Starting phenix.real_space_refine on Thu Feb 13 01:34:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmo_7964/02_2025/6dmo_7964.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmo_7964/02_2025/6dmo_7964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dmo_7964/02_2025/6dmo_7964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmo_7964/02_2025/6dmo_7964.map" model { file = "/net/cci-nas-00/data/ceres_data/6dmo_7964/02_2025/6dmo_7964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmo_7964/02_2025/6dmo_7964.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 764 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5117 2.51 5 N 1284 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7853 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7755 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 939} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.84, per 1000 atoms: 0.62 Number of scatterers: 7853 At special positions: 0 Unit cell: (90.553, 78.552, 142.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1410 8.00 N 1284 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.02 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG B 1 " - " ASN A1000 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 972.2 milliseconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 60.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 74 through 97 removed outlier: 3.595A pdb=" N TRP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.785A pdb=" N PHE A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 216 through 223 removed outlier: 3.598A pdb=" N ILE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.879A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 3.734A pdb=" N ALA A 239 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.867A pdb=" N PHE A 259 " --> pdb=" O TRP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.840A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 389 through 411 removed outlier: 4.270A pdb=" N VAL A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.280A pdb=" N ASP A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 435 No H-bonds generated for 'chain 'A' and resid 434 through 435' Processing helix chain 'A' and resid 436 through 437 No H-bonds generated for 'chain 'A' and resid 436 through 437' Processing helix chain 'A' and resid 438 through 457 Processing helix chain 'A' and resid 466 through 491 removed outlier: 4.131A pdb=" N GLY A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 526 removed outlier: 3.622A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 563 removed outlier: 3.929A pdb=" N THR A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 604 Proline residue: A 593 - end of helix Processing helix chain 'A' and resid 732 through 744 Proline residue: A 742 - end of helix Processing helix chain 'A' and resid 750 through 770 removed outlier: 3.890A pdb=" N ILE A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 815 through 829 removed outlier: 4.100A pdb=" N LEU A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 863 removed outlier: 4.311A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 885 removed outlier: 3.630A pdb=" N VAL A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 882 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 919 through 930 Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.860A pdb=" N TYR A 934 " --> pdb=" O ASP A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1003 removed outlier: 3.612A pdb=" N PHE A 987 " --> pdb=" O ASP A 983 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1019 Processing helix chain 'A' and resid 1026 through 1046 Processing helix chain 'A' and resid 1052 through 1075 removed outlier: 4.015A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1106 removed outlier: 5.137A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1138 removed outlier: 3.716A pdb=" N ALA A1118 " --> pdb=" O ARG A1114 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Proline residue: A1125 - end of helix Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1146 through 1178 removed outlier: 5.043A pdb=" N ALA A1157 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Proline residue: A1172 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 366 removed outlier: 3.931A pdb=" N LEU A 360 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 158 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 156 " --> pdb=" O PHE A 