Starting phenix.real_space_refine on Thu Mar 13 03:16:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmo_7964/03_2025/6dmo_7964.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmo_7964/03_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_7964/03_2025/6dmo_7964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmo_7964/03_2025/6dmo_7964.map" model { file = "/net/cci-nas-00/data/ceres_data/6dmo_7964/03_2025/6dmo_7964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmo_7964/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.75, per 1000 atoms: 0.60 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.83 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: 2.13 Time building geometry restraints manager: 2.34 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.520 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- 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 : 0.823 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: 0.2122 time to fit residues: 90.1083 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 : 0.895 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.110572 restraints weight = 20375.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113667 restraints weight = 12003.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115911 restraints weight = 8215.234| |-----------------------------------------------------------------------------| 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 : 0.779 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: 0.8461 (pttt) cc_final: 0.8093 (tptt) REVERT: A 196 GLN cc_start: 0.7815 (tm-30) cc_final: 0.6870 (tm-30) REVERT: A 373 TYR cc_start: 0.8047 (t80) cc_final: 0.7425 (t80) REVERT: A 476 LEU cc_start: 0.9338 (tt) cc_final: 0.8924 (pp) REVERT: A 791 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 795 PHE cc_start: 0.7438 (m-80) cc_final: 0.7234 (m-80) REVERT: A 971 TYR cc_start: 0.5577 (t80) cc_final: 0.5116 (t80) REVERT: A 1087 ILE cc_start: 0.8181 (mm) cc_final: 0.7891 (mm) REVERT: A 1117 LEU cc_start: 0.8711 (mp) cc_final: 0.8414 (mt) REVERT: A 1178 PHE cc_start: 0.7862 (p90) cc_final: 0.7495 (t80) outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.1773 time to fit residues: 56.9955 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 : 0.772 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.127624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108275 restraints weight = 20600.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.111301 restraints weight = 12296.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.113466 restraints weight = 8468.435| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8044 Z= 0.208 Angle : 0.804 10.842 10937 Z= 0.398 Chirality : 0.047 0.306 1266 Planarity : 0.006 0.067 1364 Dihedral : 7.322 56.829 1208 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 0.24 % Allowed : 5.93 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.42 (0.27), residues: 976 helix: 0.43 (0.22), residues: 542 sheet: -1.82 (0.76), residues: 51 loop : -2.92 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 926 HIS 0.004 0.001 HIS A 178 PHE 0.029 0.002 PHE A 790 TYR 0.016 0.001 TYR A 224 ARG 0.005 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 213 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.793 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: 0.8082 (tptt) REVERT: A 103 VAL cc_start: 0.7471 (t) cc_final: 0.7149 (p) REVERT: A 373 TYR cc_start: 0.8012 (t80) cc_final: 0.7275 (t80) REVERT: A 423 THR cc_start: 0.7381 (p) cc_final: 0.7166 (t) REVERT: A 791 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8413 (mp) REVERT: A 795 PHE cc_start: 0.7469 (m-10) cc_final: 0.7235 (m-80) REVERT: A 1066 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 1087 ILE cc_start: 0.8167 (mm) cc_final: 0.7878 (mm) REVERT: A 1162 LEU cc_start: 0.8513 (tp) cc_final: 0.8275 (tp) outliers start: 2 outliers final: 0 residues processed: 213 average time/residue: 0.1838 time to fit residues: 54.2455 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 : 0.901 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 466 GLN A 802 ASN A 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.126749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.107839 restraints weight = 20689.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110894 restraints weight = 12442.