Starting phenix.real_space_refine on Sun May 3 04:03:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vcs_64966/05_2026/9vcs_64966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vcs_64966/05_2026/9vcs_64966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vcs_64966/05_2026/9vcs_64966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vcs_64966/05_2026/9vcs_64966.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vcs_64966/05_2026/9vcs_64966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vcs_64966/05_2026/9vcs_64966.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.033 sd= 0.306 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 6522 2.51 5 N 1674 2.21 5 O 1931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10158 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 10158 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 37, 'TRANS': 1207} Chain breaks: 8 Time building chain proxies: 2.54, per 1000 atoms: 0.25 Number of scatterers: 10158 At special positions: 0 Unit cell: (98.889, 111.354, 122.988, 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 31 16.00 O 1931 8.00 N 1674 7.00 C 6522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 378.9 milliseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 33.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.798A pdb=" N THR A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 216 through 233 Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.895A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 299 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.776A pdb=" N MET A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.706A pdb=" N ASN A 410 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET A 411 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 549 through 558 removed outlier: 3.566A pdb=" N TYR A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 601 through 619 removed outlier: 4.594A pdb=" N GLY A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 687 through 720 Processing helix chain 'A' and resid 720 through 753 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 766 through 800 removed outlier: 3.616A pdb=" N MET A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 826 removed outlier: 3.818A pdb=" N GLY A 804 " --> pdb=" O MET A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 859 through 872 removed outlier: 3.686A pdb=" N ASN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 934 through 939 removed outlier: 3.598A pdb=" N GLU A 939 " --> pdb=" O ASN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1091 Processing helix chain 'A' and resid 1266 through 1269 Processing helix chain 'A' and resid 1288 through 1292 removed outlier: 3.632A pdb=" N TRP A1291 " --> pdb=" O ASP A1288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 148 removed outlier: 4.767A pdb=" N TYR A 21 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214 removed outlier: 4.492A pdb=" N VAL A 373 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 458 Processing sheet with id=AA5, first strand: chain 'A' and resid 479 through 481 removed outlier: 7.611A pdb=" N GLU A 479 " --> pdb=" O ALA A 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 569 Processing sheet with id=AA7, first strand: chain 'A' and resid 887 through 890 removed outlier: 3.751A pdb=" N LEU A 879 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A1072 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N TYR A 883 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 12.199A pdb=" N LYS A1070 " --> pdb=" O TYR A 883 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 914 " --> pdb=" O ILE A1069 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 905 " --> pdb=" O GLN A 915 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 887 through 890 removed outlier: 3.751A pdb=" N LEU A 879 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A1072 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N TYR A 883 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 12.199A pdb=" N LYS A1070 " --> pdb=" O TYR A 883 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A1069 " --> pdb=" O ARG A 948 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG A 948 " --> pdb=" O ILE A1069 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR A1071 " --> pdb=" O TRP A 946 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP A 946 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A1039 " --> pdb=" O SER A1027 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 898 through 900 removed outlier: 3.562A pdb=" N ILE A 924 " --> pdb=" O PHE A1055 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 964 " --> pdb=" O LYS A1056 