734 sheet: -0.52 (0.34), residues: 212 loop : 0.09 (0.28), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 863 TYR 0.015 0.001 TYR A 698 PHE 0.008 0.001 PHE B1094 TRP 0.004 0.001 TRP B1170 HIS 0.002 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (14368) covalent geometry : angle 0.53856 / 0.29 (19684) hydrogen bonds : bond 0.03570 / 2.37 ( 636) hydrogen bonds : angle 4.33099 / 3.03 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 934 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9277 (pp) REVERT: A 1050 GLU cc_start: 0.9132 (tp30) cc_final: 0.8826 (tp30) REVERT: A 1173 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8682 (mt-10) REVERT: B 514 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8700 (pp) REVERT: B 929 ARG cc_start: 0.8749 (tpm170) cc_final: 0.8529 (tpm170) REVERT: B 934 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9303 (pp) REVERT: B 1050 GLU cc_start: 0.9153 (tp30) cc_final: 0.8845 (tp30) REVERT: B 1173 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8693 (mt-10) outliers start: 17 outliers final: 9 residues processed: 61 average time/residue: 0.6455 time to fit residues: 43.4195 Evaluate side-chains 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050839 restraints weight = 45977.232| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.10 r_work: 0.2892 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14368 Z= 0.135 Angle : 0.551 11.318 19684 Z= 0.293 Chirality : 0.041 0.367 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.054 177.917 2502 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.24 % Allowed : 11.20 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1552 helix: 1.32 (0.19), residues: 734 sheet: -0.50 (0.34), residues: 212 loop : 0.08 (0.28), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 718 TYR 0.015 0.001 TYR A 698 PHE 0.008 0.001 PHE A 990 TRP 0.004 0.001 TRP B1170 HIS 0.002 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14368) covalent geometry : angle 0.55082 / 0.29 (19684) hydrogen bonds : bond 0.03548 / 2.35 ( 636) hydrogen bonds : angle 4.30023 / 3.00 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 934 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9284 (pp) REVERT: A 1050 GLU cc_start: 0.9130 (tp30) cc_final: 0.8826 (tp30) REVERT: A 1173 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8695 (mt-10) REVERT: B 514 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8710 (pp) REVERT: B 934 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9303 (pp) REVERT: B 1050 GLU cc_start: 0.9140 (tp30) cc_final: 0.8824 (tp30) REVERT: B 1173 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8697 (mt-10) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 0.6021 time to fit residues: 38.6497 Evaluate side-chains 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 122 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 102 optimal weight: 0.1980 chunk 143 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.051214 restraints weight = 45663.051| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.11 r_work: 0.2898 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14368 Z= 0.121 Angle : 0.554 12.742 19684 Z= 0.294 Chirality : 0.041 0.354 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.040 178.334 2502 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.88 % Allowed : 11.49 % Favored : 87.63 % 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 are not related in a simple way. whole: 0.84 (0.22), residues: 1552 helix: 1.35 (0.19), residues: 734 sheet: -0.47 (0.35), residues: 212 loop : 0.11 (0.28), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 929 TYR 0.014 0.001 TYR A 698 PHE 0.007 0.001 PHE A 990 TRP 0.004 0.001 TRP A1189 HIS 0.002 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (14368) covalent geometry : angle 0.55412 / 0.29 (19684) hydrogen bonds : bond 0.03453 / 2.29 ( 636) hydrogen bonds : angle 4.26412 / 2.98 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 934 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9280 (pp) REVERT: A 1050 GLU cc_start: 0.9127 (tp30) cc_final: 0.8817 (tp30) REVERT: A 1173 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8692 (mt-10) REVERT: B 514 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8690 (pp) REVERT: B 934 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9295 (pp) REVERT: B 1050 GLU cc_start: 0.9139 (tp30) cc_final: 0.8864 (tp30) REVERT: B 1173 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8643 (mt-10) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 0.6287 time to fit residues: 40.2391 Evaluate side-chains 56 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 152 optimal weight: 0.0030 chunk 117 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.0270 chunk 119 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051888 restraints weight = 45324.065| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.06 r_work: 0.2901 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14368 Z= 0.111 Angle : 0.544 11.590 19684 Z= 0.290 Chirality : 0.041 0.345 2154 Planarity : 0.003 0.047 2290 Dihedral : 16.980 178.241 2502 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.66 % Allowed : 11.93 % Favored : 87.41 % 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 are not related in a simple way. whole: 0.87 (0.22), residues: 1552 helix: 1.36 (0.19), residues: 736 sheet: -0.39 (0.35), residues: 212 loop : 0.12 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 799 TYR 0.013 0.001 TYR A 698 PHE 0.006 0.001 PHE A 990 TRP 0.005 0.001 TRP A1189 HIS 0.007 0.001 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (14368) covalent geometry : angle 0.54397 / 0.29 (19684) hydrogen bonds : bond 0.03325 / 2.21 ( 636) hydrogen bonds : angle 4.19683 / 2.93 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.15 seconds wall clock time: 52 minutes 25.37 seconds (3145.37 seconds total)