Starting phenix.real_space_refine on Wed Jan 15 10:25:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8roy_19407/01_2025/8roy_19407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8roy_19407/01_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_19407/01_2025/8roy_19407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8roy_19407/01_2025/8roy_19407.map" model { file = "/net/cci-nas-00/data/ceres_data/8roy_19407/01_2025/8roy_19407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8roy_19407/01_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-5571/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: 5.37, per 1000 atoms: 0.65 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: 2.28 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: 1.38 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: 3.35 Time building geometry restraints manager: 2.60 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: 2.590 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.440 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- 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 8471 Z= 0.230 Angle : 0.558 6.126 11614 Z= 0.331 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 *********************** 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 : 0.960 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: 0.1885 time to fit residues: 34.3331 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 : 0.946 ------------------------------------------------------------------------------- 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 = 0.104881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083408 restraints weight = 20410.402| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.05 r_work: 0.3178 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8471 Z= 0.176 Angle : 0.537 7.109 11614 Z= 0.280 Chirality : 0.044 0.146 1415 Planarity : 0.003 0.033 1469 Dihedral : 5.328 62.448 1262 Min Nonbonded Distance : 2.555 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: 2.44 (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 *********************** 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 144 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8440 (mp) cc_final: 0.7935 (tp) REVERT: D 11 TYR cc_start: 0.9164 (m-80) cc_final: 0.8896 (m-80) REVERT: D 47 ILE cc_start: 0.9087 (mt) cc_final: 0.8815 (mp) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 0.1591 time to fit residues: 30.6681 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 : 0.976 ------------------------------------------------------------------------------- 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: 7.9990 chunk 91 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 0.0020 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 overall best weight: 3.9594 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.099138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077517 restraints weight = 20958.241| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.98 r_work: 0.3045 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 8471 Z= 0.414 Angle : 0.616 6.362 11614 Z= 0.324 Chirality : 0.046 0.145 1415 Planarity : 0.003 0.026 1469 Dihedral : 4.638 25.669 1260 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.49 % Allowed : 19.54 % 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: -1.23 (0.24), residues: 1136 helix: 2.43 (0.48), residues: 120 sheet: -0.78 (0.24), residues: 463 loop : -1.56 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 207 HIS 0.003 0.001 HIS A 219 PHE 0.012 0.002 PHE B 733 TYR 0.017 0.002 TYR B 3 ARG 0.004 0.001 ARG B 134 *********************** 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: 41 poor density : 109 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: B 710 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9107 (mt) outliers start: 41 outliers final: 29 residues processed: 134 average time/residue: 0.1669 time to fit residues: 33.0921 Evaluate side-chains 133 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 489 LEU 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 178 ILE Chi-restraints excluded: chain B residue 181 VAL 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 253 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 1055 GLN 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: 0.9980 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 0.0000 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.101942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.080389 restraints weight = 20501.451| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.01 r_work: 0.3101 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8471 Z= 0.151 Angle : 0.505 5.876 11614 Z= 0.264 Chirality : 0.044 0.138 1415 Planarity : 0.003 0.029 1469 Dihedral : 4.049 19.500 1259 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.28 % Allowed : 22.76 % Favored : 72.96 % 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: -0.90 (0.25), residues: 1136 helix: 2.74 (0.50), residues: 115 sheet: -0.57 (0.25), residues: 447 loop : -1.30 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 207 HIS 0.002 0.001 HIS B 22 PHE 0.012 0.001 PHE B1030 TYR 0.023 0.001 TYR B 3 ARG 0.003 0.000 ARG B 134 *********************** 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 147 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: B 722 ARG cc_start: 0.8195 (mtt-85) cc_final: 0.7875 (mtt-85) REVERT: B 884 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7527 (mm) outliers start: 32 outliers final: 22 residues processed: 134 average time/residue: 0.1668 time to fit residues: 32.7508 Evaluate side-chains 