Starting phenix.real_space_refine on Sun May 11 02:23:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rox_19406/05_2025/8rox_19406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rox_19406/05_2025/8rox_19406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rox_19406/05_2025/8rox_19406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rox_19406/05_2025/8rox_19406.map" model { file = "/net/cci-nas-00/data/ceres_data/8rox_19406/05_2025/8rox_19406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rox_19406/05_2025/8rox_19406.cif" } resolution = 3.3 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= 0.019 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 22 5.16 5 Cl 2 4.86 5 C 4651 2.51 5 N 1244 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7249 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2101 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 15, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 324 Chain: "B" Number of atoms: 4783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 4783 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 348} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 736} Chain breaks: 9 Unresolved non-hydrogen bonds: 1212 Unresolved non-hydrogen angles: 1500 Unresolved non-hydrogen dihedrals: 939 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 18, 'ASP:plan': 35, 'PHE:plan': 2, 'GLU:plan': 64, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 672 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 339 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'A1H17': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.74 Number of scatterers: 7249 At special positions: 0 Unit cell: (90.522, 98.226, 105.288, 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 22 16.00 O 1330 8.00 N 1244 7.00 C 4651 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 958.9 milliseconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 20 sheets defined 14.0% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.974A pdb=" N HIS A 466 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.050A pdb=" N LYS B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 255 " --> pdb=" O PRO B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 987 through 990 Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1064 through 1068 removed outlier: 3.946A pdb=" N ILE B1068 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1091 through 1100 removed outlier: 3.910A pdb=" N LEU B1098 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B1099 " --> pdb=" O GLU B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1110 Processing helix chain 'B' and resid 1127 through 1137 Processing helix chain 'D' and resid 53 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 83 removed outlier: 7.333A pdb=" N LEU A 91 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE A 83 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR A 89 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 109 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 125 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TRP A 111 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.625A pdb=" N THR A 184 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 224 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 178 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP A 179 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A 158 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.647A pdb=" N LEU A 251 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 448 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 482 removed outlier: 6.698A pdb=" N LEU A 489 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A 481 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN A 487 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 3.778A pdb=" N VAL B1006 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.583A pdb=" N TYR B 42 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU B 39 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU B 54 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 41 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER D 33 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 67 removed outlier: 3.637A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 104 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU B 90 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR B 102 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS B 92 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE B 100 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N GLN D 45 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG B 103 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 47 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 105 