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 removed outlier: 7.165A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.618A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 801 " --> pdb=" O LEU A 978 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1245 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: 2.15 Time building geometry restraints manager: 2.57 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: 2410 1.34 - 1.46: 1907 1.46 - 1.58: 3658 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 8044 Sorted by residual: bond pdb=" C MET A 869 " pdb=" N PRO A 870 " ideal model delta sigma weight residual 1.336 1.370 -0.034 9.80e-03 1.04e+04 1.23e+01 bond pdb=" C1 NAG A1804 " pdb=" O5 NAG A1804 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C PRO A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.83e+00 bond pdb=" C1 NAG A1801 " pdb=" O5 NAG A1801 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" CB PRO A1082 " pdb=" CG PRO A1082 " ideal model delta sigma weight residual 1.492 1.382 0.110 5.00e-02 4.00e+02 4.86e+00 ... (remaining 8039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 10374 2.58 - 5.16: 455 5.16 - 7.74: 82 7.74 - 10.33: 19 10.33 - 12.91: 7 Bond angle restraints: 10937 Sorted by residual: angle pdb=" N TYR A 224 " pdb=" CA TYR A 224 " pdb=" C TYR A 224 " ideal model delta sigma weight residual 109.48 96.78 12.70 1.75e+00 3.27e-01 5.26e+01 angle pdb=" N GLU A 534 " pdb=" CA GLU A 534 " pdb=" C GLU A 534 " ideal model delta sigma weight residual 112.72 106.95 5.77 1.28e+00 6.10e-01 2.04e+01 angle pdb=" C PHE A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta sigma weight residual 121.80 132.76 -10.96 2.44e+00 1.68e-01 2.02e+01 angle pdb=" N ILE A 219 " pdb=" CA ILE A 219 " pdb=" C ILE A 219 " ideal model delta sigma weight residual 111.05 116.54 -5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" CG1 ILE A 815 " pdb=" CB ILE A 815 " pdb=" CG2 ILE A 815 " ideal model delta sigma weight residual 110.70 97.79 12.91 3.00e+00 1.11e-01 1.85e+01 ... (remaining 10932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4419 17.81 - 35.62: 323 35.62 - 53.43: 78 53.43 - 71.23: 9 71.23 - 89.04: 11 Dihedral angle restraints: 4840 sinusoidal: 1974 harmonic: 2866 Sorted by residual: dihedral pdb=" CA ASN A1049 " pdb=" C ASN A1049 " pdb=" N PRO A1050 " pdb=" CA PRO A1050 " ideal model delta harmonic sigma weight residual 180.00 -124.52 -55.48 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 -177.96 -89.04 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CA LYS A 867 " pdb=" C LYS A 867 " pdb=" N ILE A 868 " pdb=" CA ILE A 868 " ideal model delta harmonic sigma weight residual -180.00 -131.82 -48.18 0 5.00e+00 4.00e-02 9.28e+01 ... (remaining 4837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 960 0.067 - 0.135: 255 0.135 - 0.202: 43 0.202 - 0.270: 6 0.270 - 0.337: 2 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CB ILE A 531 " pdb=" CA ILE A 531 " pdb=" CG1 ILE A 531 " pdb=" CG2 ILE A 531 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE A 815 " pdb=" CA ILE A 815 " pdb=" CG1 ILE A 815 " pdb=" CG2 ILE A 815 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.79e+00 ... (remaining 1263 not shown) Planarity restraints: 1370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1049 " 0.051 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO A1050 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1050 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1050 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 741 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO A 742 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 742 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 742 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1165 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C LEU A1165 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A1165 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A1166 " -0.015 2.00e-02 2.50e+03 ... (remaining 1367 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 21 2.39 - 3.02: 4207 3.02 - 3.65: 12274 3.65 - 4.27: 16593 4.27 - 4.90: 26909 Nonbonded interactions: 60004 Sorted by model distance: nonbonded pdb=" O ASN A 120 " pdb=" OG SER A 494 " model vdw 1.764 3.040 nonbonded pdb=" O GLU A 864 " pdb=" CG2 THR A 865 " model vdw 2.038 3.460 nonbonded pdb=" O ALA A 939 " pdb=" CD1 ILE A 941 " model vdw 2.276 3.460 nonbonded pdb=" OE1 GLN A 400 " pdb=" OG1 THR A 425 " model vdw 2.280 3.040 nonbonded pdb=" O ASN A 154 " pdb=" NE2 GLN A 156 " model vdw 2.285 3.120 ... (remaining 59999 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 group one per residue 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 24.