Starting phenix.real_space_refine on Sat Sep 12 05:46:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9v_36116/09_2026/8j9v_36116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9v_36116/09_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_36116/09_2026/8j9v_36116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9v_36116/09_2026/8j9v_36116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j9v_36116/09_2026/8j9v_36116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9v_36116/09_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-2.2.1-6174/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: 3.21, per 1000 atoms: 0.23 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: 1.30 Conformation dependent library (CDL) restraints added in 539.4 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: 1.77 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: 2.55 Time building geometry restraints manager: 1.72 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: 467 3.50 - 5.25: 48 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: 0.03 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: 8.960 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.320 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- 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 : 0.622 8.758 19684 Z= 0.412 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 0.62162 / 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 : 0.526 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: 0.9123 time to fit residues: 55.8804 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 : 0.513 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.066963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052083 restraints weight = 46106.998| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.10 r_work: 0.2896 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14368 Z= 0.148 Angle : 0.573 7.697 19684 Z= 0.315 Chirality : 0.043 0.371 2154 Planarity : 0.004 0.047 2290 Dihedral : 17.506 177.990 2504 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.29 % Allowed : 5.12 % Favored : 94.58 % 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: 0.67 (0.22), residues: 1552 helix: 1.20 (0.19), residues: 736 sheet: -0.36 (0.34), residues: 208 loop : -0.04 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 799 TYR 0.013 0.001 TYR A 698 PHE 0.010 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 0.57293 / 0.31 (19684) hydrogen bonds : bond 0.04591 / 3.02 ( 636) hydrogen bonds : angle 4.79005 / 3.35 ( 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 48 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.417 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: 0.8701 (OUTLIER) cc_final: 0.8204 (ttm) REVERT: B 929 ARG cc_start: 0.8755 (tpm170) cc_final: 0.8540 (tpm170) REVERT: B 1050 GLU cc_start: 0.9120 (tp30) cc_final: 0.8813 (tp30) outliers start: 4 outliers final: 1 residues processed: 45 average time/residue: 0.7646 time to fit residues: 37.4931 Evaluate side-chains 42 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 1060 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: 0.7980 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.065573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.050404 restraints weight = 46343.373| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.15 r_work: 0.2875 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14368 Z= 0.180 Angle : 0.565 7.669 19684 Z= 0.308 Chirality : 0.043 0.422 2154 Planarity : 0.004 0.047 2290 Dihedral : 17.315 178.102 2502 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.59 % Allowed : 6.44 % Favored : 92.97 % 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: 0.70 (0.22), residues: 1552 helix: 1.22 (0.19), residues: 736 sheet: -0.47 (0.34), residues: 208 loop : 0.02 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 799 TYR 0.015 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 0.00393 / 0.18 (14368) covalent geometry : angle 0.56457 / 0.31 (19684) hydrogen bonds : bond 0.04321 / 2.88 ( 636) hydrogen bonds : angle 4.64097 / 3.24 ( 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 53 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9121 (tp30) cc_final: 0.8799 (tp30) REVERT: B 929 ARG cc_start: 0.8831 (tpm170) cc_final: 0.8624 (tpm170) REVERT: B 1050 GLU cc_start: 0.9140 (tp30) cc_final: 0.8832 (tp30) outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 0.7386 time to fit residues: 38.0632 Evaluate side-chains 44 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 493 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 27 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.066029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051054 restraints weight = 45894.938| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.08 r_work: 0.2869 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14368 Z= 0.144 Angle : 0.537 8.274 19684 Z= 0.294 Chirality : 0.042 0.394 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.217 179.355 2502 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.10 % Allowed : 7.91 % Favored : 91.00 % 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: 0.74 (0.22), residues: 1552 helix: 1.23 (0.19), residues: 738 sheet: -0.09 (0.37), residues: 180 loop : -0.08 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 929 TYR 0.015 0.001 TYR A 698 PHE 0.010 0.001 PHE B1094 TRP 0.004 0.001 TRP B1170 HIS 0.003 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14368) covalent geometry : angle 0.53750 / 0.29 (19684) hydrogen bonds : bond 0.03800 / 2.52 ( 636) hydrogen bonds : angle 4.51420 / 3.15 ( 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 61 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9119 (tp30) cc_final: 0.8830 (tp30) REVERT: B 1050 GLU cc_start: 0.9131 (tp30) cc_final: 0.8819 (tp30) REVERT: B 1060 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8335 (ttm) REVERT: B 1173 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8717 (mt-10) outliers start: 15 outliers final: 4 residues processed: 55 average time/residue: 0.6423 time to fit residues: 39.1039 Evaluate side-chains 48 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 157 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.065169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050325 