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N THR D 49 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N ASN B 107 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 152 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS B 153 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.955A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 178 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 193 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 201 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.955A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 178 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 193 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AB2, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.310A pdb=" N GLY B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 272 " --> pdb=" O HIS B 261 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ARG B 263 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG B 270 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 316 through 317 removed outlier: 3.681A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 332 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER B 331 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR B 352 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.832A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 376 " --> pdb=" O CYS B 363 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.227A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 742 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 750 " --> pdb=" O VAL B 742 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.227A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N HIS B 789 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 806 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 811 through 819 removed outlier: 6.258A pdb=" N GLY B 832 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 816 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 830 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER B 818 " --> pdb=" O TYR B 828 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR B 828 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLN B 845 " --> pdb=" O MET B 835 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN B 852 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR B 860 " --> pdb=" O GLN B 852 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 854 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 874 through 876 Processing sheet with id=AB9, first strand: chain 'B' and resid 911 through 917 Processing sheet with id=AC1, first strand: chain 'B' and resid 956 through 961 removed outlier: 3.529A pdb=" N ALA B 956 " --> pdb=" O ALA B 968 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B 964 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1076 through 1077 330 hydrogen bonds defined for protein. 882 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: 3.50 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1991 1.33 - 1.45: 1462 1.45 - 1.57: 3922 1.57 - 1.69: 2 1.69 - 1.81: 25 Bond restraints: 7402 Sorted by residual: bond pdb=" C3 A1H17 A 701 " pdb=" S A1H17 A 701 " ideal model delta sigma weight residual 1.750 1.644 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.456 1.494 -0.038 9.50e-03 1.11e+04 1.60e+01 bond pdb=" N VAL B 957 " pdb=" CA VAL B 957 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.22e+01 bond pdb=" N VAL B 322 " pdb=" CA VAL B 322 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.14e-02 7.69e+03 1.17e+01 bond pdb=" N VAL B 212 " pdb=" CA VAL B 212 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.10e+01 ... (remaining 7397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 9472 1.97 - 3.94: 705 3.94 - 5.91: 32 5.91 - 7.89: 3 7.89 - 9.86: 4 Bond angle restraints: 10216 Sorted by residual: angle pdb=" N SER B 955 " pdb=" CA SER B 955 " pdb=" C SER B 955 " ideal model delta sigma weight residual 113.97 108.48 5.49 1.28e+00 6.10e-01 1.84e+01 angle pdb=" C ASN B 885 " pdb=" CA ASN B 885 " pdb=" CB ASN B 885 " ideal model delta sigma weight residual 116.54 111.96 4.58 1.15e+00 7.56e-01 1.59e+01 angle pdb=" N LEU B 717 " pdb=" CA LEU B 717 " pdb=" C LEU B 717 " ideal model delta sigma weight residual 114.31 109.18 5.13 1.29e+00 6.01e-01 1.58e+01 angle pdb=" CA VAL A 126 " pdb=" C VAL A 126 " pdb=" O VAL A 126 " ideal model delta sigma weight residual 121.63 117.75 3.88 9.90e-01 1.02e+00 1.54e+01 angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 ... (remaining 10211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 3856 15.78 - 31.56: 237 31.56 - 47.33: 59 47.33 - 63.11: 21 63.11 - 78.89: 2 Dihedral angle restraints: 4175 sinusoidal: 890 harmonic: 3285 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 