Starting phenix.real_space_refine on Wed Sep 17 11:05:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8roy_19407/09_2025/8roy_19407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8roy_19407/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8roy_19407/09_2025/8roy_19407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8roy_19407/09_2025/8roy_19407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8roy_19407/09_2025/8roy_19407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8roy_19407/09_2025/8roy_19407.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 15, 'GLN:plan1': 7, 'ARG:plan': 14, 'ASP:plan': 10, 'PHE:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 3, 'TRP:plan': 1} 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, 'ARG:plan': 11, 'ASP:plan': 24} 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, 'ARG:plan': 3, 'GLU: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: 2.40, per 1000 atoms: 0.29 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: 1.02 Conformation dependent library (CDL) restraints added in 362.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.57 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: 1.75 Time building geometry restraints manager: 1.21 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG B 188 TYR 0.009 0.001 TYR A 89 PHE 0.007 0.001 PHE A 231 TRP 0.015 0.001 TRP B 207 HIS 0.003 0.001 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8471) covalent geometry : angle 0.55787 (11614) SS BOND : bond 0.02688 ( 1) SS BOND : angle 3.85600 ( 2) hydrogen bonds : bond 0.22353 ( 299) hydrogen bonds : angle 9.29077 ( 804) *********************** 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 : 0.387 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: 0.0861 time to fit residues: 15.8333 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 : 0.308 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.104216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082248 restraints weight = 20929.539| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 4.12 r_work: 0.3159 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8472 Z= 0.139 Angle : 0.553 8.767 11616 Z= 0.289 Chirality : 0.045 0.142 1415 Planarity : 0.003 0.030 1469 Dihedral : 5.517 66.929 1262 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.61 % Allowed : 20.75 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.25), residues: 1136 helix: 2.39 (0.48), residues: 127 sheet: -0.67 (0.25), residues: 443 loop : -1.56 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 134 TYR 0.010 0.001 TYR B 5 PHE 0.011 0.001 PHE B1030 TRP 0.019 0.002 TRP B 207 HIS 0.004 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8471) covalent geometry : angle 0.55344 (11614) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.55233 ( 2) hydrogen bonds : bond 0.03363 ( 299) hydrogen bonds : angle 6.12536 ( 804) *********************** 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 146 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8448 (mp) cc_final: 0.7940 (tp) REVERT: D 47 ILE cc_start: 0.9111 (mt) cc_final: 0.8834 (mp) outliers start: 27 outliers final: 18 residues processed: 132 average time/residue: 0.0766 time to fit residues: 15.0088 Evaluate side-chains 132 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 377 THR 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 105 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.102822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080692 restraints weight = 20915.348| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.09 r_work: 0.3127 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8472 Z= 0.145 Angle : 0.516 6.223 11616 Z= 0.270 Chirality : 0.044 0.137 1415 Planarity : 0.003 0.025 1469 Dihedral : 4.144 25.658 1260 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.28 % Allowed : 20.21 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.25), residues: 1136 helix: 2.55 (0.49), residues: 121 sheet: -0.62 (0.25), residues: 448 loop : -1.46 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.018 0.001 TYR B 3 PHE 0.009 0.001 PHE B1030 TRP 0.020 0.001 TRP B 207 HIS 0.002 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8471) covalent geometry : angle 0.51574 (11614) SS BOND : bond 0.00238 ( 1) SS BOND : angle 0.95383 ( 2) hydrogen bonds : bond 0.03138 ( 299) hydrogen bonds : angle 5.37836 ( 804) *********************** 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 146 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8501 (mp) cc_final: 0.7973 (tp) REVERT: A 178 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7568 (ttt180) REVERT: D 53 ASN cc_start: 0.9213 (t0) cc_final: 0.8980 (t0) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 0.0726 time to fit residues: 14.4662 Evaluate side-chains 130 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 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 831 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 Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1096 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 104 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.104082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082491 restraints weight = 20812.200| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.07 r_work: 0.3146 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8472 Z= 0.097 Angle : 0.490 6.192 11616 Z= 0.253 Chirality : 0.044 0.135 1415 Planarity : 0.003 0.028 1469 Dihedral : 3.819 21.237 1259 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.88 % Allowed : 22.49 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.25), residues: 1136 helix: 2.75 (0.50), residues: 115 sheet: -0.54 (0.25), residues: 455 loop : -1.30 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.029 0.001 TYR B 3 PHE 0.011 0.001 PHE B1030 TRP 0.020 0.001 TRP B 207 HIS 0.002 0.000 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8471) covalent geometry : angle 0.48956 (11614) SS BOND : bond 0.00553 ( 1) SS BOND : angle 1.99646 ( 2) hydrogen bonds : bond 0.02641 ( 299) hydrogen bonds : angle 5.02925 ( 804) *********************** 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: 29 poor density : 118 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8513 (mp) cc_final: 0.7966 (tp) REVERT: A 112 TRP cc_start: 0.8283 (m100) cc_final: 0.7517 (m100) REVERT: B 710 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9055 (mt) REVERT: B 884 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7498 (mm) outliers start: 29 outliers final: 23 residues processed: 138 average time/residue: 0.0752 time to fit residues: 15.4191 Evaluate side-chains 135 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 490 ILE Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 564 VAL 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 322 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 710 LEU 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 976 VAL Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain D residue 38 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.099313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077831 restraints weight = 20816.909| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.01 r_work: 0.3017 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8472 Z= 0.207 Angle : 0.552 5.771 11616 Z= 0.289 Chirality : 0.044 0.157 1415 Planarity : 0.003 0.035 1469 Dihedral : 4.173 20.925 1259 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.76 % Allowed : 21.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1136 helix: 2.70 (0.50), residues: 114 sheet: -0.62 (0.24), residues: 463 loop : -1.27 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 722 TYR 0.024 0.002 TYR B 3 PHE 0.011 0.002 PHE B1030 TRP 0.019 0.001 TRP B 207 HIS 0.003 0.001 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 8471) covalent geometry : angle 0.55212 (11614) SS BOND : bond 0.00428 ( 1) SS BOND : angle 1.64668 ( 2) hydrogen bonds : bond 0.03170 ( 299) hydrogen bonds : angle 5.04744 ( 804) *********************** 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 151 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8546 (mp) cc_final: 0.8123 (tp) REVERT: A 148 ASP cc_start: 0.8665 (t0) cc_final: 0.8447 (t0) REVERT: B 710 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9135 (mt) outliers start: 43 outliers final: 34 residues processed: 139 average time/residue: 0.0736 time to fit residues: 15.3109 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 : 0.396 ------------------------------------------------------------------------------- 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 491 ASN 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 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 253 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 322 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 792 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 945 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.101039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080046 restraints weight = 20407.191| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.03 r_work: 0.3044 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2602 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= 0.107 Angle : 0.490 5.906 11616 Z= 0.256 Chirality : 0.044 0.141 1415 Planarity : 0.003 0.030 1469 Dihedral : 3.869 17.754 1259 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.69 % Allowed : 23.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.25), residues: 1136 helix: 2.55 (0.50), residues: 116 sheet: -0.52 (0.25), residues: 454 loop : -1.18 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 722 TYR 0.021 0.001 TYR B 3 PHE 0.012 0.001 PHE B1030 TRP 0.020 0.001 TRP B 207 HIS 0.002 0.000 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8471) covalent geometry : angle 0.48956 (11614) SS BOND : bond 0.00433 ( 1) SS BOND : angle 1.37579 ( 2) hydrogen bonds : bond 0.02613 ( 299) hydrogen bonds : angle 4.79460 ( 804) *********************** 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 148 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8525 (mp) cc_final: 0.8086 (tp) REVERT: A 148 ASP cc_start: 0.8668 (t0) cc_final: 0.8440 (t0) REVERT: B 884 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7368 (mm) outliers start: 35 outliers final: 27 residues processed: 138 average time/residue: 0.0726 time to fit residues: 15.1154 Evaluate side-chains 138 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 550 SER Chi-restraints excluded: chain A residue 564 VAL 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 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 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 1036 MET Chi-restraints excluded: chain B residue 1061 VAL 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 55 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.099664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.078320 restraints weight = 20925.628| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.07 r_work: 0.3022 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8472 Z= 0.147 Angle : 0.497 5.911 11616 Z= 0.260 Chirality : 0.043 0.145 1415 Planarity : 0.003 0.030 1469 Dihedral : 3.867 17.847 1259 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.42 % Allowed : 24.36 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.25), residues: 1136 helix: 2.56 (0.49), residues: 115 sheet: -0.49 (0.25), residues: 453 loop : -1.15 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 722 TYR 0.020 0.001 TYR B 3 PHE 0.010 0.001 PHE B1030 TRP 0.019 0.001 TRP B 207 HIS 0.002 0.000 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8471) covalent geometry : angle 0.49640 (11614) SS BOND : bond 0.00428 ( 1) SS BOND : angle 1.52111 ( 2) hydrogen bonds : bond 0.02725 ( 299) hydrogen bonds : angle 4.74454 ( 804) *********************** 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 145 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8527 (mp) cc_final: 0.8091 (tp) REVERT: B 722 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7954 (mtt-85) REVERT: B 884 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7464 (mm) outliers start: 33 outliers final: 29 residues processed: 137 average time/residue: 0.0720 time to fit residues: 14.7312 Evaluate side-chains 138 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 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 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 1082 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.099256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078026 restraints weight = 