Starting phenix.real_space_refine on Tue Apr 29 02:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8roy_19407/04_2025/8roy_19407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8roy_19407/04_2025/8roy_19407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8roy_19407/04_2025/8roy_19407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8roy_19407/04_2025/8roy_19407.map" model { file = "/net/cci-nas-00/data/ceres_data/8roy_19407/04_2025/8roy_19407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8roy_19407/04_2025/8roy_19407.cif" } resolution = 3.1 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= 0.009 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 Cl 2 4.86 5 C 5345 2.51 5 N 1431 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8294 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2295 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 14, 'TRANS': 316} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 442 Unresolved non-hydrogen angles: 548 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 264 Chain: "B" Number of atoms: 5550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 5550 Classifications: {'peptide': 786} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 759} Chain breaks: 5 Unresolved non-hydrogen bonds: 643 Unresolved non-hydrogen angles: 782 Unresolved non-hydrogen dihedrals: 504 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 61, 'ASN:plan1': 4, 'ASP:plan': 24, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 419 Chain: "D" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 416 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'A1H18': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.04, per 1000 atoms: 0.61 Number of scatterers: 8294 At special positions: 0 Unit cell: (84.495, 106.425, 109.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 38 16.00 O 1478 8.00 N 1431 7.00 C 5345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.06 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 25 sheets defined 11.8% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.665A pdb=" N ILE A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 449 through 461 Processing helix chain 'A' and resid 548 through 562 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 985 through 990 Processing helix chain 'B' and resid 1044 through 1062 removed outlier: 3.828A pdb=" N LYS B1060 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B1061 " --> pdb=" O ARG B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1091 through 1097 removed outlier: 3.778A pdb=" N PHE B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1109 Processing helix chain 'B' and resid 1126 through 1138 Processing helix chain 'D' and resid 53 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.631A pdb=" N VAL A 61 " --> pdb=" O TRP A 597 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 83 removed outlier: 6.274A pdb=" N LEU A 91 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 109 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN A 125 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP A 111 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 123 " --> pdb=" O TRP A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 482 removed outlier: 6.587A pdb=" N LEU A 489 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 481 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN A 487 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER A 516 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLY A 534 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS A 518 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 6.773A pdb=" N GLY B1031 " --> pdb=" O ASN B1005 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B1007 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B1029 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N HIS B1009 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N SER B1027 " --> pdb=" O HIS B1009 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B1039 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR B 8 " --> pdb=" O LEU B1039 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR B1041 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 6 " --> pdb=" O THR B1041 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 21 removed outlier: 3.513A pdb=" N LYS B 53 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N TYR D 35 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU B 54 " --> pdb=" O TYR D 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 67 removed outlier: 6.367A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N GLN D 45 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG B 103 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE D 47 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N HIS B 105 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR D 49 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 121 through 124 removed outlier: 4.312A pdb=" N LEU B 135 