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP A1058 " --> pdb=" O TYR A 962 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR A 962 " --> pdb=" O ASP A1058 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL A 976 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN A 966 " --> pdb=" O TRP A 974 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TRP A 974 " --> pdb=" O ASN A 966 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 973 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 988 " --> pdb=" O GLY A 973 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 983 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 999 " --> pdb=" O ILE A 983 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1208 through 1209 removed outlier: 5.907A pdb=" N ILE A1182 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1114 " --> pdb=" O GLU A1283 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A1235 " --> pdb=" O TRP A1282 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET A1237 " --> pdb=" O PHE A1249 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE A1249 " --> pdb=" O MET A1237 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A1239 " --> pdb=" O ILE A1247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1208 through 1209 removed outlier: 5.907A pdb=" N ILE A1182 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A1180 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A1220 " --> pdb=" O GLN A1240 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A1240 " --> pdb=" O VAL A1220 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET A1237 " --> pdb=" O PHE A1249 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE A1249 " --> pdb=" O MET A1237 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A1239 " --> pdb=" O ILE A1247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1121 through 1125 removed outlier: 6.235A pdb=" N TYR A1122 " --> pdb=" O LYS A1137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1203 through 1205 412 hydrogen bonds defined for protein. 1179 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: 2.60 Time building geometry restraints manager: 1.16 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: 3265 1.34 - 1.46: 1888 1.46 - 1.57: 5164 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 10370 Sorted by residual: bond pdb=" N PHE A 188 " pdb=" CA PHE A 188 " ideal model delta sigma weight residual 1.455 1.437 0.018 1.27e-02 6.20e+03 1.95e+00 bond pdb=" CA PHE A 188 " pdb=" C PHE A 188 " ideal model delta sigma weight residual 1.521 1.504 0.017 1.23e-02 6.61e+03 1.94e+00 bond pdb=" CA SER A 587 " pdb=" C SER A 587 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.41e-02 5.03e+03 1.88e+00 bond pdb=" CA ILE A1036 " pdb=" CB ILE A1036 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.71e+00 bond pdb=" CG1 ILE A 348 " pdb=" CD1 ILE A 348 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.21e+00 ... (remaining 10365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 13559 1.26 - 2.52: 373 2.52 - 3.78: 80 3.78 - 5.05: 14 5.05 - 6.31: 5 Bond angle restraints: 14031 Sorted by residual: angle pdb=" N TYR A 87 " pdb=" CA TYR A 87 " pdb=" C TYR A 87 " ideal model delta sigma weight residual 111.14 106.26 4.88 1.08e+00 8.57e-01 2.04e+01 angle pdb=" C ASP A1171 " pdb=" N ASN A1172 " pdb=" CA ASN A1172 " ideal model delta sigma weight residual 122.61 128.81 -6.20 1.56e+00 4.11e-01 1.58e+01 angle pdb=" N SER A 622 " pdb=" CA SER A 622 " pdb=" C SER A 622 " ideal model delta sigma weight residual 108.23 113.08 -4.85 1.38e+00 5.25e-01 1.23e+01 angle pdb=" N THR A 50 " pdb=" CA THR A 50 " pdb=" C THR A 50 " ideal model delta sigma weight residual 114.62 110.75 3.87 1.14e+00 7.69e-01 1.15e+01 angle pdb=" C TYR A1107 " pdb=" N ASP A1108 " pdb=" CA ASP A1108 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.09e+00 ... (remaining 14026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5796 16.81 - 33.62: 361 33.62 - 50.43: 40 50.43 - 67.23: 6 67.23 - 84.04: 4 Dihedral angle restraints: 6207 sinusoidal: 2529 harmonic: 3678 Sorted by residual: dihedral pdb=" CA GLU A 347 " pdb=" C GLU A 347 " pdb=" N ILE A 348 " pdb=" CA ILE A 348 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN A 174 " pdb=" C ASN A 174 " pdb=" N LEU A 175 " pdb=" CA LEU A 175 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LYS A1070 " pdb=" C LYS A1070 " pdb=" N TYR A1071 " pdb=" CA TYR A1071 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 945 0.032 - 0.064: 373 0.064 - 0.096: 145 0.096 - 0.128: 74 0.128 - 0.160: 8 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CA GLU A 347 " pdb=" N GLU A 347 " pdb=" C GLU A 347 " pdb=" CB GLU A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA VAL A 621 " pdb=" N VAL A 621 " pdb=" C VAL A 621 " pdb=" CB VAL A 621 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ASP A1108 " pdb=" N ASP A1108 " pdb=" C ASP A1108 " pdb=" CB ASP A1108 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1542 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 86 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ASN A 86 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 86 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 87 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1171 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ASP A1171 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP A1171 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A1172 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 238 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 239 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " -0.018 5.00e-02 4.00e+02 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1670 2.76 - 3.29: 10503 3.29 - 3.83: 17311 3.83 - 4.36: 20705 4.36 - 4.90: 34824 Nonbonded interactions: 85013 Sorted by model distance: nonbonded pdb=" OG1 THR A 963 " pdb=" OD1 ASP A1058 " model vdw 2.224 3.040 nonbonded pdb=" O ASN A 842 " pdb=" OG SER A 846 " model vdw 2.249 3.040 nonbonded pdb=" O SER A 622 " pdb=" OG1 THR A 623 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 121 " pdb=" O ILE A 123 " model vdw 2.254 3.040 nonbonded pdb=" O SER A1008 " pdb=" NH1 ARG A1013 " model vdw 2.283 3.120 ... (remaining 85008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.004 0.043 10370 Z= 0.162 Angle : 0.532 6.308 14031 Z= 0.298 Chirality : 0.044 0.160 1545 Planarity : 0.003 0.032 1802 Dihedral : 10.913 84.044 3837 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.26 % Allowed : 0.35 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.24), residues: 1227 helix: 1.33 (0.26), residues: 372 sheet: -0.03 (0.37), residues: 206 loop : -0.93 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.017 0.001 TYR A 822 PHE 0.019 0.001 PHE A 866 TRP 0.010 0.001 TRP A 717 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00357 (10370) covalent geometry : angle 0.53183 (14031) hydrogen bonds : bond 0.19456 ( 400) hydrogen bonds : angle 6.94854 ( 1179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.6972 (p90) cc_final: 0.6657 (p90) REVERT: A 326 ASP cc_start: 0.7969 (m-30) cc_final: 0.7456 (m-30) REVERT: A 452 ASP cc_start: 0.7442 (t0) cc_final: 0.7177 (t0) REVERT: A 498 LEU cc_start: 0.8841 (tp) cc_final: 0.8420 (tp) REVERT: A 682 VAL cc_start: 0.8857 (t) cc_final: 0.8541 (m) REVERT: A 767 ASP cc_start: 0.7102 (t70) cc_final: 0.6893 (t0) REVERT: A 962 TYR cc_start: 0.8518 (p90) cc_final: 0.8226 (p90) REVERT: A 1053 ILE cc_start: 0.8407 (mt) cc_final: 0.8058 (mp) REVERT: A 1066 TYR cc_start: 0.9423 (p90) cc_final: 0.8915 (p90) REVERT: A 1088 TYR cc_start: 0.7674 (t80) cc_final: 0.7458 (t80) REVERT: A 1101 TRP cc_start: 0.7268 (m100) cc_final: 0.6938 (m100) outliers start: 3 outliers final: 1 residues processed: 201 average time/residue: 0.5738 time to fit residues: 124.1696 Evaluate side-chains 145 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 123 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.144982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.101645 restraints weight = 24591.904| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.82 r_work: 0.3441 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10370 Z= 0.170 Angle : 0.626 9.614 14031 Z= 0.332 Chirality : 0.045 0.151 1545 Planarity : 0.004 0.052 1802 Dihedral : 4.608 38.787 1350 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.76 % Allowed : 9.07 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1227 helix: 1.30 (0.25), residues: 376 sheet: 0.12 (0.37), residues: 204 loop : -0.89 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 861 TYR 0.026 0.002 TYR A 751 PHE 0.020 0.002 PHE A 425 TRP 0.014 0.001 TRP A 946 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00383 (10370) covalent geometry : angle 0.62637 (14031) hydrogen bonds : bond 0.05356 ( 400) hydrogen bonds : angle 5.45412 ( 1179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8454 (t) cc_final: 0.8204 (p) REVERT: A 283 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8133 (ttm-80) REVERT: A 476 ASN cc_start: 0.6601 (OUTLIER) cc_final: 0.6377 (p0) REVERT: A 826 ASN cc_start: 0.8090 (p0) cc_final: 0.7830 (p0) REVERT: A 839 ASP cc_start: 0.7369 (p0) cc_final: 0.7148 (p0) REVERT: A 962 TYR cc_start: 0.8483 (p90) cc_final: 0.8257 (p90) REVERT: A 1050 SER cc_start: 0.5089 (OUTLIER) cc_final: 0.4443 (m) REVERT: A 1066 TYR cc_start: 0.9540 (p90) cc_final: 0.9024 (p90) REVERT: A 1071 TYR cc_start: 