Starting phenix.real_space_refine on Mon Jun 16 11:02:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r87_18997/06_2025/8r87_18997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r87_18997/06_2025/8r87_18997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r87_18997/06_2025/8r87_18997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r87_18997/06_2025/8r87_18997.map" model { file = "/net/cci-nas-00/data/ceres_data/8r87_18997/06_2025/8r87_18997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r87_18997/06_2025/8r87_18997.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 11712 2.51 5 N 3042 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18372 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6124 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 41, 'TRANS': 747} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Restraints were copied for chains: C, B Time building chain proxies: 14.78, per 1000 atoms: 0.80 Number of scatterers: 18372 At special positions: 0 Unit cell: (128.52, 126.84, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3540 8.00 N 3042 7.00 C 11712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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: 4.29 Conformation dependent library (CDL) restraints added in 2.4 seconds 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 28.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.543A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.754A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 946 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.046A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.143A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.543A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.755A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.046A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.143A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.543A pdb=" N GLY C 744 " --> pdb=" O MET C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.755A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 946 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.046A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.143A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.391A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.517A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.916A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.834A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.596A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.517A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.500A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.962A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.779A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.966A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.502A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.776A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.179A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.390A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.916A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.834A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.597A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.517A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.500A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.967A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.779A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.966A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.502A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.178A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.391A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.915A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.834A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.596A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.500A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.780A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.966A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.501A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.179A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.32 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5958 1.34 - 1.46: 4346 1.46 - 1.58: 8338 1.58 - 1.70: 0 1.70 - 1.81: 102 Bond restraints: 18744 Sorted by residual: bond pdb=" N PRO B 899 " pdb=" CA PRO B 899 " ideal model delta sigma weight residual 1.472 1.458 0.014 1.32e-02 5.74e+03 1.14e+00 bond pdb=" N PRO A 899 " pdb=" CA PRO A 899 " ideal model delta sigma weight residual 1.472 1.458 0.014 1.32e-02 5.74e+03 1.09e+00 bond pdb=" N PRO B 892 " pdb=" CA PRO B 892 " ideal model delta sigma weight residual 1.467 1.454 0.013 1.21e-02 6.83e+03 1.09e+00 bond pdb=" N PRO A 892 " pdb=" CA PRO A 892 " ideal model delta sigma weight residual 1.467 1.454 0.013 1.21e-02 6.83e+03 1.08e+00 bond pdb=" N PRO C 899 " pdb=" CA PRO C 899 " ideal model delta sigma weight residual 1.472 1.458 0.014 1.32e-02 5.74e+03 1.05e+00 ... (remaining 18739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 24932 1.40 - 2.79: 409 2.79 - 4.19: 129 4.19 - 5.58: 6 5.58 - 6.98: 6 Bond angle restraints: 25482 Sorted by residual: angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.31 110.29 -6.98 8.90e-01 1.26e+00 6.15e+01 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.31 110.27 -6.96 8.90e-01 1.26e+00 6.11e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.31 110.26 -6.95 8.90e-01 1.26e+00 6.10e+01 angle pdb=" N PRO A 899 " pdb=" CA PRO A 899 " pdb=" CB PRO A 899 " ideal model delta sigma weight residual 103.33 110.06 -6.73 1.10e+00 8.26e-01 3.74e+01 angle pdb=" N PRO C 899 " pdb=" CA PRO C 899 " pdb=" CB PRO C 899 " ideal model delta sigma weight residual 103.33 110.05 -6.72 1.10e+00 8.26e-01 3.73e+01 ... (remaining 25477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 10688 17.53 - 35.06: 373 35.06 - 52.59: 90 52.59 - 70.11: 60 70.11 - 87.64: 12 Dihedral angle restraints: 11223 sinusoidal: 