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.760A pdb=" N ASP B 166 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 216 through 221 removed outlier: 3.533A pdb=" N MET B 218 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.815A pdb=" N GLY B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 272 " --> pdb=" O HIS B 261 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG B 263 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ARG B 270 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AB7, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AB8, first strand: chain 'B' and resid 362 through 365 removed outlier: 3.641A pdb=" N VAL B 376 " --> pdb=" O CYS B 363 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 388 " --> pdb=" O THR B 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.640A pdb=" N SER B 738 " --> pdb=" O PRO B 721 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 723 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 805 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS B 803 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP B 795 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 801 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER B 762 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN B 806 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 811 through 819 removed outlier: 5.240A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 849 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 848 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 863 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL B 850 " --> pdb=" O VAL B 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 875 through 876 Processing sheet with id=AC3, first strand: chain 'B' and resid 883 through 884 removed outlier: 6.627A pdb=" N VAL B 888 " --> pdb=" O ASN B 904 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN B 904 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 911 through 917 removed outlier: 3.539A pdb=" N TYR B 913 " --> pdb=" O GLY B 924 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 941 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 911 through 917 removed outlier: 3.539A pdb=" N TYR B 913 " --> pdb=" O GLY B 924 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 946 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 954 through 959 removed outlier: 6.866A pdb=" N ALA B 968 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL B 957 " --> pdb=" O LEU B 966 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 966 " --> pdb=" O VAL B 957 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE B 959 " --> pdb=" O ASN B 964 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN B 964 " --> pdb=" O ILE B 959 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1076 through 1077 308 hydrogen bonds defined for protein. 804 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: 3.79 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2680 1.34 - 1.46: 1748 1.46 - 1.57: 3989 1.57 - 1.69: 2 1.69 - 1.81: 52 Bond restraints: 8471 Sorted by residual: bond pdb=" C3 A1H18 A 701 " pdb=" S A1H18 A 701 " ideal model delta sigma weight residual 1.745 1.661 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" N VAL B 19 " pdb=" CA VAL B 19 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.13e+01 bond pdb=" CA PHE A 129 " pdb=" CB PHE A 129 " ideal model delta sigma weight residual 1.524 1.571 -0.046 1.46e-02 4.69e+03 1.00e+01 bond pdb=" N THR B 20 " pdb=" CA THR B 20 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.87e+00 bond pdb=" N LEU A 138 " pdb=" CA LEU A 138 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.66e+00 ... (remaining 8466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 11191 1.23 - 2.45: 316 2.45 - 3.68: 78 3.68 - 4.90: 26 4.90 - 6.13: 3 Bond angle restraints: 11614 Sorted by residual: angle pdb=" CA VAL B 19 " pdb=" C VAL B 19 " pdb=" O VAL B 19 " ideal model delta sigma weight residual 121.63 117.33 4.30 9.90e-01 1.02e+00 1.89e+01 angle pdb=" CA ASP A 137 " pdb=" C ASP A 137 " pdb=" O ASP A 137 " ideal model delta sigma weight residual 121.00 116.57 4.43 1.05e+00 9.07e-01 1.78e+01 angle pdb=" N CYS B 313 " pdb=" CA CYS B 313 " pdb=" C CYS B 313 " ideal model delta sigma weight residual 108.79 114.64 -5.85 1.53e+00 4.27e-01 1.46e+01 angle pdb=" CA THR B 20 " pdb=" C THR B 20 " pdb=" O THR B 20 " ideal model delta sigma weight residual 120.99 117.09 3.90 1.12e+00 7.97e-01 1.21e+01 angle pdb=" CA GLY B 17 " pdb=" C GLY B 17 " pdb=" O GLY B 17 " ideal model delta sigma weight residual 121.23 117.66 3.57 1.08e+00 8.57e-01 1.09e+01 ... (remaining 11609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4412 17.95 - 35.91: 387 35.91 - 53.86: 86 53.86 - 71.82: 8 71.82 - 89.77: 5 Dihedral angle restraints: 4898 sinusoidal: 1489 harmonic: 3409 Sorted by residual: dihedral pdb=" CB CYS B 18 " pdb=" SG CYS B 18 " pdb=" SG CYS B 313 " pdb=" CB CYS B 313 " ideal model delta sinusoidal sigma