0.7960 (m-10) cc_final: 0.7599 (m-10) REVERT: A 1088 TYR cc_start: 0.7360 (t80) cc_final: 0.7143 (t80) REVERT: A 1237 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.5411 (mmp) outliers start: 20 outliers final: 2 residues processed: 158 average time/residue: 0.5843 time to fit residues: 99.3893 Evaluate side-chains 140 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1237 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 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 = 0.4319 r_free = 0.4319 target = 0.143709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099628 restraints weight = 24221.824| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.64 r_work: 0.3413 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10370 Z= 0.186 Angle : 0.629 10.629 14031 Z= 0.330 Chirality : 0.045 0.146 1545 Planarity : 0.004 0.032 1802 Dihedral : 4.489 18.869 1348 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.03 % Allowed : 13.13 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1227 helix: 1.21 (0.25), residues: 375 sheet: 0.11 (0.36), residues: 214 loop : -0.91 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.035 0.002 TYR A 751 PHE 0.037 0.002 PHE A 419 TRP 0.023 0.001 TRP A 946 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00424 (10370) covalent geometry : angle 0.62865 (14031) hydrogen bonds : bond 0.05253 ( 400) hydrogen bonds : angle 5.34372 ( 1179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.322 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 30 MET cc_start: 0.6220 (tpp) cc_final: 0.5984 (tpt) REVERT: A 157 SER cc_start: 0.8517 (t) cc_final: 0.8255 (p) REVERT: A 283 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8086 (ttm-80) REVERT: A 606 TRP cc_start: 0.8022 (t60) cc_final: 0.7768 (t60) REVERT: A 632 ILE cc_start: 0.7915 (pp) cc_final: 0.7667 (pt) REVERT: A 684 TYR cc_start: 0.7315 (m-10) cc_final: 0.6378 (m-10) REVERT: A 690 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7554 (tp) REVERT: A 800 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7287 (mtt) REVERT: A 839 ASP cc_start: 0.7407 (p0) cc_final: 0.7204 (p0) REVERT: A 924 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8494 (pt) REVERT: A 962 TYR cc_start: 0.8473 (p90) cc_final: 0.8252 (p90) REVERT: A 1066 TYR cc_start: 0.9505 (p90) cc_final: 0.8993 (p90) REVERT: A 1088 TYR cc_start: 0.7456 (t80) cc_final: 0.7163 (t80) REVERT: A 1221 VAL cc_start: 0.3461 (OUTLIER) cc_final: 0.2673 (p) REVERT: A 1237 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5641 (mmp) outliers start: 23 outliers final: 7 residues processed: 146 average time/residue: 0.5074 time to fit residues: 80.5781 Evaluate side-chains 136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1237 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 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 = 0.4318 r_free = 0.4318 target = 0.143558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.099439 restraints weight = 24425.077| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.84 r_work: 0.3388 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10370 Z= 0.179 Angle : 0.616 15.481 14031 Z= 0.323 Chirality : 0.045 0.144 1545 Planarity : 0.003 0.032 1802 Dihedral : 4.495 19.013 1348 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.64 % Allowed : 13.57 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1227 helix: 1.12 (0.25), residues: 373 sheet: 0.20 (0.36), residues: 218 loop : -0.92 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 113 TYR 0.029 0.002 TYR A 250 PHE 0.021 0.002 PHE A 419 TRP 0.032 0.002 TRP A 946 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00407 (10370) covalent geometry : angle 0.61594 (14031) hydrogen bonds : bond 0.05108 ( 400) hydrogen bonds : angle 5.21505 ( 1179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8496 (t) cc_final: 0.8234 (p) REVERT: A 283 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8084 (ttm-80) REVERT: A 684 TYR cc_start: 0.7284 (m-10) cc_final: 0.6461 (m-10) REVERT: A 690 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7688 (tp) REVERT: A 800 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7224 (mtt) REVERT: A 839 ASP cc_start: 0.7457 (p0) cc_final: 0.7253 (p0) REVERT: A 845 LEU cc_start: 0.8539 (tm) cc_final: 0.8128 (tm) REVERT: A 946 TRP cc_start: 0.5895 (m100) cc_final: 0.5674 (m100) REVERT: A 962 TYR cc_start: 0.8471 (p90) cc_final: 0.8236 (p90) REVERT: A 1050 SER cc_start: 0.4030 (OUTLIER) cc_final: 0.3589 (m) REVERT: A 1066 TYR cc_start: 0.9519 (p90) cc_final: 0.9016 (p90) REVERT: A 1088 TYR cc_start: 0.7510 (t80) cc_final: 0.7177 (t80) REVERT: A 1221 VAL cc_start: 0.3450 (OUTLIER) cc_final: 0.2598 (p) REVERT: A 1237 