4371 harmonic: 6852 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 176.02 -83.02 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 176.02 -83.02 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 176.02 -83.02 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 11220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2355 0.044 - 0.088: 365 0.088 - 0.132: 229 0.132 - 0.175: 12 0.175 - 0.219: 6 Chirality restraints: 2967 Sorted by residual: chirality pdb=" CA PRO B 899 " pdb=" N PRO B 899 " pdb=" C PRO B 899 " pdb=" CB PRO B 899 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO C 899 " pdb=" N PRO C 899 " pdb=" C PRO C 899 " pdb=" CB PRO C 899 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO A 899 " pdb=" N PRO A 899 " pdb=" C PRO A 899 " pdb=" CB PRO A 899 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2964 not shown) Planarity restraints: 3291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B1052 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO B1053 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B1053 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B1053 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1052 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO A1053 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A1053 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A1053 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C1052 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO C1053 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO C1053 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C1053 " 0.014 5.00e-02 4.00e+02 ... (remaining 3288 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4554 2.80 - 3.32: 16985 3.32 - 3.85: 29873 3.85 - 4.37: 35622 4.37 - 4.90: 61709 Nonbonded interactions: 148743 Sorted by model distance: nonbonded pdb=" NZ LYS A 790 " pdb=" OE2 GLU C 702 " model vdw 2.273 3.120 nonbonded pdb=" OE2 GLU A 702 " pdb=" NZ LYS B 790 " model vdw 2.277 3.120 nonbonded pdb=" OE2 GLU B 702 " pdb=" NZ LYS C 790 " model vdw 2.279 3.120 nonbonded pdb=" OD2 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 2.317 3.040 nonbonded pdb=" OD2 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.317 3.040 ... (remaining 148738 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 49.180 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 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 : 0.003 0.033 18771 Z= 0.140 Angle : 0.519 6.979 25536 Z= 0.308 Chirality : 0.043 0.219 2967 Planarity : 0.003 0.025 3291 Dihedral : 11.244 87.644 6708 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.14 % Allowed : 3.32 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2301 helix: 3.27 (0.20), residues: 600 sheet: 0.58 (0.21), residues: 513 loop : -0.47 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 104 HIS 0.002 0.001 HIS C1088 PHE 0.006 0.001 PHE B 55 TYR 0.011 0.001 TYR C1067 ARG 0.002 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.09753 ( 925) hydrogen bonds : angle 6.31838 ( 2550) SS BOND : bond 0.00308 ( 27) SS BOND : angle 0.84987 ( 54) covalent geometry : bond 0.00272 (18744) covalent geometry : angle 0.51762 (25482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 1.994 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8368 (t60) cc_final: 0.7254 (t60) REVERT: A 104 TRP cc_start: 0.7557 (m-90) cc_final: 0.7299 (m-90) REVERT: B 64 TRP cc_start: 0.8315 (t60) cc_final: 0.7806 (t60) REVERT: B 104 TRP cc_start: 0.7501 (m-90) cc_final: 0.7061 (m-90) REVERT: C 64 TRP cc_start: 0.8345 (t60) cc_final: 0.7396 (t60) REVERT: C 104 TRP cc_start: 0.7513 (m-90) cc_final: 0.6996 (m-90) REVERT: C 201 PHE cc_start: 0.8112 (t80) cc_final: 0.7888 (t80) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 1.1030 time to fit residues: 81.6611 Evaluate side-chains 55 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain B residue 140 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 183 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN B 207 HIS B 755 GLN C 755 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.045816 restraints weight = 59955.406| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.16 r_work: 0.2691 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18771 Z= 0.272 Angle : 0.567 6.878 25536 Z= 0.299 Chirality : 0.045 0.133 2967 Planarity : 0.003 0.030 3291 Dihedral : 4.337 37.401 2491 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.63 % Allowed : 3.76 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.17), residues: 2301 helix: 3.30 (0.21), residues: 582 sheet: 0.84 (0.22), residues: 507 loop : -0.42 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 886 HIS 0.003 0.001 HIS C1064 PHE 0.019 0.001 PHE B 201 TYR 0.019 0.002 TYR C1067 ARG 0.005 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 925) hydrogen bonds : angle 5.36720 ( 2550) SS BOND : bond 0.00621 ( 27) SS BOND : angle 1.60621 ( 54) covalent geometry : bond 0.00630 (18744) covalent geometry : angle 0.56239 (25482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7342 (m-90) cc_final: 0.7108 (m-90) REVERT: B 64 TRP cc_start: 0.8474 (t60) cc_final: 0.7991 (t60) REVERT: B 104 TRP cc_start: 0.7408 (m-90) cc_final: 0.6907 (m-90) REVERT: C 104 TRP cc_start: 0.7400 (m-90) cc_final: 0.6979 (m-90) outliers start: 13 outliers final: 6 residues processed: 54 average time/residue: 1.1391 time to fit residues: 72.4646 Evaluate side-chains 53 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 205 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 217 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.071042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.046944 restraints weight = 59615.559| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.15 r_work: 0.2726 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18771 Z= 0.153 Angle : 0.473 6.051 25536 Z= 0.249 Chirality : 0.042 0.135 2967 Planarity : 0.003 0.032 3291 Dihedral : 3.879 15.483 2487 