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 0.110 8044 Z= 0.502 Angle : 1.271 12.908 10937 Z= 0.656 Chirality : 0.063 0.337 1266 Planarity : 0.009 0.078 1364 Dihedral : 13.720 82.995 2987 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.07 % Favored : 88.63 % Rotamer: Outliers : 2.78 % Allowed : 10.77 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.21 % 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: -4.11 (0.21), residues: 976 helix: -2.12 (0.17), residues: 553 sheet: -2.15 (0.71), residues: 47 loop : -3.63 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 399 HIS 0.020 0.003 HIS A1099 PHE 0.037 0.004 PHE A1153 TYR 0.035 0.003 TYR A 812 ARG 0.010 0.002 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8126 (pttt) cc_final: 0.7917 (tptt) REVERT: A 86 LEU cc_start: 0.8533 (mt) cc_final: 0.8271 (tp) REVERT: A 94 ILE cc_start: 0.8773 (mt) cc_final: 0.8545 (tp) REVERT: A 172 THR cc_start: 0.7547 (p) cc_final: 0.7152 (p) REVERT: A 254 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6163 (tm) REVERT: A 319 MET cc_start: 0.7461 (mpm) cc_final: 0.7065 (mmm) REVERT: A 373 TYR cc_start: 0.8123 (t80) cc_final: 0.7571 (t80) REVERT: A 430 ILE cc_start: 0.8330 (mm) cc_final: 0.8116 (pt) REVERT: A 791 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 1087 ILE cc_start: 0.8253 (mm) cc_final: 0.8041 (mm) REVERT: A 1105 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7614 (tm) REVERT: A 1166 ASN cc_start: 0.8414 (t0) cc_final: 0.8050 (t0) REVERT: A 1178 PHE cc_start: 0.7848 (p90) cc_final: 0.7575 (t80) outliers start: 23 outliers final: 4 residues processed: 316 average time/residue: 0.2174 time to fit residues: 91.2156 Evaluate side-chains 201 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.0000 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 289 HIS A 358 HIS ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 802 ASN A 853 GLN A 929 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.129904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.110573 restraints weight = 20375.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113669 restraints weight = 12003.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115921 restraints weight = 8214.803| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8044 Z= 0.234 Angle : 0.864 9.622 10937 Z= 0.427 Chirality : 0.051 0.531 1266 Planarity : 0.006 0.064 1364 Dihedral : 7.873 54.394 1208 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.11 % 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: -2.17 (0.26), residues: 976 helix: -0.25 (0.21), residues: 548 sheet: -1.82 (0.78), residues: 51 loop : -3.23 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 129 HIS 0.009 0.001 HIS A 178 PHE 0.036 0.002 PHE A 790 TYR 0.025 0.002 TYR A 224 ARG 0.006 0.001 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8462 (pttt) cc_final: 0.8093 (tptt) REVERT: A 196 GLN cc_start: 0.7811 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 373 TYR cc_start: 0.8052 (t80) cc_final: 0.7429 (t80) REVERT: A 476 LEU cc_start: 0.9339 (tt) cc_final: 0.8924 (pp) REVERT: A 791 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 795 PHE cc_start: 0.7437 (m-80) cc_final: 0.7232 (m-80) REVERT: A 971 TYR cc_start: 0.5573 (t80) cc_final: 0.5115 (t80) REVERT: A 1087 ILE cc_start: 0.8179 (mm) cc_final: 0.7891 (mm) REVERT: A 1117 LEU cc_start: 0.8711 (mp) cc_final: 0.8412 (mt) REVERT: A 1178 PHE cc_start: 0.7863 (p90) cc_final: 0.7495 (t80) outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.1943 time to fit residues: 62.3938 Evaluate side-chains 166 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 160 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN A 915 ASN A 950 HIS A1166 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.127180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107864 restraints weight = 20618.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110888 restraints weight = 12307.