restraints weight = 46198.366| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.05 r_work: 0.2843 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14368 Z= 0.183 Angle : 0.570 9.621 19684 Z= 0.307 Chirality : 0.043 0.423 2154 Planarity : 0.004 0.047 2290 Dihedral : 17.161 176.847 2502 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.02 % Allowed : 9.22 % Favored : 89.75 % 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: 1.24 (0.19), residues: 734 sheet: -0.52 (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 0.011 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 0.00400 / 0.18 (14368) covalent geometry : angle 0.56985 / 0.31 (19684) hydrogen bonds : bond 0.03956 / 2.63 ( 636) hydrogen bonds : angle 4.50334 / 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 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9144 (tp30) cc_final: 0.8859 (tp30) REVERT: B 514 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 1050 GLU cc_start: 0.9163 (tp30) cc_final: 0.8856 (tp30) REVERT: B 1060 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8427 (ttm) REVERT: B 1173 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8721 (mt-10) outliers start: 14 outliers final: 8 residues processed: 53 average time/residue: 0.6644 time to fit residues: 38.7590 Evaluate side-chains 53 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 493 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1060 MET Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 146 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.065648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050634 restraints weight = 45640.711| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.08 r_work: 0.2883 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14368 Z= 0.148 Angle : 0.551 9.663 19684 Z= 0.297 Chirality : 0.042 0.395 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.115 178.700 2502 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.95 % Allowed : 10.40 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1552 helix: 1.27 (0.19), residues: 734 sheet: -0.60 (0.34), residues: 212 loop : 0.06 (0.28), residues: 606 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 0.00316 / 0.15 (14368) covalent geometry : angle 0.55075 / 0.30 (19684) hydrogen bonds : bond 0.03714 / 2.46 ( 636) hydrogen bonds : angle 4.44449 / 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 : 0.372 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9146 (tp30) cc_final: 0.8862 (tp30) REVERT: B 514 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 934 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9301 (pp) REVERT: B 1050 GLU cc_start: 0.9172 (tp30) cc_final: 0.8868 (tp30) REVERT: B 1060 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8374 (ttm) REVERT: B 1173 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8721 (mt-10) outliers start: 13 outliers final: 6 residues processed: 53 average time/residue: 0.6766 time to fit residues: 39.5433 Evaluate side-chains 52 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 1060 MET 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: 4.9990 chunk 45 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 930 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050731 restraints weight = 45766.026| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.08 r_work: 0.2885 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14368 Z= 0.145 Angle : 0.552 10.201 19684 Z= 0.295 Chirality : 0.042 0.398 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.062 177.978 2502 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.17 % Allowed : 10.47 % Favored : 88.36 % 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: 0.74 (0.22), residues: 1552 helix: 1.28 (0.19), residues: 734 sheet: -0.57 (0.34), residues: 212 loop : 0.07 (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 B1094 TRP 0.004 0.001 TRP B1170 HIS 0.003 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14368) covalent geometry : angle 0.55234 / 0.30 (19684) hydrogen bonds : bond 0.03654 / 2.43 ( 636) hydrogen bonds : angle 4.38364 / 3.06 ( 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 60 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 934 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9278 (pp) REVERT: A 1050 GLU cc_start: 0.9137 (tp30) cc_final: 0.8854 (tp30) REVERT: A 1173 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8691 (mt-10) REVERT: B 514 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8595 (pp) REVERT: B 934 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9301 (pp) REVERT: B 1050 GLU cc_start: 0.9162 (tp30) cc_final: 0.8868 (tp30) REVERT: B 1060 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8374 (ttm) REVERT: B 1173 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8713 (mt-10) outliers start: 16 outliers final: 9 residues processed: 56 average time/residue: 0.6875 time to fit residues: 42.5036 Evaluate side-chains 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 1060 MET 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: 1.9990 chunk 109 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.066389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051413 restraints weight = 45449.400| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.08 r_work: 0.2908 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14368 Z= 0.117 Angle : 0.540 11.277 19684 Z= 0.288 Chirality : 0.041 0.379 2154 Planarity : 0.003 0.047 2290 Dihedral : 17.015 178.664 2502 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.02 % Allowed : 10.83 % 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: 0.79 (0.22), residues: 1552 helix: 1.32 (0.19), residues: 736 sheet: -0.47 (0.35), residues: 212 loop : 0.06 (0.28), residues: 604 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 B 814 TRP 0.004 0.001 TRP A1189 HIS 0.002 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (14368) covalent geometry : angle 0.53960 / 0.29 (19684) hydrogen bonds : bond 0.03449 / 2.29 ( 636) hydrogen bonds : angle 4.29886 / 3.00 ( 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 60 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9125 (tp30) cc_final: 0.8820 (tp30) REVERT: A 1173 