130 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 A residue 550 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain B residue 162 LEU 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 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 1036 MET Chi-restraints excluded: chain B residue 1061 VAL 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: 9.9990 chunk 99 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 12 optimal weight: 0.0670 chunk 98 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.102880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082916 restraints weight = 20883.675| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.90 r_work: 0.3121 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 8471 Z= 0.123 Angle : 0.476 6.239 11614 Z= 0.248 Chirality : 0.043 0.142 1415 Planarity : 0.003 0.030 1469 Dihedral : 3.751 17.943 1259 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.42 % Allowed : 23.16 % Favored : 72.42 % 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: -0.87 (0.25), residues: 1136 helix: 2.58 (0.50), residues: 115 sheet: -0.57 (0.25), residues: 450 loop : -1.22 (0.25), residues: 571 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 0.011 0.001 PHE B1030 TYR 0.018 0.001 TYR B 3 ARG 0.004 0.000 ARG A 178 *********************** 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 153 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8902 (pt) cc_final: 0.8518 (tp) REVERT: B 722 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7911 (mtt-85) REVERT: B 884 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7486 (mm) REVERT: B 969 GLU cc_start: 0.9084 (pt0) cc_final: 0.8826 (pt0) outliers start: 33 outliers final: 23 residues processed: 144 average time/residue: 0.1855 time to fit residues: 38.6821 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 : 1.061 ------------------------------------------------------------------------------- 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 547 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain B residue 162 LEU 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 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 1061 VAL Chi-restraints excluded: chain B residue 1096 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.099272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.078052 restraints weight = 20715.479| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.00 r_work: 0.3057 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8471 Z= 0.245 Angle : 0.512 6.900 11614 Z= 0.267 Chirality : 0.044 0.142 1415 Planarity : 0.003 0.029 1469 Dihedral : 3.913 18.306 1259 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.35 % Allowed : 22.89 % 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: -0.78 (0.25), residues: 1136 helix: 2.71 (0.50), residues: 114 sheet: -0.52 (0.25), residues: 452 loop : -1.16 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 207 HIS 0.003 0.001 HIS B 189 PHE 0.009 0.001 PHE B 733 TYR 0.015 0.001 TYR B 3 ARG 0.002 0.000 ARG B 134 *********************** 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 151 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: B 722 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7813 (mtt-85) REVERT: B 884 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7532 (mm) outliers start: 40 outliers final: 33 residues processed: 142 average time/residue: 0.1786 time to fit residues: 36.5436 Evaluate side-chains 144 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 365 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 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 Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1096 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.100354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.079388 restraints weight = 20656.598| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.03 r_work: 0.3066 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8471 Z= 0.183 Angle : 0.490 6.932 11614 Z= 0.255 Chirality : 0.043 0.136 1415 Planarity : 0.003 0.031 1469 Dihedral : 3.780 16.919 1259 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.09 % Allowed : 22.76 % Favored : 72.16 % 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: 2.57 (0.50), residues: 115 sheet: -0.47 (0.25), residues: 449 loop : -1.17 (0.25), residues: 572 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 0.012 0.001 PHE B1030 TYR 0.012 0.001 TYR B 3 ARG 0.003 0.000 ARG B 134 *********************** 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 156 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: B 884 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7525 (mm) outliers start: 38 outliers final: 30 residues processed: 146 average time/residue: 0.1839 time to fit residues: 39.1340 Evaluate side-chains 142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 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 A residue 547 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain B residue 162 LEU 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 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 945 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1096 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 76 optimal weight: 0.0170 chunk 85 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 2.5624 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.099342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.078058 restraints weight = 20918.740| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.02 r_work: 0.3034 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8471 Z= 0.281 Angle : 0.529 9.501 11614 