20955.172| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.01 r_work: 0.3021 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8472 Z= 0.145 Angle : 0.496 6.032 11616 Z= 0.261 Chirality : 0.043 0.148 1415 Planarity : 0.003 0.030 1469 Dihedral : 3.863 16.910 1259 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.95 % Allowed : 23.83 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.25), residues: 1136 helix: 2.52 (0.49), residues: 115 sheet: -0.46 (0.25), residues: 453 loop : -1.13 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 722 TYR 0.019 0.001 TYR B 3 PHE 0.010 0.001 PHE B1030 TRP 0.019 0.001 TRP B 207 HIS 0.002 0.000 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8471) covalent geometry : angle 0.49570 (11614) SS BOND : bond 0.00418 ( 1) SS BOND : angle 1.44698 ( 2) hydrogen bonds : bond 0.02649 ( 299) hydrogen bonds : angle 4.70417 ( 804) *********************** 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 148 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8544 (mp) cc_final: 0.8114 (tp) REVERT: B 276 MET cc_start: 0.9504 (tpp) cc_final: 0.9277 (tpp) REVERT: B 884 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7513 (mm) outliers start: 37 outliers final: 31 residues processed: 138 average time/residue: 0.0741 time to fit residues: 15.2928 Evaluate side-chains 140 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 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 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 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 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 74 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.098659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077428 restraints weight = 21035.128| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.03 r_work: 0.3004 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8472 Z= 0.164 Angle : 0.520 8.403 11616 Z= 0.270 Chirality : 0.044 0.147 1415 Planarity : 0.003 0.037 1469 Dihedral : 3.907 16.584 1259 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.95 % Allowed : 24.10 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.25), residues: 1136 helix: 2.44 (0.49), residues: 116 sheet: -0.47 (0.25), residues: 453 loop : -1.14 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 722 TYR 0.018 0.001 TYR B 3 PHE 0.009 0.001 PHE B 733 TRP 0.020 0.001 TRP A 562 HIS 0.002 0.001 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8471) covalent geometry : angle 0.51945 (11614) SS BOND : bond 0.00414 ( 1) SS BOND : angle 1.51939 ( 2) hydrogen bonds : bond 0.02701 ( 299) hydrogen bonds : angle 4.70583 ( 804) *********************** 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 148 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8563 (mp) cc_final: 0.8129 (tp) REVERT: B 276 MET cc_start: 0.9528 (tpp) cc_final: 0.9311 (tpp) REVERT: B 884 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7399 (mm) REVERT: B 929 SER cc_start: 0.8875 (t) cc_final: 0.8650 (t) outliers start: 37 outliers final: 31 residues processed: 139 average time/residue: 0.0690 time to fit residues: 14.8447 Evaluate side-chains 142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 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 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 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 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 47 optimal weight: 0.0060 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.100371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.079074 restraints weight = 20863.225| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.05 r_work: 0.3043 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8472 Z= 0.095 Angle : 0.502 6.509 11616 Z= 0.258 Chirality : 0.043 0.145 1415 Planarity : 0.003 0.048 1469 Dihedral : 3.718 14.946 1259 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.48 % Allowed : 25.84 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.25), residues: 1136 helix: 2.37 (0.50), residues: 116 sheet: -0.47 (0.25), residues: 452 loop : -1.09 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 947 TYR 0.016 0.001 TYR B 3 PHE 0.009 0.001 PHE B1030 TRP 0.020 0.001 TRP B 207 HIS 0.003 0.000 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8471) covalent geometry : angle 0.50157 (11614) SS BOND : bond 0.00349 ( 1) SS BOND : angle 1.19102 ( 2) hydrogen bonds : bond 0.02427 ( 299) hydrogen bonds : angle 4.58559 ( 804) ********************** 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 142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8552 (mp) cc_final: 0.8116 (tp) REVERT: B 276 MET cc_start: 0.9507 (tpp) cc_final: 0.9296 (tpp) REVERT: B 884 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7461 (mm) outliers start: 26 outliers final: 22 residues processed: 134 average time/residue: 0.0698 time to fit residues: 14.1245 Evaluate side-chains 135 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 550 SER Chi-restraints excluded: chain A residue 564 VAL 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 930 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 0.0770 chunk 111 optimal weight: 0.0670 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.100126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078926 restraints weight = 20964.199| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.01 r_work: 0.3082 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8472 Z= 0.102 Angle : 0.499 7.551 11616 Z= 0.255 Chirality : 0.043 0.140 1415 Planarity : 0.003 0.048 1469 Dihedral : 3.622 15.372 1259 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.61 % Allowed : 26.24 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.25), residues: 1136 helix: 2.26 (0.50), residues: 116 sheet: -0.47 (0.25), residues: 456 loop : -1.06 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 947 TYR 0.016 0.001 TYR B 3 PHE 0.010 0.001 PHE B1030 TRP 0.019 0.001 TRP B 207 HIS 0.002 0.000 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8471) covalent geometry : angle 0.49833 (11614) SS BOND : bond 0.00365 ( 1) SS BOND : angle 1.20014 ( 2) hydrogen bonds : bond 0.02433 ( 299) hydrogen bonds : angle 4.51206 ( 804) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2037.02 seconds wall clock time: 35 minutes 15.80 seconds (2115.80 seconds total)