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.113042 restraints weight = 8501.864| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8044 Z= 0.221 Angle : 0.800 11.888 10937 Z= 0.396 Chirality : 0.047 0.297 1266 Planarity : 0.006 0.067 1364 Dihedral : 7.321 57.792 1208 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 0.24 % Allowed : 5.33 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % 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: -1.43 (0.27), residues: 976 helix: 0.42 (0.22), residues: 542 sheet: -1.77 (0.78), residues: 51 loop : -2.92 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 926 HIS 0.005 0.001 HIS A 178 PHE 0.030 0.002 PHE A 790 TYR 0.015 0.001 TYR A 224 ARG 0.004 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8355 (pttt) cc_final: 0.8085 (tptt) REVERT: A 103 VAL cc_start: 0.7487 (t) cc_final: 0.7166 (p) REVERT: A 373 TYR cc_start: 0.8015 (t80) cc_final: 0.7263 (t80) REVERT: A 423 THR cc_start: 0.7433 (p) cc_final: 0.7212 (t) REVERT: A 475 LEU cc_start: 0.9005 (tt) cc_final: 0.8804 (pp) REVERT: A 791 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 795 PHE cc_start: 0.7523 (m-10) cc_final: 0.7302 (m-80) REVERT: A 1066 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 1087 ILE cc_start: 0.8101 (mm) cc_final: 0.7841 (mm) REVERT: A 1162 LEU cc_start: 0.8522 (tp) cc_final: 0.8301 (tp) outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.1785 time to fit residues: 52.4505 Evaluate side-chains 161 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 915 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.121683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102733 restraints weight = 20746.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105667 restraints weight = 12216.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107735 restraints weight = 8351.425| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8044 Z= 0.246 Angle : 0.802 9.039 10937 Z= 0.404 Chirality : 0.048 0.274 1266 Planarity : 0.005 0.071 1364 Dihedral : 6.932 56.167 1208 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % 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: -1.22 (0.27), residues: 976 helix: 0.62 (0.22), residues: 546 sheet: -1.76 (0.76), residues: 51 loop : -2.91 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 129 HIS 0.006 0.001 HIS A 358 PHE 0.028 0.002 PHE A 790 TYR 0.010 0.002 TYR A 204 ARG 0.004 0.000 ARG A 962 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8519 (pttt) cc_final: 0.8122 (tptt) REVERT: A 103 VAL cc_start: 0.7615 (t) cc_final: 0.7333 (p) REVERT: A 192 MET cc_start: 0.5494 (ttp) cc_final: 0.5087 (ttp) REVERT: A 292 MET cc_start: 0.4926 (mmp) cc_final: 0.3830 (mmp) REVERT: A 432 LYS cc_start: 0.8358 (tppt) cc_final: 0.7957 (tppt) REVERT: A 475 LEU cc_start: 0.9013 (tt) cc_final: 0.8761 (pp) REVERT: A 791 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8590 (mp) REVERT: A 1066 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 1068 PHE cc_start: 0.7761 (t80) cc_final: 0.7262 (t80) REVERT: A 1077 LYS cc_start: 0.7520 (mttp) cc_final: 0.6372 (mttp) REVERT: A 1087 ILE cc_start: 0.8318 (mm) cc_final: 0.8076 (mm) REVERT: A 1146 ASP cc_start: 0.7006 (t0) cc_final: 0.6761 (t0) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.1743 time to fit residues: 49.4587 Evaluate side-chains 153 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 0.0470 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN A 871 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.119652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.100753 restraints weight = 20633.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103634 restraints weight = 12197.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.105672 restraints weight = 8371.962| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8044 Z= 0.225 Angle : 0.780 9.757 10937 Z= 0.387 Chirality : 0.048 0.315 1266 Planarity : 0.005 0.070 1364 Dihedral : 6.287 46.545 1208 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.12 % Allowed : 3.75 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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 (0.27), residues: 976 helix: 0.79 (0.22), residues: 549 sheet: -1.73 (0.75), residues: 51 loop : -2.78 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 129 HIS 0.004 0.001 HIS A 178 PHE 0.037 0.002 PHE A 795 TYR 0.015 0.001 TYR A 873 ARG 0.004 0.000 ARG A 772 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8491 (pttt) cc_final: 0.8213 (tptt) REVERT: A 103 VAL cc_start: 0.7702 (t) cc_final: 0.7456 (p) REVERT: A 372 MET cc_start: 0.7842 (ttm) cc_final: 0.7614 (ttm) REVERT: A 432 LYS cc_start: 0.8311 (tppt) cc_final: 0.7927 (tppt) REVERT: A 475 LEU cc_start: 0.9065 (tt) cc_final: 0.8775 (pp) REVERT: A 1146 ASP cc_start: 0.7197 (t0) cc_final: 0.6892 (t0) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.1751 time to fit residues: 47.8445 Evaluate side-chains 139 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.119188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100449 restraints weight = 20501.