weight residual 93.00 30.89 62.11 1 1.00e+01 1.00e-02 5.11e+01 dihedral pdb=" CD ARG B 188 " pdb=" NE ARG B 188 " pdb=" CZ ARG B 188 " pdb=" NH1 ARG B 188 " ideal model delta sinusoidal sigma weight residual 0.00 -39.62 39.62 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA ALA B 311 " pdb=" C ALA B 311 " pdb=" N GLU B 312 " pdb=" CA GLU B 312 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 940 0.033 - 0.066: 289 0.066 - 0.099: 95 0.099 - 0.132: 88 0.132 - 0.165: 3 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA VAL B 19 " pdb=" N VAL B 19 " pdb=" C VAL B 19 " pdb=" CB VAL B 19 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA PHE A 129 " pdb=" N PHE A 129 " pdb=" C PHE A 129 " pdb=" CB PHE A 129 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE B 848 " pdb=" N ILE B 848 " pdb=" C ILE B 848 " pdb=" CB ILE B 848 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1412 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N A1H18 A 701 " -0.009 2.00e-02 2.50e+03 5.92e-01 5.25e+03 pdb=" C10 A1H18 A 701 " 0.690 2.00e-02 2.50e+03 pdb=" C4 A1H18 A 701 " 0.787 2.00e-02 2.50e+03 pdb=" C5 A1H18 A 701 " -0.060 2.00e-02 2.50e+03 pdb=" C6 A1H18 A 701 " -0.633 2.00e-02 2.50e+03 pdb=" O1 A1H18 A 701 " -0.775 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 188 " -0.673 9.50e-02 1.11e+02 3.02e-01 5.56e+01 pdb=" NE ARG B 188 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 188 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 188 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 188 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 128 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C LEU A 128 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU A 128 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE A 129 " 0.007 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3099 2.86 - 3.37: 7364 3.37 - 3.88: 12928 3.88 - 4.39: 14241 4.39 - 4.90: 25649 Nonbonded interactions: 63281 Sorted by model distance: nonbonded pdb=" O THR B 37 " pdb=" OG1 THR B 37 " model vdw 2.346 3.040 nonbonded pdb=" O SER D 14 " pdb=" OG SER D 17 " model vdw 2.358 3.040 nonbonded pdb=" O VAL B 6 " pdb=" N GLY B1091 " model vdw 2.368 3.120 nonbonded pdb=" O LYS B 936 " pdb=" N GLY B 940 " model vdw 2.398 3.120 nonbonded pdb=" O GLU B 286 " pdb=" N LYS B 298 " model vdw 2.417 3.120 ... (remaining 63276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 0.084 8472 Z= 0.195 Angle : 0.560 6.126 11616 Z= 0.332 Chirality : 0.044 0.165 1415 Planarity : 0.017 0.592 1469 Dihedral : 14.453 89.771 2687 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.40 % Allowed : 21.82 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.39 (0.25), residues: 1136 helix: 2.56 (0.47), residues: 124 sheet: -0.87 (0.25), residues: 446 loop : -1.78 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 207 HIS 0.003 0.001 HIS B 261 PHE 0.007 0.001 PHE A 231 TYR 0.009 0.001 TYR A 89 ARG 0.006 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.22353 ( 299) hydrogen bonds : angle 9.29077 ( 804) SS BOND : bond 0.02688 ( 1) SS BOND : angle 3.85600 ( 2) covalent geometry : bond 0.00339 ( 8471) covalent geometry : angle 0.55787 (11614) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8068 (mp) cc_final: 0.7835 (tp) REVERT: B 276 MET cc_start: 0.9321 (tpp) cc_final: 0.9104 (tpp) REVERT: D 47 ILE cc_start: 0.8986 (mt) cc_final: 0.8744 (mp) outliers start: 3 outliers final: 2 residues processed: 128 average time/residue: 0.1803 time to fit residues: 32.9415 Evaluate side-chains 114 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 TRP Chi-restraints excluded: chain B residue 18 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 chunk 30 optimal weight: 0.0050 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 0.3980 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.104869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.083247 restraints weight = 20405.159| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.07 r_work: 0.3177 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8472 Z= 0.121 Angle : 0.537 7.104 11616 Z= 0.280 Chirality : 0.044 0.146 1415 Planarity : 0.003 0.032 1469 Dihedral : 5.313 62.076 1262 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.48 % Allowed : 20.48 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.12 (0.25), residues: 1136 helix: 2.45 (0.48), residues: 127 sheet: -0.68 (0.25), residues: 448 loop : -1.54 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 207 HIS 0.004 0.001 HIS B 805 PHE 0.010 0.001 PHE B1030 TYR 0.010 0.001 TYR B 193 ARG 0.005 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 299) hydrogen bonds : angle 6.20539 ( 804) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.32263 ( 2) covalent geometry : bond 0.00262 ( 8471) covalent geometry : angle 0.53678 (11614) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8441 (mp) cc_final: 0.7935 (tp) REVERT: D 11 TYR cc_start: 0.9164 (m-80) cc_final: 0.8897 (m-80) REVERT: D 47 ILE cc_start: 