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.113096 restraints weight = 8574.229| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8044 Z= 0.205 Angle : 0.778 8.724 10937 Z= 0.387 Chirality : 0.047 0.277 1266 Planarity : 0.005 0.069 1364 Dihedral : 6.906 59.706 1208 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.12 % Allowed : 3.39 % Favored : 96.49 % 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: -1.19 (0.27), residues: 976 helix: 0.69 (0.22), residues: 538 sheet: -1.94 (0.73), residues: 51 loop : -2.87 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 129 HIS 0.009 0.001 HIS A 358 PHE 0.025 0.002 PHE A 790 TYR 0.014 0.001 TYR A 191 ARG 0.004 0.000 ARG A 772 *********************** 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 213 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8306 (pttt) cc_final: 0.8065 (tptt) REVERT: A 93 TYR cc_start: 0.8496 (t80) cc_final: 0.8194 (t80) REVERT: A 103 VAL cc_start: 0.7567 (t) cc_final: 0.7286 (p) REVERT: A 292 MET cc_start: 0.4343 (mmp) cc_final: 0.3172 (mmp) REVERT: A 373 TYR cc_start: 0.7981 (t80) cc_final: 0.7306 (t80) REVERT: A 423 THR cc_start: 0.7553 (p) cc_final: 0.7224 (t) REVERT: A 432 LYS cc_start: 0.8282 (tppt) cc_final: 0.7884 (tppt) REVERT: A 791 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 1056 ILE cc_start: 0.8485 (mm) cc_final: 0.8090 (mm) REVERT: A 1066 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 1087 ILE cc_start: 0.8009 (mm) cc_final: 0.7769 (mm) REVERT: A 1097 THR cc_start: 0.8417 (p) cc_final: 0.8011 (p) REVERT: A 1162 LEU cc_start: 0.8614 (tp) cc_final: 0.8305 (tp) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1809 time to fit residues: 53.7282 Evaluate side-chains 155 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 78 optimal weight: 0.0270 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 73 optimal weight: 0.0980 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.125035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106067 restraints weight = 20498.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109006 restraints weight = 12280.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111132 restraints weight = 8537.536| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8044 Z= 0.217 Angle : 0.756 9.422 10937 Z= 0.376 Chirality : 0.046 0.246 1266 Planarity : 0.005 0.069 1364 Dihedral : 6.581 49.228 1208 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.12 % Allowed : 3.27 % Favored : 96.61 % 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: -0.94 (0.28), residues: 976 helix: 0.90 (0.22), residues: 538 sheet: -1.92 (0.74), residues: 51 loop : -2.75 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 129 HIS 0.004 0.001 HIS A 178 PHE 0.029 0.002 PHE A 795 TYR 0.016 0.002 TYR A 934 ARG 0.002 0.000 ARG A 401 *********************** 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 198 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8348 (pttt) cc_final: 0.8042 (tptt) REVERT: A 103 VAL cc_start: 0.7706 (t) cc_final: 0.7415 (p) REVERT: A 191 TYR cc_start: 0.7560 (m-80) cc_final: 0.7211 (m-10) REVERT: A 373 TYR cc_start: 0.7971 (t80) cc_final: 0.7279 (t80) REVERT: A 432 LYS cc_start: 0.8335 (tppt) cc_final: 0.7939 (tppt) REVERT: A 992 GLU cc_start: 0.8338 (pt0) cc_final: 0.7931 (pp20) REVERT: A 1056 ILE cc_start: 0.8553 (mm) cc_final: 0.8193 (mm) REVERT: A 1087 ILE cc_start: 0.8135 (mm) cc_final: 0.7905 (mm) REVERT: A 1097 THR cc_start: 0.8529 (p) cc_final: 0.8133 (p) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1849 time to fit residues: 50.8361 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 : 0.858 ------------------------------------------------------------------------------- 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: 8.9990 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 51 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1044 ------------------------------------------------------------------------------- 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 520 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.122885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.103362 restraints weight = 20620.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106447 restraints weight = 11982.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.108535 restraints weight = 8206.630| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.6671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8044 Z= 0.211 Angle : 0.765 13.496 10937 Z= 0.374 Chirality : 0.047 0.442 1266 Planarity : 0.005 0.070 1364 Dihedral : 6.425 55.006 1208 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % 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: -0.84 (0.28), residues: 976 helix: 0.93 (0.22), residues: 544 sheet: -1.92 (0.74), residues: 51 loop : -2.66 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 129 HIS 0.004 0.001 HIS A 178 PHE 0.023 0.002 PHE A 790 TYR 0.015 0.001 TYR A 446 ARG 0.003 0.000 ARG A 906 *********************** 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 183 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.813 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: 0.8404 (pttt) cc_final: 0.8038 (tptt) REVERT: A 103 VAL cc_start: 