93.00 157.91 -64.91 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CA THR A 447 " pdb=" C THR A 447 " pdb=" N LEU A 448 " pdb=" CA LEU A 448 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LEU A 53 " pdb=" C LEU A 53 " pdb=" N PHE A 54 " pdb=" CA PHE A 54 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 814 0.054 - 0.107: 282 0.107 - 0.161: 122 0.161 - 0.215: 49 0.215 - 0.268: 1 Chirality restraints: 1268 Sorted by residual: 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 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE B 41 " pdb=" N ILE B 41 " pdb=" C ILE B 41 " pdb=" CB ILE B 41 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA VAL B 850 " pdb=" N VAL B 850 " pdb=" C VAL B 850 " pdb=" CB VAL B 850 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1265 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " -0.434 9.50e-02 1.11e+02 1.95e-01 2.33e+01 pdb=" NE ARG B 134 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 117 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C GLU B 117 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU B 117 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 118 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 132 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C GLY B 132 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY B 132 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 133 " -0.011 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2481 2.83 - 3.35: 6380 3.35 - 3.87: 11245 3.87 - 4.38: 11631 4.38 - 4.90: 20853 Nonbonded interactions: 52590 Sorted by model distance: nonbonded pdb=" O SER A 96 " pdb=" N TYR A 107 " model vdw 2.316 3.120 nonbonded pdb=" OG1 THR A 247 " pdb=" O SER A 250 " model vdw 2.403 3.040 nonbonded pdb=" N LEU A 109 " pdb=" O VAL A 126 " model vdw 2.410 3.120 nonbonded pdb=" OG SER A 250 " pdb=" O LEU A 448 " model vdw 2.414 3.040 nonbonded pdb=" N SER B 955 " pdb=" O ALA B 968 " model vdw 2.443 3.120 ... (remaining 52585 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: 3.210 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: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.008 0.106 7403 Z= 0.607 Angle : 1.015 9.856 10218 Z= 0.716 Chirality : 0.070 0.268 1268 Planarity : 0.006 0.195 1319 Dihedral : 12.768 78.888 2040 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.59 % Allowed : 20.28 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.84 (0.25), residues: 1088 helix: 0.06 (0.44), residues: 142 sheet: -1.26 (0.24), residues: 449 loop : -1.44 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 464 HIS 0.005 0.001 HIS A 259 PHE 0.021 0.002 PHE D 19 TYR 0.024 0.001 TYR B 913 ARG 0.006 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.23680 ( 322) hydrogen bonds : angle 9.50797 ( 882) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.58744 ( 2) covalent geometry : bond 0.00833 ( 7402) covalent geometry : angle 1.01512 (10216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.7598 (m100) cc_final: 0.7303 (m100) REVERT: A 114 PHE cc_start: 0.8289 (t80) cc_final: 0.8076 (t80) REVERT: B 990 GLN cc_start: 0.9265 (mt0) cc_final: 0.9057 (mp10) outliers start: 8 outliers final: 1 residues processed: 133 average time/residue: 0.1531 time to fit residues: 29.2933 Evaluate side-chains 103 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.098923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083196 restraints weight = 25832.144| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.82 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7403 Z= 0.110 Angle : 0.520 8.110 10218 Z= 0.273 Chirality : 0.044 0.139 1268 Planarity : 0.003 0.028 1319 Dihedral : 5.537 53.695 1172 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.38 % Allowed : 21.27 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.14 (0.25), residues: 1088 helix: 1.28 (0.46), residues: 143 sheet: -0.91 (0.24), residues: 463 loop : -1.09 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 112 HIS 0.004 0.001 HIS A 514 PHE 0.018 0.001 PHE B 323 TYR 0.020 0.001 TYR A 226 ARG 0.002 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 322) hydrogen bonds : angle 6.53949 ( 882) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.39395 ( 2) covalent geometry : bond 0.00216 ( 7402) covalent geometry : angle 0.52031 (10216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 473 ASP cc_start: 0.7921 (p0) cc_final: 0.7586 (p0) REVERT: A 548 TRP cc_start: 0.8239 (m100) cc_final: 0.7097 (m100) REVERT: B 326 SER cc_start: 0.8824 (t) cc_final: 0.8083 (p) REVERT: B 732 CYS cc_start: 0.8704 (m) cc_final: 0.8417 (t) REVERT: B 733 PHE cc_start: 0.8874 (m-80) cc_final: 0.8472 (m-80) outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.1263 time to fit residues: 24.0441 Evaluate side-chains 