Starting phenix.real_space_refine on Wed Jan 22 12:39:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r87_18997/01_2025/8r87_18997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r87_18997/01_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_18997/01_2025/8r87_18997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r87_18997/01_2025/8r87_18997.map" model { file = "/net/cci-nas-00/data/ceres_data/8r87_18997/01_2025/8r87_18997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r87_18997/01_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-5571/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: 14.05, per 1000 atoms: 0.76 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=9, 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 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: 5.02 Conformation dependent library (CDL) restraints added in 2.3 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: 2.93 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: 7.91 Time building geometry restraints manager: 5.25 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: 10666 17.53 - 35.06: 355 35.06 - 52.59: 80 52.59 - 70.11: 58 70.11 - 87.64: 10 Dihedral angle restraints: 11169 sinusoidal: 4317 harmonic: 6852 Sorted by residual: 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 A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 56.72 36.28 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 11166 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: 2.02 - 2.60: 159 2.60 - 3.17: 15878 3.17 - 3.75: 27028 3.75 - 4.32: 39513 4.32 - 4.90: 66219 Nonbonded interactions: 148797 Sorted by model distance: nonbonded pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " model vdw 2.029 3.760 ... (remaining 148792 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: 0.14 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: 4.020 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.260 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.380 ------------------------------------------------------------------------------- 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 18744 Z= 0.177 Angle : 0.518 6.979 25482 Z= 0.308 Chirality : 0.043 0.219 2967 Planarity : 0.003 0.025 3291 Dihedral : 11.244 87.644 6708 Min Nonbonded Distance : 2.024 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 *********************** 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 : 2.121 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: 1.2405 time to fit residues: 91.4945 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 : 2.093 ------------------------------------------------------------------------------- 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: 4.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 183 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 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 = 0.3490 r_free = 0.3490 target = 0.069665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.045486 restraints weight = 60662.176| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.15 r_work: 0.2683 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18744 Z= 0.408 Angle : 0.569 7.106 25482 Z= 0.302 Chirality : 0.045 0.133 2967 Planarity : 0.003 0.031 3291 Dihedral : 4.332 37.488 2491 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.63 % Allowed : 3.52 % Favored : 95.86 % 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: 1.24 (0.17), residues: 2301 helix: 3.19 (0.20), residues: 600 sheet: 0.83 (0.22), residues: 507 loop : -0.43 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 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 0.000 ARG C 328 *********************** 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 64 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7347 (m-90) cc_final: 0.7115 (m-90) REVERT: B 64 TRP cc_start: 0.8474 (t60) cc_final: 0.8000 (t60) REVERT: B 104 TRP cc_start: 0.7413 (m-90) cc_final: 0.6913 (m-90) REVERT: C 104 TRP cc_start: 0.7421 (m-90) cc_final: 0.6993 (m-90) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 1.2646 time to fit residues: 81.9972 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 : 1.999 ------------------------------------------------------------------------------- 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: 0.7980 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.071545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047698 restraints weight = 60122.523| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.14 r_work: 0.2754 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18744 Z= 0.141 Angle : 0.444 6.143 25482 Z= 0.236 Chirality : 0.041 0.140 2967 Planarity : 0.003 0.032 3291 Dihedral : 3.739 15.214 2487 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.29 % Allowed : 4.38 % Favored : 95.33 % 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: 1.48 (0.17), residues: 2301 helix: 3.52 (0.20), residues: 582 sheet: 0.89 (0.22), residues: 528 loop : -0.28 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 PHE 0.019 0.001 PHE B 201 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG C 328 *********************** 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 61 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7207 (m-90) cc_final: 0.6962 (m-90) REVERT: B 64 TRP cc_start: 0.8422 (t60) cc_final: 0.7971 (t60) REVERT: B 104 TRP cc_start: 0.7225 (m-90) cc_final: 0.6713 (m-90) REVERT: C 104 TRP cc_start: 0.7238 (m-90) cc_final: 0.6797 (m-90) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 1.3698 time to fit residues: 91.7872 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 : 2.082 ------------------------------------------------------------------------------- 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: 8.9990 chunk 83 optimal weight: 0.0870 