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103445 restraints weight = 11686.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.105481 restraints weight = 7908.104| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8044 Z= 0.205 Angle : 0.757 9.245 10937 Z= 0.372 Chirality : 0.046 0.231 1266 Planarity : 0.005 0.069 1364 Dihedral : 6.085 45.532 1208 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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 (0.28), residues: 976 helix: 0.97 (0.22), residues: 541 sheet: -1.47 (0.78), residues: 51 loop : -2.66 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 129 HIS 0.005 0.001 HIS A1121 PHE 0.020 0.002 PHE A1096 TYR 0.013 0.001 TYR A 873 ARG 0.002 0.000 ARG A 960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8890 (tt) cc_final: 0.7910 (tt) REVERT: A 103 VAL cc_start: 0.7744 (t) cc_final: 0.7542 (p) REVERT: A 475 LEU cc_start: 0.9031 (tt) cc_final: 0.8803 (pp) REVERT: A 561 MET cc_start: 0.7823 (tpt) cc_final: 0.7568 (tpt) REVERT: A 592 PHE cc_start: 0.6819 (m-80) cc_final: 0.6585 (m-80) REVERT: A 992 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 1068 PHE cc_start: 0.7548 (t80) cc_final: 0.7050 (t80) REVERT: A 1146 ASP cc_start: 0.7309 (t0) cc_final: 0.6987 (t0) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1799 time to fit residues: 48.7400 Evaluate side-chains 141 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.119746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.100834 restraints weight = 20719.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.103799 restraints weight = 11874.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105886 restraints weight = 8080.350| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.7494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8044 Z= 0.193 Angle : 0.752 10.834 10937 Z= 0.369 Chirality : 0.046 0.211 1266 Planarity : 0.005 0.073 1364 Dihedral : 5.892 43.860 1208 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.28), residues: 976 helix: 0.93 (0.22), residues: 535 sheet: -1.48 (0.77), residues: 51 loop : -2.58 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 844 HIS 0.005 0.001 HIS A 823 PHE 0.022 0.002 PHE A 826 TYR 0.013 0.001 TYR A 452 ARG 0.003 0.000 ARG A 960 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8830 (tt) cc_final: 0.7825 (tt) REVERT: A 103 VAL cc_start: 0.7635 (t) cc_final: 0.7398 (p) REVERT: A 158 MET cc_start: 0.8071 (tmm) cc_final: 0.7473 (tmm) REVERT: A 281 MET cc_start: 0.7876 (mtp) cc_final: 0.7614 (mtp) REVERT: A 475 LEU cc_start: 0.9045 (tt) cc_final: 0.8780 (pp) REVERT: A 1068 PHE cc_start: 0.7552 (t80) cc_final: 0.7102 (t80) REVERT: A 1146 ASP cc_start: 0.7339 (t0) cc_final: 0.7073 (t0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1752 time to fit residues: 48.9338 Evaluate side-chains 142 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.120540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101588 restraints weight = 20486.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.104594 restraints weight = 11741.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106710 restraints weight = 8006.918| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.7844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8044 Z= 0.203 Angle : 0.771 10.593 10937 Z= 0.377 Chirality : 0.046 0.241 1266 Planarity : 0.005 0.071 1364 Dihedral : 5.762 43.434 1208 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.12 % Allowed : 1.57 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.75 (0.28), residues: 976 helix: 0.99 (0.23), residues: 534 sheet: -1.48 (0.77), residues: 50 loop : -2.58 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 844 HIS 0.005 0.001 HIS A 823 PHE 0.025 0.001 PHE A1096 TYR 0.012 0.001 TYR A 191 ARG 0.007 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8876 (tt) cc_final: 0.8528 (tt) REVERT: A 158 MET cc_start: 0.8038 (tmm) cc_final: 0.7491 (tmm) REVERT: A 585 PHE cc_start: 0.8171 (t80) cc_final: 0.7930 (t80) REVERT: A 795 PHE cc_start: 0.7738 (m-80) cc_final: 0.7417 (m-80) REVERT: A 1068 PHE cc_start: 0.7505 (t80) cc_final: 0.7058 (t80) REVERT: A 1146 ASP cc_start: 0.7364 (t0) cc_final: 0.7098 (t0) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1531 time to fit residues: 42.2682 Evaluate side-chains 140 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.120272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101237 restraints weight = 20791.