0.9088 (mt) cc_final: 0.8816 (mp) outliers start: 26 outliers final: 17 residues processed: 131 average time/residue: 0.1581 time to fit residues: 30.7630 Evaluate side-chains 131 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 460 HIS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 0.0670 chunk 91 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 overall best weight: 2.4122 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.101686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079898 restraints weight = 20968.231| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.07 r_work: 0.3108 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8472 Z= 0.182 Angle : 0.541 6.339 11616 Z= 0.283 Chirality : 0.044 0.139 1415 Planarity : 0.003 0.025 1469 Dihedral : 4.217 24.099 1260 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.82 % Allowed : 20.21 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.05 (0.25), residues: 1136 helix: 2.59 (0.49), residues: 120 sheet: -0.62 (0.25), residues: 458 loop : -1.49 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 207 HIS 0.003 0.001 HIS B 805 PHE 0.009 0.001 PHE B 799 TYR 0.014 0.001 TYR B 3 ARG 0.005 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 299) hydrogen bonds : angle 5.39103 ( 804) SS BOND : bond 0.00183 ( 1) SS BOND : angle 1.41611 ( 2) covalent geometry : bond 0.00411 ( 8471) covalent geometry : angle 0.54120 (11614) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8536 (mp) cc_final: 0.8133 (tp) REVERT: B 710 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9069 (mt) REVERT: D 53 ASN cc_start: 0.9280 (t0) cc_final: 0.9056 (t0) outliers start: 36 outliers final: 26 residues processed: 135 average time/residue: 0.1628 time to fit residues: 32.4786 Evaluate side-chains 132 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1082 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 114 optimal weight: 0.0970 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 overall best weight: 1.8182 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.101899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080183 restraints weight = 20633.176| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.03 r_work: 0.3108 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8472 Z= 0.141 Angle : 0.506 6.263 11616 Z= 0.264 Chirality : 0.044 0.151 1415 Planarity : 0.003 0.026 1469 Dihedral : 3.986 20.958 1259 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.42 % Allowed : 23.03 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.84 (0.25), residues: 1136 helix: 2.82 (0.50), residues: 115 sheet: -0.51 (0.25), residues: 449 loop : -1.29 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 207 HIS 0.002 0.001 HIS B 22 PHE 0.012 0.001 PHE B1030 TYR 0.025 0.001 TYR B 3 ARG 0.003 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02845 ( 299) hydrogen bonds : angle 5.07907 ( 804) SS BOND : bond 0.00584 ( 1) SS BOND : angle 2.39337 ( 2) covalent geometry : bond 0.00319 ( 8471) covalent geometry : angle 0.50470 (11614) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8538 (mp) cc_final: 0.8110 (tp) REVERT: B 722 ARG cc_start: 0.8237 (mtt-85) cc_final: 0.7898 (mtt-85) REVERT: B 884 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7537 (mm) outliers start: 33 outliers final: 23 residues processed: 135 average time/residue: 0.1606 time to fit residues: 32.1824 Evaluate side-chains 135 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1096 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 111 optimal weight: 0.0070 chunk 12 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.104147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082545 restraints weight = 20385.165| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 4.06 r_work: 0.3131 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8472 Z= 0.089 Angle : 0.480 5.953 11616 Z= 0.250 Chirality : 0.043 0.144 1415 Planarity : 0.003 0.031 1469 Dihedral : 3.703 18.112 1259 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.61 % Allowed : 23.83 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.79 (0.25), residues: 1136 helix: 2.84 (0.50), residues: 115 sheet: -0.56 (0.25), residues: 456 loop : -1.16 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 207 HIS 0.002 0.000 HIS B 22 PHE 0.014 0.001 PHE B1030 TYR 0.017 0.001 TYR B 3 ARG 0.003 0.000 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.02495 ( 299) hydrogen bonds : angle 4.74185 ( 804) SS BOND : bond 0.00483 ( 1) SS BOND : angle 1.64894 ( 2) covalent geometry : bond 0.00197 ( 8471) covalent geometry : angle 0.47943 (11614) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8516 (mp) cc_final: 0.8066 (tp) REVERT: A 112 TRP cc_start: 0.8296 (m100) cc_final: 0.7866 (m100) REVERT: A 148 ASP cc_start: 0.8655 (t0) cc_final: 0.8430 (t0) REVERT: B 722 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7922 (mtt-85) REVERT: B 884 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7526 (mm) outliers