0.7710 (t) cc_final: 0.7430 (p) REVERT: A 191 TYR cc_start: 0.7443 (m-80) cc_final: 0.7234 (m-10) REVERT: A 281 MET cc_start: 0.7799 (mtp) cc_final: 0.7544 (mtp) REVERT: A 822 LEU cc_start: 0.9069 (tt) cc_final: 0.8860 (tt) REVERT: A 1139 MET cc_start: 0.8575 (pmm) cc_final: 0.7634 (ptm) REVERT: A 1146 ASP cc_start: 0.6945 (t0) cc_final: 0.6642 (t0) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1731 time to fit residues: 44.9530 Evaluate side-chains 137 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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: 0.0030 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 2 optimal weight: 0.0000 chunk 88 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 871 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.123252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.104179 restraints weight = 20462.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107248 restraints weight = 11809.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.109377 restraints weight = 8015.172| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.7022 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= 0.189 Angle : 0.750 11.148 10937 Z= 0.365 Chirality : 0.047 0.337 1266 Planarity : 0.005 0.073 1364 Dihedral : 6.217 52.887 1208 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % 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: -0.75 (0.28), residues: 976 helix: 1.00 (0.23), residues: 532 sheet: -1.86 (0.74), residues: 51 loop : -2.51 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 129 HIS 0.004 0.001 HIS A 178 PHE 0.020 0.002 PHE A 790 TYR 0.015 0.001 TYR A 934 ARG 0.003 0.000 ARG A 906 *********************** 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 185 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.820 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: 0.8442 (pttt) cc_final: 0.8088 (tptt) REVERT: A 79 LEU cc_start: 0.8808 (tt) cc_final: 0.7822 (tt) REVERT: A 103 VAL cc_start: 0.7636 (t) cc_final: 0.7378 (p) REVERT: A 191 TYR cc_start: 0.7335 (m-80) cc_final: 0.7068 (m-10) REVERT: A 397 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 475 LEU cc_start: 0.8977 (tt) cc_final: 0.8741 (pp) REVERT: A 1139 MET cc_start: 0.8488 (pmm) cc_final: 0.7412 (ptm) REVERT: A 1146 ASP cc_start: 0.7020 (t0) cc_final: 0.6727 (t0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1683 time to fit residues: 44.1722 Evaluate side-chains 134 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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: 0.1980 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 0.0970 chunk 22 optimal weight: 0.0570 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 overall best weight: 0.2454 ------------------------------------------------------------------------------- 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 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.124862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.105736 restraints weight = 20281.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108727 restraints weight = 11907.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.110896 restraints weight = 8183.786| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.7363 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= 0.192 Angle : 0.778 14.713 10937 Z= 0.371 Chirality : 0.046 0.280 1266 Planarity : 0.005 0.070 1364 Dihedral : 5.779 42.789 1208 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -0.82 (0.28), residues: 976 helix: 0.92 (0.23), residues: 536 sheet: -1.87 (0.74), residues: 50 loop : -2.54 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 129 HIS 0.003 0.001 HIS A 178 PHE 0.020 0.002 PHE A 592 TYR 0.012 0.001 TYR A 934 ARG 0.012 0.000 ARG A 960 *********************** 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 188 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 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: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8457 (pttt) cc_final: 0.8200 (tptt) REVERT: A 93 TYR cc_start: 0.8327 (t80) cc_final: 0.8119 (t80) REVERT: A 94 ILE cc_start: 0.9200 (mt) cc_final: 0.8813 (tp) REVERT: A 103 VAL cc_start: 0.7688 (t) cc_final: 0.7451 (p) REVERT: A 191 TYR cc_start: 0.7431 (m-80) cc_final: 0.7147 (m-10) REVERT: A 397 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 475 LEU cc_start: 0.8991 (tt) cc_final: 0.8763 (pp) REVERT: A 561 MET cc_start: 0.7841 (tpt) cc_final: 0.7440 (tpt) REVERT: A 1146 ASP cc_start: 0.7075 (t0) cc_final: 0.6819 (t0) REVERT: A 1162 LEU cc_start: 0.7979 (tp) cc_final: 0.7677 (tp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1582 time to fit residues: 42.9061 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 : 0.850 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 196 GLN A 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.122964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103603 restraints weight = 20567.