chunk 171 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 176 optimal weight: 0.1980 chunk 216 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.4564 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.069604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045700 restraints weight = 61009.003| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.11 r_work: 0.2700 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18744 Z= 0.326 Angle : 0.502 6.795 25482 Z= 0.262 Chirality : 0.043 0.136 2967 Planarity : 0.003 0.033 3291 Dihedral : 3.909 16.478 2487 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.67 % Allowed : 4.72 % Favored : 94.61 % 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: 1.40 (0.17), residues: 2301 helix: 3.39 (0.21), residues: 582 sheet: 0.90 (0.22), residues: 528 loop : -0.32 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.002 0.001 HIS C1064 PHE 0.013 0.001 PHE B 201 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG C 905 *********************** 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 73 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7351 (m-90) cc_final: 0.7131 (m-90) REVERT: B 64 TRP cc_start: 0.8419 (t60) cc_final: 0.7921 (t60) REVERT: B 104 TRP cc_start: 0.7401 (m-90) cc_final: 0.7139 (m-90) REVERT: C 104 TRP cc_start: 0.7421 (m-90) cc_final: 0.7170 (m-90) outliers start: 14 outliers final: 7 residues processed: 66 average time/residue: 1.0525 time to fit residues: 82.9314 Evaluate side-chains 62 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE 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 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: 2.9990 chunk 171 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.069214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045327 restraints weight = 61542.934| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.11 r_work: 0.2691 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18744 Z= 0.353 Angle : 0.521 7.764 25482 Z= 0.269 Chirality : 0.043 0.136 2967 Planarity : 0.003 0.034 3291 Dihedral : 3.978 16.625 2487 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.92 % Allowed : 5.15 % 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: 1.35 (0.18), residues: 2301 helix: 3.33 (0.21), residues: 582 sheet: 0.86 (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 A 886 HIS 0.003 0.001 HIS C1064 PHE 0.014 0.001 PHE C 898 TYR 0.019 0.001 TYR A1067 ARG 0.002 0.000 ARG A 328 *********************** 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 83 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7247 (m-90) cc_final: 0.7012 (m-90) REVERT: A 197 ILE cc_start: 0.9019 (mt) cc_final: 0.8755 (pp) REVERT: A 200 TYR cc_start: 0.9098 (m-80) cc_final: 0.8676 (OUTLIER) REVERT: B 64 TRP cc_start: 0.8431 (t60) cc_final: 0.7899 (t60) REVERT: B 104 TRP cc_start: 0.7339 (m-90) cc_final: 0.7131 (m-90) REVERT: C 104 TRP cc_start: 0.7455 (m-90) cc_final: 0.7229 (m-90) REVERT: C 197 ILE cc_start: 0.9039 (mt) cc_final: 0.8837 (pp) outliers start: 19 outliers final: 9 residues processed: 77 average time/residue: 0.9716 time to fit residues: 89.8208 Evaluate side-chains 67 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 158 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.069985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046240 restraints weight = 61288.132| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.11 r_work: 0.2721 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18744 Z= 0.209 Angle : 0.463 6.995 25482 Z= 0.241 Chirality : 0.041 0.138 2967 Planarity : 0.003 0.072 3291 Dihedral : 3.764 15.164 2487 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.63 % Allowed : 5.59 % Favored : 93.79 % 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: 1.48 (0.18), residues: 2301 helix: 3.47 (0.20), residues: 582 sheet: 0.92 (0.22), residues: 525 loop : -0.25 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 886 HIS 0.002 0.000 HIS A1088 PHE 0.014 0.001 PHE C 106 TYR 0.017 0.001 TYR B1067 ARG 0.001 0.000 ARG C 328 *********************** 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 77 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7224 (m-90) cc_final: 0.7017 (m-90) REVERT: A 197 ILE cc_start: 0.8980 (mt) cc_final: 0.8760 (pp) REVERT: A 200 TYR cc_start: 0.9047 (m-80) cc_final: 0.8686 (m-80) REVERT: B 64 TRP cc_start: 0.8391 (t60) cc_final: 0.7861 (t60) REVERT: B 104 TRP cc_start: 0.7303 (m-90) cc_final: 0.7089 (m-90) REVERT: C 104 TRP cc_start: 0.7361 (m-90) cc_final: 0.7139 (m-90) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 1.0345 time to fit residues: 89.2629 Evaluate side-chains 68 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 214 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.068323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.044501 restraints weight = 61350.210| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.08 r_work: 0.2666 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 18744 Z= 0.477 Angle : 0.581 7.655 25482 Z= 0.299 Chirality : 0.045 0.179 2967 Planarity : 0.004 0.059 3291 Dihedral : 4.164 17.470 2487 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.82 % Allowed : 5.54 % Favored : 93.64 % 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: 1.24 (0.17), residues: 2301 helix: 3.22 (0.20), residues: 600 sheet: 0.78 (0.22), residues: 525 loop : -0.44 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 886 HIS 0.003 0.001 HIS C1064 PHE 0.015 0.001 PHE B 898 TYR 0.019 0.002 TYR A1067 ARG 0.002 0.000 ARG C1107 *********************** 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: 17 poor density : 57 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.9003 (mt) cc_final: 0.8792 (pp) REVERT: A 200 TYR cc_start: 0.9123 (m-80) cc_final: 0.8794 (m-80) REVERT: B 64 TRP cc_start: 0.8427 (t60) cc_final: 0.7933 (t60) REVERT: C 104 TRP cc_start: 0.7411 (m-90) cc_final: 0.7211 (m-90) outliers start: 17 outliers final: 15 residues processed: 69 average time/residue: 1.0115 time to fit residues: 83.8492 Evaluate side-chains 69 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1145 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 129 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 151 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 231 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.070901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047474 restraints weight = 60728.391| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.10 r_work: 0.2759 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18744 Z= 0.130 Angle : 0.446 6.653 25482 Z= 0.233 Chirality : 0.041 0.138 2967 Planarity : 0.003 0.053 3291 Dihedral : 3.628 15.116 2487 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.77 % Allowed : 5.54 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2301 helix: 3.54 (0.20), residues: 600 sheet: 0.93 (0.22), residues: 543 loop : -0.29 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 104 HIS 0.003 0.000 HIS A1048 PHE 0.017 0.001 PHE B 565 TYR 0.015 0.001 TYR B1067 ARG 0.002 0.000 ARG B 328 *********************** 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 78 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7195 (m-90) cc_final: 0.6924 (m-90) REVERT: A 200 TYR cc_start: 0.9064 (m-80) cc_final: 0.8751 (m-80) REVERT: B 64 TRP cc_start: 0.8379 (t60) cc_final: 0.7788 (t60) REVERT: C 104 TRP cc_start: 0.7244 (m-90) cc_final: 0.7033 (m-90) outliers start: 16 outliers final: 13 residues processed: 73 average time/residue: 0.9904 time to fit residues: 87.0821 Evaluate side-chains 69 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE 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 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 C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.069295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.045529 restraints weight = 61378.325| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.10 r_work: 0.2716 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18744 Z= 0.309 Angle : 0.504 7.748 25482 Z= 0.262 Chirality : 0.042 0.136 2967 Planarity : 0.003 0.051 3291 Dihedral : 3.803 15.772 2487 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.67 % Allowed : 5.88 % Favored : 93.45 % 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: 1.46 (0.18), residues: 2301 helix: 3.45 (0.20), residues: 600 sheet: 0.89 (0.22), residues: 525 loop : -0.33 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.002 0.001 HIS C1064 PHE 0.012 0.001 PHE C 898 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG C1107 *********************** 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 69 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9061 (m-80) cc_final: 0.8851 (m-80) REVERT: B 64 TRP cc_start: 0.8404 (t60) cc_final: 0.7818 (t60) REVERT: C 104 TRP cc_start: 0.7362 (m-90) cc_final: 0.7127 (m-90) outliers start: 14 outliers final: 14 residues processed: 66 average time/residue: 0.9293 time to fit residues: 74.3611 Evaluate side-chains 70 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE 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 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 1145 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR 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: 0.8980 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 111 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.070887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047335 restraints weight = 61071.015| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.11 r_work: 0.2753 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18744 Z= 0.139 Angle : 0.449 7.126 25482 Z= 0.234 Chirality : 0.041 0.136 2967 Planarity : 0.003 0.050 3291 Dihedral : 3.543 14.961 2487 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.77 % Allowed : 5.78 % Favored : 93.45 % 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: 1.63 (0.18), residues: 2301 helix: 3.61 (0.20), residues: 600 sheet: 0.98 (0.22), residues: 543 loop : -0.24 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.002 0.000 HIS A1088 PHE 0.015 0.001 PHE C 106 TYR 0.016 0.001 TYR B1067 ARG 0.001 0.000 ARG C 328 ********************** 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: 16 poor density : 59 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7171 (m-90) cc_final: 0.6905 (m-90) REVERT: B 64 TRP cc_start: 0.8383 (t60) cc_final: 0.7827 (t60) REVERT: C 104 TRP cc_start: 0.7247 (m-90) cc_final: 0.7021 (m-90) outliers start: 16 outliers final: 14 residues processed: 70 average time/residue: 0.9396 time to fit residues: 79.6689 Evaluate side-chains 72 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 79 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.070338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046706 restraints weight = 61038.405| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.11 r_work: 0.2752 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18744 Z= 0.193 Angle : 0.459 7.065 25482 Z= 0.239 Chirality : 0.041 0.138 2967 Planarity : 0.003 0.049 3291 Dihedral : 3.561 14.702 2487 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.72 % Allowed : 5.92 % Favored : 93.35 % 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: 1.65 (0.18), residues: 2301 helix: 3.59 (0.20), residues: 600 sheet: 1.03 (0.22), residues: 543 loop : -0.22 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.002 0.000 HIS A1088 PHE 0.015 0.001 PHE B 106 TYR 0.016 0.001 TYR C1067 ARG 0.001 0.000 ARG C1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8325.03 seconds wall clock time: 153 minutes 12.34 seconds (9192.34 seconds total)