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8677 (mt-10) REVERT: B 934 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9298 (pp) REVERT: B 1050 GLU cc_start: 0.9153 (tp30) cc_final: 0.8840 (tp30) REVERT: B 1060 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8352 (ttm) REVERT: B 1173 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8637 (mt-10) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.6720 time to fit residues: 42.2633 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 : 0.394 ------------------------------------------------------------------------------- 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 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 1060 MET 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: 0.5980 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.0570 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 153 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 930 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.066502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051677 restraints weight = 45895.537| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.08 r_work: 0.2917 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14368 Z= 0.116 Angle : 0.543 10.730 19684 Z= 0.289 Chirality : 0.041 0.379 2154 Planarity : 0.003 0.048 2290 Dihedral : 16.985 177.895 2502 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.24 % Allowed : 11.05 % Favored : 87.70 % 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: 736 sheet: -0.40 (0.35), residues: 212 loop : 0.07 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 863 TYR 0.014 0.001 TYR A 698 PHE 0.007 0.001 PHE A 990 TRP 0.005 0.001 TRP A1189 HIS 0.002 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (14368) covalent geometry : angle 0.54311 / 0.29 (19684) hydrogen bonds : bond 0.03402 / 2.26 ( 636) hydrogen bonds : angle 4.23733 / 2.96 ( 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 66 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 934 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9280 (pp) REVERT: A 1050 GLU cc_start: 0.9119 (tp30) cc_final: 0.8805 (tp30) REVERT: A 1173 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8701 (mt-10) REVERT: B 934 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9296 (pp) REVERT: B 1050 GLU cc_start: 0.9144 (tp30) cc_final: 0.8843 (tp30) REVERT: B 1060 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8351 (ttm) REVERT: B 1173 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8652 (mt-10) outliers start: 17 outliers final: 8 residues processed: 61 average time/residue: 0.6812 time to fit residues: 45.6856 Evaluate side-chains 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 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 1060 MET 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: 0.7980 chunk 102 optimal weight: 0.0870 chunk 143 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.066893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.051979 restraints weight = 45710.085| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.10 r_work: 0.2896 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14368 Z= 0.116 Angle : 0.545 11.568 19684 Z= 0.289 Chirality : 0.041 0.372 2154 Planarity : 0.003 0.054 2290 Dihedral : 16.959 177.766 2502 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.95 % Allowed : 11.86 % Favored : 87.19 % 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: 0.86 (0.22), residues: 1552 helix: 1.37 (0.19), residues: 736 sheet: -0.37 (0.35), residues: 212 loop : 0.08 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 799 TYR 0.014 0.001 TYR A 698 PHE 0.007 0.001 PHE A 990 TRP 0.005 0.001 TRP A1189 HIS 0.002 0.001 HIS B 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (14368) covalent geometry : angle 0.54516 / 0.29 (19684) hydrogen bonds : bond 0.03335 / 2.21 ( 636) hydrogen bonds : angle 4.19556 / 2.92 ( 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 63 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 934 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9282 (pp) REVERT: A 1050 GLU cc_start: 0.9116 (tp30) cc_final: 0.8799 (tp30) REVERT: A 1173 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8706 (mt-10) REVERT: B 514 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8667 (pp) REVERT: B 934 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9290 (pp) REVERT: B 1050 GLU cc_start: 0.9143 (tp30) cc_final: 0.8869 (tp30) REVERT: B 1060 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8365 (ttm) REVERT: B 1173 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8671 (mt-10) outliers start: 13 outliers final: 9 residues processed: 60 average time/residue: 0.7157 time to fit residues: 47.0601 Evaluate side-chains 61 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 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 1060 MET 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: 0.5980 chunk 59 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 117 optimal weight: 0.0010 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 chunk 119 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.066779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.052015 restraints weight = 45266.327| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.07 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: 0.8765 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14368 Z= 0.114 Angle : 0.542 11.576 19684 Z= 0.288 Chirality : 0.041 0.372 2154 Planarity : 0.003 0.048 2290 Dihedral : 16.921 177.691 2502 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.95 % Allowed : 12.15 % Favored : 86.90 % 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: 0.90 (0.22), residues: 1552 helix: 1.39 (0.19), residues: 736 sheet: -0.32 (0.35), residues: 212 loop : 0.09 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 799 TYR 0.014 0.001 TYR A 698 PHE 0.007 0.001 PHE A 990 TRP 0.005 0.001 TRP A1189 HIS 0.005 0.001 HIS A1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (14368) covalent geometry : angle 0.54181 / 0.29 (19684) hydrogen bonds : bond 0.03285 / 2.18 ( 636) hydrogen bonds : angle 4.16443 / 2.90 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3432.57 seconds wall clock time: 59 minutes 44.37 seconds (3584.37 seconds total)