start: 27 outliers final: 19 residues processed: 142 average time/residue: 0.1786 time to fit residues: 36.9416 Evaluate side-chains 132 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.0040 chunk 65 optimal weight: 0.0020 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.103348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081860 restraints weight = 20424.250| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.00 r_work: 0.3128 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8472 Z= 0.098 Angle : 0.483 7.431 11616 Z= 0.248 Chirality : 0.043 0.157 1415 Planarity : 0.003 0.031 1469 Dihedral : 3.640 18.072 1259 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.15 % Allowed : 23.29 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.78 (0.25), residues: 1136 helix: 2.69 (0.50), residues: 115 sheet: -0.54 (0.25), residues: 455 loop : -1.14 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 207 HIS 0.002 0.000 HIS B 805 PHE 0.010 0.001 PHE B1030 TYR 0.021 0.001 TYR B 3 ARG 0.003 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02494 ( 299) hydrogen bonds : angle 4.66407 ( 804) SS BOND : bond 0.00422 ( 1) SS BOND : angle 1.51830 ( 2) covalent geometry : bond 0.00220 ( 8471) covalent geometry : angle 0.48276 (11614) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8554 (mp) cc_final: 0.8106 (tp) REVERT: A 112 TRP cc_start: 0.8322 (m100) cc_final: 0.7889 (m100) REVERT: A 148 ASP cc_start: 0.8677 (t0) cc_final: 0.8424 (t0) REVERT: A 577 ASN cc_start: 0.7016 (m-40) cc_final: 0.6795 (m-40) REVERT: B 722 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7953 (mtt-85) REVERT: B 875 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8782 (tm-30) REVERT: B 884 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7525 (mm) REVERT: B 1036 MET cc_start: 0.8965 (ppp) cc_final: 0.8736 (ptp) outliers start: 31 outliers final: 23 residues processed: 137 average time/residue: 0.1713 time to fit residues: 34.3321 Evaluate side-chains 136 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.0020 chunk 49 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.102902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.081797 restraints weight = 20344.783| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.05 r_work: 0.3085 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8472 Z= 0.086 Angle : 0.478 8.663 11616 Z= 0.244 Chirality : 0.043 0.229 1415 Planarity : 0.003 0.031 1469 Dihedral : 3.537 17.315 1259 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.15 % Allowed : 23.56 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.71 (0.25), residues: 1136 helix: 2.70 (0.50), residues: 115 sheet: -0.48 (0.25), residues: 455 loop : -1.10 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 207 HIS 0.002 0.000 HIS B 22 PHE 0.010 0.001 PHE B1030 TYR 0.019 0.001 TYR D 58 ARG 0.003 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02386 ( 299) hydrogen bonds : angle 4.52992 ( 804) SS BOND : bond 0.00419 ( 1) SS BOND : angle 1.28755 ( 2) covalent geometry : bond 0.00192 ( 8471) covalent geometry : angle 0.47797 (11614) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8501 (mp) cc_final: 0.8050 (tp) REVERT: A 112 TRP cc_start: 0.8252 (m100) cc_final: 0.7836 (m100) REVERT: A 148 ASP cc_start: 0.8619 (t0) cc_final: 0.8338 (t0) REVERT: A 577 ASN cc_start: 0.6985 (m-40) cc_final: 0.6771 (m-40) REVERT: B 875 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8826 (tm-30) REVERT: B 884 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7410 (mm) REVERT: B 969 GLU cc_start: 0.9081 (pt0) cc_final: 0.8657 (mt-10) REVERT: B 1036 MET cc_start: 0.9008 (ppp) cc_final: 0.8770 (ptm) outliers start: 31 outliers final: 22 residues processed: 141 average time/residue: 0.1657 time to fit residues: 34.2596 Evaluate side-chains 136 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.101875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080506 restraints weight = 20750.496| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.07 r_work: 0.3048 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8472 Z= 0.136 Angle : 0.503 11.040 11616 Z= 0.256 Chirality : 0.044 0.347 1415 Planarity : 0.003 0.029 1469 Dihedral : 3.653 17.681 1259 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.55 % Allowed : 23.43 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.65 (0.25), residues: 1136 helix: 2.73 (0.50), residues: 114 sheet: -0.47 (0.25), residues: 458 loop : -1.01 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 207 HIS 0.002 0.000 HIS B 805 PHE 0.009 0.001 PHE B 733 TYR 0.019 0.001 TYR B 3 ARG 0.007 0.000 ARG B 722 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 299) hydrogen bonds : angle 4.58731 ( 804) SS BOND : bond 0.00450 ( 1) SS BOND : angle 1.38590 ( 2) covalent geometry : bond 0.00311 ( 8471) covalent geometry : angle 0.50264 (11614) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.939 Fit side-chains REVERT: A 106 ILE cc_start: 0.8516 (mp) cc_final: 0.8060 (tp) REVERT: A 112 TRP cc_start: 0.8238 (m100) cc_final: 0.7762 (m100) REVERT: B 850 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.9015 (p) REVERT: B 884 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7468 (mm) REVERT: B 1036 MET cc_start: 0.8949 (ppp) cc_final: 0.8693 (ppp) outliers start: 34 outliers final: 29 residues processed: 143 average time/residue: 0.1675 time to fit residues: 34.9975 Evaluate side-chains 144 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 28 optimal weight: 30.0000 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.099746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078432 restraints weight = 21173.982| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.01 r_work: 0.3033 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8472 Z= 0.156 Angle : 0.527 11.713 11616 Z= 0.268 Chirality : 0.045 0.349 1415 Planarity : 0.003 0.030 1469 Dihedral : 3.787 17.254 1259 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.69 % Allowed : 23.29 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.61 (0.25), residues: 1136 helix: 2.80 (0.50), residues: 114 sheet: -0.40 (0.25), residues: 448 loop : -1.05 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 207 HIS 0.002 0.000 HIS B 805 PHE 0.022 0.001 PHE A 528 TYR 0.017 0.001 TYR B 3 ARG 0.007 0.000 ARG B 722 Details of bonding type rmsd hydrogen bonds : bond 0.02626 ( 299) hydrogen bonds : angle 4.63550 ( 804) SS BOND : bond 0.00452 ( 1) SS BOND : angle 1.43405 ( 2) covalent geometry : bond 0.00354 ( 8471) covalent geometry : angle 0.52702 (11614) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.875 Fit side-chains REVERT: A 522 ASP cc_start: 0.9240 (t0) cc_final: 0.8639 (p0) REVERT: B 276 MET cc_start: 0.9508 (tpp) cc_final: 0.9279 (tpp) REVERT: B 850 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9074 (p) REVERT: B 884 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7533 (mm) outliers start: 35 outliers final: 30 residues processed: 143 average time/residue: 0.1716 time to fit residues: 36.5005 Evaluate side-chains 143 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 0.0270 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 0.0670 chunk 64 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.103814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082966 restraints weight = 20702.996| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.02 r_work: 0.3068 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8472 Z= 0.090 Angle : 0.511 12.492 11616 Z= 0.257 Chirality : 0.044 0.312 1415 Planarity : 0.003 0.032 1469 Dihedral : 3.650 18.690 1259 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.88 % Allowed : 24.36 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.64 (0.25), residues: 1136 helix: 2.58 (0.50), residues: 115 sheet: -0.41 (0.25), residues: 449 loop : -1.03 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 207 HIS 0.005 0.001 HIS A 108 PHE 0.009 0.001 PHE B1030 TYR 0.021 0.001 TYR D 58 ARG 0.007 0.000 ARG B 722 Details of bonding type rmsd hydrogen bonds : bond 0.02325 ( 299) hydrogen bonds : angle 4.50139 ( 804) SS BOND : bond 0.00353 ( 1) SS BOND : angle 1.08815 ( 2) covalent geometry : bond 0.00198 ( 8471) covalent geometry : angle 0.51118 (11614) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.628 Fit side-chains REVERT: A 112 TRP cc_start: 0.8221 (m100) cc_final: 0.7755 (m100) REVERT: B 276 MET cc_start: 0.9527 (tpp) cc_final: 0.9296 (tpp) REVERT: B 850 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9046 (p) REVERT: B 884 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7419 (mm) REVERT: B 969 GLU cc_start: 0.9095 (pt0) cc_final: 0.8679 (mt-10) outliers start: 29 outliers final: 24 residues processed: 145 average time/residue: 0.1901 time to fit residues: 40.9214 Evaluate side-chains 142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.100208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079001 restraints weight = 21024.458| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.03 r_work: 0.3060 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8472 Z= 0.173 Angle : 0.545 12.336 11616 Z= 0.276 Chirality : 0.045 0.359 1415 Planarity : 0.003 0.053 1469 Dihedral : 3.816 18.523 1259 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.15 % Allowed : 25.03 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.64 (0.25), residues: 1136 helix: 2.79 (0.49), residues: 112 sheet: -0.43 (0.25), residues: 458 loop : -1.04 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 207 HIS 0.005 0.001 HIS A 108 PHE 0.010 0.001 PHE B 733 TYR 0.019 0.001 TYR D 58 ARG 0.006 0.001 ARG B 722 Details of bonding type rmsd hydrogen bonds : bond 0.02644 ( 299) hydrogen bonds : angle 4.61851 ( 804) SS BOND : bond 0.00434 ( 1) SS BOND : angle 1.46112 ( 2) covalent geometry : bond 0.00390 ( 8471) covalent geometry : angle 0.54427 (11614) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4277.20 seconds wall clock time: 74 minutes 1.03 seconds (4441.03 seconds total)