110 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 866 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.096473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.081409 restraints weight = 26381.126| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 4.52 r_work: 0.3242 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7403 Z= 0.158 Angle : 0.509 7.945 10218 Z= 0.268 Chirality : 0.044 0.128 1268 Planarity : 0.003 0.032 1319 Dihedral : 5.423 51.476 1172 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.77 % Allowed : 20.08 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.77 (0.26), residues: 1088 helix: 1.98 (0.47), residues: 134 sheet: -0.77 (0.25), residues: 459 loop : -0.83 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 464 HIS 0.005 0.001 HIS A 514 PHE 0.011 0.001 PHE B1097 TYR 0.012 0.001 TYR B 913 ARG 0.003 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 322) hydrogen bonds : angle 5.82575 ( 882) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.42270 ( 2) covalent geometry : bond 0.00324 ( 7402) covalent geometry : angle 0.50885 (10216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.914 Fit side-chains REVERT: A 473 ASP cc_start: 0.8505 (p0) cc_final: 0.8040 (p0) REVERT: A 548 TRP cc_start: 0.8097 (m100) cc_final: 0.6895 (m100) REVERT: B 183 GLN cc_start: 0.7877 (pp30) cc_final: 0.7647 (pm20) REVERT: B 733 PHE cc_start: 0.9018 (m-80) cc_final: 0.8772 (m-80) REVERT: B 1093 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8765 (tt) REVERT: B 1096 SER cc_start: 0.9488 (m) cc_final: 0.9258 (p) outliers start: 29 outliers final: 22 residues processed: 121 average time/residue: 0.1163 time to fit residues: 22.3351 Evaluate side-chains 115 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.091906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075931 restraints weight = 27663.177| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.88 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7403 Z= 0.353 Angle : 0.665 8.639 10218 Z= 0.361 Chirality : 0.046 0.154 1268 Planarity : 0.004 0.055 1319 Dihedral : 6.327 54.782 1172 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.96 % Allowed : 20.48 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.98 (0.25), residues: 1088 helix: 1.81 (0.47), residues: 134 sheet: -0.77 (0.25), residues: 439 loop : -1.13 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 562 HIS 0.008 0.002 HIS A 514 PHE 0.020 0.002 PHE B1097 TYR 0.018 0.002 TYR B 193 ARG 0.004 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 322) hydrogen bonds : angle 6.32043 ( 882) SS BOND : bond 0.00486 ( 1) SS BOND : angle 0.65519 ( 2) covalent geometry : bond 0.00728 ( 7402) covalent geometry : angle 0.66533 (10216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.777 Fit side-chains REVERT: A 473 ASP cc_start: 0.8320 (p0) cc_final: 0.7868 (p0) REVERT: A 548 TRP cc_start: 0.8284 (m100) cc_final: 0.7225 (m100) REVERT: B 183 GLN cc_start: 0.8027 (pp30) cc_final: 0.7443 (pm20) outliers start: 35 outliers final: 27 residues processed: 115 average time/residue: 0.1100 time to fit residues: 20.1577 Evaluate side-chains 107 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.093599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.077988 restraints weight = 26787.502| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.79 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7403 Z= 0.121 Angle : 0.500 7.288 10218 Z= 0.261 Chirality : 0.044 0.137 1268 Planarity : 0.003 0.041 1319 Dihedral : 5.504 48.459 1172 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.97 % Allowed : 23.26 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.73 (0.26), residues: 1088 helix: 2.10 (0.48), residues: 135 sheet: -0.58 (0.26), residues: 435 loop : -1.03 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 562 HIS 0.007 0.001 HIS A 514 PHE 0.012 0.001 PHE B1030 TYR 0.014 0.001 TYR B 5 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02853 ( 322) hydrogen bonds : angle 5.55237 ( 882) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.42314 ( 2) covalent geometry : bond 0.00249 ( 7402) covalent geometry : angle 0.49983 (10216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.780 Fit side-chains REVERT: A 267 CYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7761 (p) REVERT: A 268 GLN cc_start: 0.8393 (mp10) cc_final: 0.7932 (mp10) REVERT: A 473 ASP cc_start: 0.8450 (p0) cc_final: 0.7963 (p0) REVERT: A 548 TRP cc_start: 0.8239 (m100) cc_final: 0.7099 (m100) REVERT: B 183 GLN cc_start: 0.7827 (pp30) cc_final: 0.7598 (pm20) REVERT: B 207 TRP cc_start: 0.8965 (OUTLIER) cc_final: 0.8567 (p-90) outliers start: 25 outliers final: 17 residues processed: 112 average time/residue: 0.1126 time to fit residues: 20.0731 Evaluate side-chains 