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106668 restraints weight = 11887.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.108809 restraints weight = 8049.501| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.7688 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 : 0.766 14.539 10937 Z= 0.371 Chirality : 0.047 0.293 1266 Planarity : 0.005 0.072 1364 Dihedral : 5.636 41.968 1208 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.64 (0.28), residues: 976 helix: 1.03 (0.23), residues: 540 sheet: -1.64 (0.75), residues: 50 loop : -2.46 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 129 HIS 0.004 0.001 HIS A 201 PHE 0.024 0.002 PHE A1096 TYR 0.014 0.001 TYR A 452 ARG 0.003 0.000 ARG A 906 *********************** 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 184 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.786 Fit side-chains 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: 0.8182 (tptt) REVERT: A 94 ILE cc_start: 0.9259 (mt) cc_final: 0.8893 (tp) REVERT: A 103 VAL cc_start: 0.7644 (t) cc_final: 0.7415 (p) REVERT: A 191 TYR cc_start: 0.7462 (m-80) cc_final: 0.7108 (m-10) REVERT: A 220 ILE cc_start: 0.5732 (mm) cc_final: 0.5241 (mm) REVERT: A 362 THR cc_start: 0.8310 (t) cc_final: 0.8065 (m) REVERT: A 397 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 475 LEU cc_start: 0.9004 (tt) cc_final: 0.8752 (pp) REVERT: A 561 MET cc_start: 0.7815 (tpt) cc_final: 0.7474 (tpt) REVERT: A 1146 ASP cc_start: 0.7175 (t0) cc_final: 0.6922 (t0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1667 time to fit residues: 44.1350 Evaluate side-chains 138 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 358 HIS A 520 HIS A 739 HIS ** A 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.120781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.101595 restraints weight = 20714.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104592 restraints weight = 12070.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.106705 restraints weight = 8211.185| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.8085 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= 0.217 Angle : 0.778 12.021 10937 Z= 0.381 Chirality : 0.046 0.216 1266 Planarity : 0.005 0.076 1364 Dihedral : 5.796 41.479 1208 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % 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: -0.64 (0.28), residues: 976 helix: 1.08 (0.23), residues: 529 sheet: -1.41 (0.78), residues: 50 loop : -2.47 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 278 HIS 0.004 0.001 HIS A1121 PHE 0.027 0.002 PHE A1096 TYR 0.014 0.001 TYR A 452 ARG 0.003 0.000 ARG A 962 ********************** 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 179 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.883 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 93 TYR cc_start: 0.8252 (t80) cc_final: 0.8002 (t80) REVERT: A 94 ILE cc_start: 0.9236 (mt) cc_final: 0.8853 (tp) REVERT: A 103 VAL cc_start: 0.7723 (t) cc_final: 0.7517 (p) REVERT: A 158 MET cc_start: 0.8046 (tmm) cc_final: 0.7819 (tmm) REVERT: A 191 TYR cc_start: 0.7455 (m-80) cc_final: 0.7078 (m-10) REVERT: A 216 MET cc_start: 0.3386 (tpt) cc_final: 0.2825 (tpp) REVERT: A 397 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 475 LEU cc_start: 0.9000 (tt) cc_final: 0.8766 (pp) REVERT: A 561 MET cc_start: 0.8039 (tpt) cc_final: 0.7611 (tpt) REVERT: A 1146 ASP cc_start: 0.7320 (t0) cc_final: 0.7026 (t0) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1688 time to fit residues: 43.3989 Evaluate side-chains 135 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN ** A 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.120759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.101988 restraints weight = 20763.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.105011 restraints weight = 11833.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.107117 restraints weight = 7965.071| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.8449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8044 Z= 0.217 Angle : 0.791 12.381 10937 Z= 0.384 Chirality : 0.047 0.309 1266 Planarity : 0.005 0.073 1364 Dihedral : 5.431 41.483 1208 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -0.64 (0.28), residues: 976 helix: 1.02 (0.23), residues: 538 sheet: -1.32 (0.78), residues: 50 loop : -2.48 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 278 HIS 0.004 0.001 HIS A 178 PHE 0.027 0.002 PHE A1096 TYR 0.015 0.001 TYR A 452 ARG 0.003 0.000 ARG A 906 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.14 seconds wall clock time: 45 minutes 52.24 seconds (2752.24 seconds total)