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104209 restraints weight = 12033.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106310 restraints weight = 8170.180| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8044 Z= 0.210 Angle : 0.779 11.742 10937 Z= 0.381 Chirality : 0.047 0.304 1266 Planarity : 0.005 0.071 1364 Dihedral : 5.714 42.375 1208 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 976 helix: 0.95 (0.22), residues: 528 sheet: -1.35 (0.78), residues: 50 loop : -2.54 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 844 HIS 0.003 0.001 HIS A 823 PHE 0.024 0.002 PHE A1096 TYR 0.009 0.001 TYR A 204 ARG 0.002 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8807 (tt) cc_final: 0.8173 (tt) REVERT: A 94 ILE cc_start: 0.9235 (mt) cc_final: 0.8904 (tp) REVERT: A 158 MET cc_start: 0.8061 (tmm) cc_final: 0.7829 (tmm) REVERT: A 366 LEU cc_start: 0.9344 (mt) cc_final: 0.9062 (mt) REVERT: A 561 MET cc_start: 0.7896 (tpt) cc_final: 0.7566 (tpt) REVERT: A 795 PHE cc_start: 0.7635 (m-80) cc_final: 0.7426 (m-80) REVERT: A 843 MET cc_start: 0.6711 (mmt) cc_final: 0.6030 (mmt) REVERT: A 1068 PHE cc_start: 0.7515 (t80) cc_final: 0.7195 (t80) REVERT: A 1146 ASP cc_start: 0.7266 (t0) cc_final: 0.7019 (t0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1620 time to fit residues: 43.9144 Evaluate side-chains 143 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.120070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.100809 restraints weight = 20881.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103723 restraints weight = 12262.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.105782 restraints weight = 8419.563| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.8491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8044 Z= 0.213 Angle : 0.779 12.020 10937 Z= 0.381 Chirality : 0.047 0.215 1266 Planarity : 0.005 0.075 1364 Dihedral : 5.755 41.814 1208 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % 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: -0.70 (0.28), residues: 976 helix: 1.00 (0.22), residues: 531 sheet: -1.23 (0.79), residues: 50 loop : -2.50 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 844 HIS 0.006 0.001 HIS A 823 PHE 0.023 0.002 PHE A1096 TYR 0.013 0.001 TYR A 193 ARG 0.002 0.000 ARG A 786 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7655 (m-80) cc_final: 0.7447 (m-80) REVERT: A 94 ILE cc_start: 0.9238 (mt) cc_final: 0.8930 (tp) REVERT: A 158 MET cc_start: 0.8106 (tmm) cc_final: 0.7804 (tmm) REVERT: A 366 LEU cc_start: 0.9363 (mt) cc_final: 0.9046 (mt) REVERT: A 475 LEU cc_start: 0.8957 (tt) cc_final: 0.8657 (mp) REVERT: A 1068 PHE cc_start: 0.7509 (t80) cc_final: 0.7135 (t80) REVERT: A 1146 ASP cc_start: 0.7306 (t0) cc_final: 0.7040 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1507 time to fit residues: 39.4356 Evaluate side-chains 143 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 371 GLN A 584 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.118096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099005 restraints weight = 20832.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102023 restraints weight = 11773.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.104156 restraints weight = 7859.134| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.8810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8044 Z= 0.210 Angle : 0.788 12.300 10937 Z= 0.389 Chirality : 0.047 0.286 1266 Planarity : 0.005 0.074 1364 Dihedral : 6.012 46.023 1208 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % 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 (0.27), residues: 976 helix: 0.94 (0.22), residues: 526 sheet: -1.21 (0.79), residues: 50 loop : -2.43 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 844 HIS 0.004 0.001 HIS A 178 PHE 0.038 0.002 PHE A 795 TYR 0.017 0.001 TYR A 193 ARG 0.002 0.000 ARG A 772 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.48 seconds wall clock time: 45 minutes 1.90 seconds (2701.90 seconds total)