104 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.089366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074046 restraints weight = 27613.168| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.73 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7403 Z= 0.315 Angle : 0.614 7.104 10218 Z= 0.332 Chirality : 0.046 0.149 1268 Planarity : 0.004 0.032 1319 Dihedral : 6.136 53.109 1172 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 7.95 % Allowed : 21.47 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.99 (0.25), residues: 1088 helix: 1.92 (0.47), residues: 134 sheet: -0.70 (0.26), residues: 431 loop : -1.26 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 562 HIS 0.009 0.001 HIS A 514 PHE 0.018 0.002 PHE B1097 TYR 0.019 0.002 TYR A 226 ARG 0.004 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 322) hydrogen bonds : angle 5.99823 ( 882) SS BOND : bond 0.00279 ( 1) SS BOND : angle 0.64660 ( 2) covalent geometry : bond 0.00656 ( 7402) covalent geometry : angle 0.61372 (10216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.860 Fit side-chains REVERT: A 226 TYR cc_start: 0.8712 (t80) cc_final: 0.8297 (t80) REVERT: A 267 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7545 (p) REVERT: A 268 GLN cc_start: 0.8388 (mp10) cc_final: 0.7881 (mp10) REVERT: A 473 ASP cc_start: 0.8419 (p0) cc_final: 0.8054 (p0) REVERT: B 207 TRP cc_start: 0.9002 (OUTLIER) cc_final: 0.8657 (p-90) outliers start: 40 outliers final: 32 residues processed: 108 average time/residue: 0.1179 time to fit residues: 20.4147 Evaluate side-chains 109 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 737 SER Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.093488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077882 restraints weight = 26963.781| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.81 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7403 Z= 0.110 Angle : 0.500 7.029 10218 Z= 0.258 Chirality : 0.045 0.131 1268 Planarity : 0.003 0.051 1319 Dihedral : 5.326 45.582 1172 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.57 % Allowed : 25.84 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.74 (0.26), residues: 1088 helix: 2.15 (0.48), residues: 134 sheet: -0.49 (0.26), residues: 428 loop : -1.15 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 562 HIS 0.005 0.001 HIS A 514 PHE 0.014 0.001 PHE B1030 TYR 0.016 0.001 TYR A 226 ARG 0.002 0.000 ARG B 739 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 322) hydrogen bonds : angle 5.30321 ( 882) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.49216 ( 2) covalent geometry : bond 0.00236 ( 7402) covalent geometry : angle 0.50041 (10216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.820 Fit side-chains REVERT: A 226 TYR cc_start: 0.8686 (t80) cc_final: 0.8296 (t80) REVERT: A 473 ASP cc_start: 0.8439 (p0) cc_final: 0.7933 (p0) REVERT: A 548 TRP cc_start: 0.8229 (m100) cc_final: 0.7122 (m100) REVERT: A 558 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8759 (tpt) REVERT: B 207 TRP cc_start: 0.9003 (OUTLIER) cc_final: 0.8631 (p-90) REVERT: B 990 GLN cc_start: 0.8704 (mp10) cc_final: 0.8473 (mp10) outliers start: 23 outliers final: 18 residues processed: 109 average time/residue: 0.1328 time to fit residues: 22.9316 Evaluate side-chains 104 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1047 TRP Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 4 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.094302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078609 restraints weight = 27061.336| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.86 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7403 Z= 0.105 Angle : 0.492 6.919 10218 Z= 0.254 Chirality : 0.044 0.150 1268 Planarity : 0.003 0.030 1319 Dihedral : 4.953 41.061 1172 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.37 % Allowed : 24.65 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.63 (0.26), residues: 1088 helix: 2.29 (0.48), residues: 134 sheet: -0.42 (0.26), residues: 428 loop : -1.09 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 562 HIS 0.004 0.001 HIS A 514 PHE 0.014 0.001 PHE B1030 TYR 0.016 0.001 TYR A 226 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02568 ( 322) hydrogen bonds : angle 5.01190 ( 882) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.53975 ( 2) covalent geometry : bond 0.00221 ( 7402) covalent geometry : angle 0.49222 (10216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.020 Fit side-chains REVERT: A 267 CYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7591 (p) REVERT: A 473 ASP cc_start: 0.8524 (p0) cc_final: 0.8034 (p0) REVERT: A 548 TRP cc_start: 0.8230 (m100) cc_final: 0.7233 (m100) REVERT: B 207 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.8744 (p-90) outliers start: 27 outliers final: 22 residues processed: 115 average time/residue: 0.1200 time to fit residues: 22.3367 Evaluate side-chains 115 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.095298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.079493 restraints weight = 26440.699| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.89 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7403 Z= 0.086 Angle : 0.480 7.346 10218 Z= 0.247 Chirality : 0.044 0.133 1268 Planarity : 0.003 0.045 1319 Dihedral : 4.645 36.737 1172 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.57 % Allowed : 26.04 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.52 (0.26), residues: 1088 helix: 2.22 (0.48), residues: 135 sheet: -0.28 (0.26), residues: 432 loop : -1.05 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 521 HIS 0.003 0.001 HIS A 514 PHE 0.015 0.001 PHE B1030 TYR 0.036 0.001 TYR A 226 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02432 ( 322) hydrogen bonds : angle 4.80544 ( 882) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.52497 ( 2) covalent geometry : bond 0.00184 ( 7402) covalent geometry : angle 0.48017 (10216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.866 Fit side-chains REVERT: A 142 VAL cc_start: 0.9547 (t) cc_final: 0.9313 (p) REVERT: A 267 CYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 473 ASP cc_start: 0.8491 (p0) cc_final: 0.8013 (p0) REVERT: A 548 TRP cc_start: 0.8204 (m100) cc_final: 0.7247 (m100) REVERT: A 562 TRP cc_start: 0.8937 (m100) cc_final: 0.8671 (m100) REVERT: B 207 TRP cc_start: 0.9036 (OUTLIER) cc_final: 0.8735 (p-90) outliers start: 23 outliers final: 20 residues processed: 111 average time/residue: 0.1171 time to fit residues: 20.6816 Evaluate side-chains 112 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 81 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.092957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077269 restraints weight = 27320.119| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.88 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7403 Z= 0.159 Angle : 0.513 10.211 10218 Z= 0.266 Chirality : 0.044 0.145 1268 Planarity : 0.003 0.031 1319 Dihedral : 4.816 38.816 1172 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.37 % Allowed : 24.85 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.48 (0.26), residues: 1088 helix: 2.45 (0.48), residues: 134 sheet: -0.32 (0.26), residues: 427 loop : -1.01 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 562 HIS 0.005 0.001 HIS A 514 PHE 0.011 0.001 PHE B1030 TYR 0.013 0.001 TYR B 5 ARG 0.003 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02746 ( 322) hydrogen bonds : angle 4.96848 ( 882) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.45600 ( 2) covalent geometry : bond 0.00336 ( 7402) covalent geometry : angle 0.51324 (10216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.889 Fit side-chains REVERT: A 142 VAL cc_start: 0.9582 (t) cc_final: 0.9378 (p) REVERT: A 267 CYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7617 (p) REVERT: A 473 ASP cc_start: 0.8510 (p0) cc_final: 0.8171 (p0) REVERT: B 207 TRP cc_start: 0.9069 (OUTLIER) cc_final: 0.8760 (p-90) outliers start: 27 outliers final: 24 residues processed: 106 average time/residue: 0.1198 time to fit residues: 20.1011 Evaluate side-chains 110 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 207 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1047 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 0.0770 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 109 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.4100 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.093798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.078032 restraints weight = 26826.282| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.86 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7403 Z= 0.112 Angle : 0.494 9.760 10218 Z= 0.252 Chirality : 0.044 0.132 1268 Planarity : 0.003 0.041 1319 Dihedral : 4.677 36.534 1172 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.37 % Allowed : 25.05 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.43 (0.26), residues: 1088 helix: 2.39 (0.47), residues: 134 sheet: -0.25 (0.26), residues: 426 loop : -0.99 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 562 HIS 0.004 0.001 HIS A 514 PHE 0.013 0.001 PHE B1030 TYR 0.020 0.001 TYR A 226 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02535 ( 322) hydrogen bonds : angle 4.86986 ( 882) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.40843 ( 2) covalent geometry : bond 0.00239 ( 7402) covalent geometry : angle 0.49355 (10216) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2836.81 seconds wall clock time: 49 minutes 52.78 seconds (2992.78 seconds total)