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.29 % Allowed : 4.58 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2301 helix: 3.46 (0.20), residues: 582 sheet: 1.00 (0.22), residues: 507 loop : -0.33 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.001 0.000 HIS B1088 PHE 0.018 0.001 PHE B 201 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG C 328 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 925) hydrogen bonds : angle 4.97415 ( 2550) SS BOND : bond 0.00493 ( 27) SS BOND : angle 1.22880 ( 54) covalent geometry : bond 0.00347 (18744) covalent geometry : angle 0.46984 (25482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7257 (m-90) cc_final: 0.7034 (m-90) REVERT: B 64 TRP cc_start: 0.8436 (t60) cc_final: 0.7932 (t60) REVERT: B 104 TRP cc_start: 0.7313 (m-90) cc_final: 0.6791 (m-90) REVERT: C 104 TRP cc_start: 0.7325 (m-90) cc_final: 0.7044 (m-90) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 1.1836 time to fit residues: 73.7759 Evaluate side-chains 55 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 189 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.068669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045212 restraints weight = 60041.905| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.06 r_work: 0.2676 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 18771 Z= 0.332 Angle : 0.593 8.270 25536 Z= 0.308 Chirality : 0.045 0.131 2967 Planarity : 0.003 0.034 3291 Dihedral : 4.287 18.090 2487 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.92 % Allowed : 5.11 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2301 helix: 3.21 (0.21), residues: 582 sheet: 0.84 (0.22), residues: 525 loop : -0.48 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 886 HIS 0.003 0.001 HIS C1064 PHE 0.015 0.001 PHE C 92 TYR 0.020 0.002 TYR A1067 ARG 0.004 0.000 ARG A1039 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 925) hydrogen bonds : angle 5.39114 ( 2550) SS BOND : bond 0.00654 ( 27) SS BOND : angle 1.73945 ( 54) covalent geometry : bond 0.00765 (18744) covalent geometry : angle 0.58847 (25482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.8458 (t60) cc_final: 0.7945 (t60) REVERT: B 104 TRP cc_start: 0.7431 (m-90) cc_final: 0.7226 (m-90) outliers start: 19 outliers final: 9 residues processed: 69 average time/residue: 0.9850 time to fit residues: 80.6927 Evaluate side-chains 64 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 130 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 207 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.071512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047842 restraints weight = 60622.463| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.14 r_work: 0.2763 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18771 Z= 0.096 Angle : 0.446 7.797 25536 Z= 0.235 Chirality : 0.041 0.135 2967 Planarity : 0.003 0.034 3291 Dihedral : 3.728 14.979 2487 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.77 % Allowed : 5.30 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2301 helix: 3.58 (0.20), residues: 582 sheet: 0.98 (0.22), residues: 543 loop : -0.31 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.002 0.000 HIS A1048 PHE 0.014 0.001 PHE B 106 TYR 0.016 0.001 TYR A1067 ARG 0.002 0.000 ARG C 328 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 925) hydrogen bonds : angle 4.75314 ( 2550) SS BOND : bond 0.00403 ( 27) SS BOND : angle 0.95912 ( 54) covalent geometry : bond 0.00206 (18744) covalent geometry : angle 0.44416 (25482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7201 (m-90) cc_final: 0.6963 (m-90) REVERT: B 64 TRP cc_start: 0.8388 (t60) cc_final: 0.7887 (t60) REVERT: B 104 TRP cc_start: 0.7262 (m-90) cc_final: 0.7056 (m-90) REVERT: C 104 TRP cc_start: 0.7264 (m-90) cc_final: 0.6999 (m-90) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 1.0592 time to fit residues: 91.3697 Evaluate side-chains 66 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 240 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 158 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 224 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.069566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.045642 restraints weight = 61034.077| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.13 r_work: 0.2693 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 18771 Z= 0.245 Angle : 0.537 7.132 25536 Z= 0.278 Chirality : 0.043 0.132 2967 Planarity : 0.003 0.034 3291 Dihedral : 3.985 16.567 2487 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.01 % Allowed : 5.59 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2301 helix: 3.45 (0.20), residues: 582 sheet: 0.93 (0.22), residues: 525 loop : -0.34 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.003 0.001 HIS C1048 PHE 0.015 0.001 PHE A 106 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 925) hydrogen bonds : angle 5.05662 ( 2550) SS BOND : bond 0.00565 ( 27) SS BOND : angle 1.45505 ( 54) covalent geometry : bond 0.00566 (18744) covalent geometry : angle 0.53319 (25482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.8433 (t60) cc_final: 0.7891 (t60) outliers start: 21 outliers final: 12 residues processed: 74 average time/residue: 0.9409 time to fit residues: 83.5149 Evaluate side-chains 66 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 760 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 214 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 178 optimal weight: 0.0770 chunk 28 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 13 optimal weight: 30.0000 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.070717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047048 restraints weight = 60198.705| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.12 r_work: 0.2743 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18771 Z= 0.120 Angle : 0.466 6.839 25536 Z= 0.243 Chirality : 0.041 0.137 2967 Planarity : 0.003 0.034 3291 Dihedral : 3.725 15.406 2487 