Z= 0.275 Chirality : 0.044 0.138 1415 Planarity : 0.003 0.028 1469 Dihedral : 3.937 17.389 1259 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.35 % Allowed : 23.16 % Favored : 71.49 % 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: -0.82 (0.25), residues: 1136 helix: 2.63 (0.49), residues: 112 sheet: -0.50 (0.25), residues: 454 loop : -1.21 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 207 HIS 0.002 0.001 HIS B 22 PHE 0.011 0.001 PHE B1030 TYR 0.014 0.001 TYR B 3 ARG 0.007 0.000 ARG B 722 *********************** 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: 40 poor density : 109 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: B 276 MET cc_start: 0.9510 (tpp) cc_final: 0.9298 (tpp) REVERT: B 850 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9103 (p) REVERT: B 884 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7428 (mm) outliers start: 40 outliers final: 33 residues processed: 138 average time/residue: 0.1665 time to fit residues: 34.2688 Evaluate side-chains 141 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 CYS 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 458 ILE 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 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 833 THR Chi-restraints excluded: chain B residue 850 VAL 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 Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1096 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.100333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078946 restraints weight = 21005.571| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.08 r_work: 0.3021 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8471 Z= 0.193 Angle : 0.513 9.736 11614 Z= 0.263 Chirality : 0.044 0.185 1415 Planarity : 0.003 0.031 1469 Dihedral : 3.811 15.925 1259 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.82 % Allowed : 24.36 % 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: -0.80 (0.25), residues: 1136 helix: 2.37 (0.50), residues: 115 sheet: -0.45 (0.25), residues: 455 loop : -1.18 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 207 HIS 0.002 0.001 HIS B 22 PHE 0.010 0.001 PHE B1030 TYR 0.010 0.001 TYR A 89 ARG 0.007 0.000 ARG B 722 *********************** 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 145 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: B 276 MET cc_start: 0.9514 (tpp) cc_final: 0.9305 (tpp) REVERT: B 850 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9108 (p) REVERT: B 884 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7383 (mm) outliers start: 36 outliers final: 31 residues processed: 136 average time/residue: 0.1651 time to fit residues: 33.5381 Evaluate side-chains 142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 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 512 THR 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 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 833 THR Chi-restraints excluded: chain B residue 850 VAL 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 Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1096 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.100010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078890 restraints weight = 20730.417| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.98 r_work: 0.3043 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8471 Z= 0.164 Angle : 0.504 9.668 11614 Z= 0.258 Chirality : 0.043 0.140 1415 Planarity : 0.003 0.029 1469 Dihedral : 3.679 15.647 1259 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.28 % Allowed : 24.90 % 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: -0.84 (0.25), residues: 1136 helix: 2.15 (0.50), residues: 116 sheet: -0.52 (0.25), residues: 457 loop : -1.12 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 207 HIS 0.004 0.001 HIS A 108 PHE 0.009 0.001 PHE B1030 TYR 0.010 0.001 TYR A 89 ARG 0.007 0.000 ARG B 722 ********************** 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 143 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.948 Fit side-chains REVERT: B 850 VAL cc_start: 0.9431 (OUTLIER) cc_final: 0.9110 (p) REVERT: B 884 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7430 (mm) outliers start: 32 outliers final: 30 residues processed: 135 average time/residue: 0.1663 time to fit residues: 33.4439 Evaluate side-chains 139 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 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 512 THR 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 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 833 THR Chi-restraints excluded: chain B residue 850 VAL 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 Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.097382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075921 restraints weight = 21403.831| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.98 r_work: 0.2969 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8471 Z= 0.397 Angle : 0.597 9.586 11614 Z= 0.309 Chirality : 0.045 0.183 1415 Planarity : 0.003 0.028 1469 Dihedral : 4.149 17.441 1259 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 4.82 % Allowed : 24.90 % Favored : 70.28 % 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: -0.87 (0.25), residues: 1136 helix: 2.13 (0.49), residues: 119 sheet: -0.57 (0.25), residues: 460 loop : -1.14 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 207 HIS 0.002 0.001 HIS A 108 PHE 0.029 0.002 PHE A 528 TYR 0.017 0.002 TYR A 107 ARG 0.007 0.001 ARG B 722 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4075.63 seconds wall clock time: 72 minutes 42.03 seconds (4362.03 seconds total)