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.72 % Allowed : 5.78 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2301 helix: 3.55 (0.20), residues: 600 sheet: 0.95 (0.22), residues: 528 loop : -0.28 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 PHE 0.015 0.001 PHE B 106 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 925) hydrogen bonds : angle 4.76074 ( 2550) SS BOND : bond 0.00407 ( 27) SS BOND : angle 1.06432 ( 54) covalent geometry : bond 0.00271 (18744) covalent geometry : angle 0.46419 (25482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.8410 (t60) cc_final: 0.7824 (t60) outliers start: 15 outliers final: 13 residues processed: 68 average time/residue: 0.9458 time to fit residues: 77.1759 Evaluate side-chains 68 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 760 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 129 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 151 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.069507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.045645 restraints weight = 60503.714| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.12 r_work: 0.2699 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18771 Z= 0.229 Angle : 0.522 6.038 25536 Z= 0.272 Chirality : 0.043 0.133 2967 Planarity : 0.003 0.035 3291 Dihedral : 3.918 16.158 2487 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.06 % Allowed : 5.78 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.18), residues: 2301 helix: 3.44 (0.20), residues: 600 sheet: 0.94 (0.22), residues: 525 loop : -0.33 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 104 HIS 0.002 0.001 HIS C1048 PHE 0.015 0.001 PHE A 106 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 925) hydrogen bonds : angle 4.98120 ( 2550) SS BOND : bond 0.00522 ( 27) SS BOND : angle 1.41983 ( 54) covalent geometry : bond 0.00529 (18744) covalent geometry : angle 0.51871 (25482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.8409 (t60) cc_final: 0.7858 (t60) outliers start: 22 outliers final: 19 residues processed: 72 average time/residue: 0.8420 time to fit residues: 74.1782 Evaluate side-chains 74 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 760 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.070939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047300 restraints weight = 60552.983| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.13 r_work: 0.2746 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18771 Z= 0.107 Angle : 0.458 6.402 25536 Z= 0.240 Chirality : 0.041 0.137 2967 Planarity : 0.003 0.034 3291 Dihedral : 3.663 15.376 2487 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.82 % Allowed : 5.97 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2301 helix: 3.62 (0.20), residues: 600 sheet: 1.01 (0.22), residues: 543 loop : -0.28 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 PHE 0.015 0.001 PHE B 106 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 925) hydrogen bonds : angle 4.69540 ( 2550) SS BOND : bond 0.00385 ( 27) SS BOND : angle 1.03263 ( 54) covalent geometry : bond 0.00237 (18744) covalent geometry : angle 0.45605 (25482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.8401 (t60) cc_final: 0.7840 (t60) outliers start: 17 outliers final: 16 residues processed: 72 average time/residue: 0.9663 time to fit residues: 84.4327 Evaluate side-chains 72 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 760 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 166 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 156 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.069640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046034 restraints weight = 61417.199| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.11 r_work: 0.2734 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18771 Z= 0.219 Angle : 0.517 5.762 25536 Z= 0.269 Chirality : 0.043 0.134 2967 Planarity : 0.003 0.048 3291 Dihedral : 3.874 15.867 2487 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.87 % Allowed : 6.07 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2301 helix: 3.47 (0.20), residues: 600 sheet: 0.98 (0.22), residues: 525 loop : -0.29 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 104 HIS 0.002 0.001 HIS C1064 PHE 0.013 0.001 PHE C 106 TYR 0.017 0.001 TYR A1067 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 925) hydrogen bonds : angle 4.93104 ( 2550) SS BOND : bond 0.00512 ( 27) SS BOND : angle 1.42515 ( 54) covalent geometry : bond 0.00502 (18744) covalent geometry : angle 0.51340 (25482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.8425 (t60) cc_final: 0.7846 (t60) outliers start: 18 outliers final: 19 residues processed: 70 average time/residue: 0.8813 time to fit residues: 75.4154 Evaluate side-chains 74 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 760 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 79 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.070735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047092 restraints weight = 60387.909| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.14 r_work: 0.2742 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18771 Z= 0.117 Angle : 0.459 6.173 25536 Z= 0.241 Chirality : 0.041 0.137 2967 Planarity : 0.003 0.034 3291 Dihedral : 3.660 15.511 2487 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.96 % Allowed : 6.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2301 helix: 3.64 (0.20), residues: 600 sheet: 1.02 (0.22), residues: 543 loop : -0.27 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 104 HIS 0.001 0.000 HIS A1088 PHE 0.015 0.001 PHE B 106 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 925) hydrogen bonds : angle 4.69192 ( 2550) SS BOND : bond 0.00402 ( 27) SS BOND : angle 1.09071 ( 54) covalent geometry : bond 0.00263 (18744) covalent geometry : angle 0.45664 (25482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8565.49 seconds wall clock time: 147 minutes 41.20 seconds (8861.20 seconds total)