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5404 (mmp) REVERT: A 1250 ILE cc_start: -0.1380 (OUTLIER) cc_final: -0.2085 (mp) outliers start: 30 outliers final: 7 residues processed: 143 average time/residue: 0.5174 time to fit residues: 80.5922 Evaluate side-chains 142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1250 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 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 = 0.4299 r_free = 0.4299 target = 0.142476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098300 restraints weight = 24610.381| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.80 r_work: 0.3368 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10370 Z= 0.219 Angle : 0.659 13.409 14031 Z= 0.345 Chirality : 0.047 0.201 1545 Planarity : 0.004 0.033 1802 Dihedral : 4.687 19.259 1348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.73 % Allowed : 16.30 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1227 helix: 0.91 (0.25), residues: 376 sheet: 0.04 (0.34), residues: 233 loop : -0.94 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.031 0.002 TYR A 751 PHE 0.022 0.002 PHE A 419 TRP 0.018 0.002 TRP A 946 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00506 (10370) covalent geometry : angle 0.65890 (14031) hydrogen bonds : bond 0.05438 ( 400) hydrogen bonds : angle 5.25585 ( 1179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8587 (t) cc_final: 0.8308 (p) REVERT: A 283 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8520 (ttp80) REVERT: A 606 TRP cc_start: 0.8039 (t60) cc_final: 0.7561 (t60) REVERT: A 632 ILE cc_start: 0.7892 (pp) cc_final: 0.7646 (pt) REVERT: A 800 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7294 (mtt) REVERT: A 824 TYR cc_start: 0.8167 (t80) cc_final: 0.7910 (t80) REVERT: A 827 ARG cc_start: 0.8214 (ptt-90) cc_final: 0.7911 (ptp90) REVERT: A 839 ASP cc_start: 0.7454 (p0) cc_final: 0.7242 (p0) REVERT: A 946 TRP cc_start: 0.5891 (m100) cc_final: 0.5610 (m100) REVERT: A 962 TYR cc_start: 0.8508 (p90) cc_final: 0.8260 (p90) REVERT: A 1050 SER cc_start: 0.4156 (OUTLIER) cc_final: 0.3884 (m) REVERT: A 1054 MET cc_start: 0.7879 (tpp) cc_final: 0.6989 (tmm) REVERT: A 1066 TYR cc_start: 0.9562 (p90) cc_final: 0.9087 (p90) REVERT: A 1088 TYR cc_start: 0.7359 (t80) cc_final: 0.7047 (t80) REVERT: A 1221 VAL cc_start: 0.3387 (OUTLIER) cc_final: 0.2514 (p) REVERT: A 1237 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5523 (mmp) REVERT: A 1250 ILE cc_start: -0.1302 (OUTLIER) cc_final: -0.1989 (mp) outliers start: 31 outliers final: 11 residues processed: 151 average time/residue: 0.5290 time to fit residues: 86.8095 Evaluate side-chains 141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1250 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 86 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 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 = 0.4313 r_free = 0.4313 target = 0.143094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.098521 restraints weight = 24557.296| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.95 r_work: 0.3379 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10370 Z= 0.181 Angle : 0.646 15.751 14031 Z= 0.335 Chirality : 0.048 0.532 1545 Planarity : 0.003 0.032 1802 Dihedral : 4.663 19.586 1348 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.73 % Allowed : 17.89 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.23), residues: 1227 helix: 0.91 (0.25), residues: 377 sheet: 0.12 (0.34), residues: 232 loop : -0.91 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 363 TYR 0.035 0.002 TYR A 751 PHE 0.019 0.002 PHE A 419 TRP 0.015 0.001 TRP A 946 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00417 (10370) covalent geometry : angle 0.64582 (14031) hydrogen bonds : bond 0.05050 ( 400) hydrogen bonds : angle 5.11702 ( 1179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8518 (t) cc_final: 0.8241 (p) REVERT: A 201 GLU cc_start: 0.8118 (tp30) cc_final: 0.7873 (tp30) REVERT: A 246 ASN cc_start: 0.8216 (t0) cc_final: 0.7865 (t0) REVERT: A 283 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7966 (ttm-80) REVERT: A 325 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 606 TRP cc_start: 0.8021 (t60) cc_final: 0.7648 (t60) REVERT: A 632 ILE cc_start: 0.7835 (pp) cc_final: 0.7616 (pt) REVERT: A 800 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7359 (mtt) REVERT: A 826 ASN cc_start: 0.8171 (p0) cc_final: 0.7898 (p0) REVERT: A 946 TRP cc_start: 0.5861 (m100) cc_final: 0.5551 (m100) REVERT: A 962 TYR cc_start: 0.8492 (p90) cc_final: 0.8236 (p90) REVERT: A 1050 SER cc_start: 0.4038 (OUTLIER) cc_final: 0.3663 (m) REVERT: A 1054 MET cc_start: 0.7794 (tpp) cc_final: 0.7015 (tmm) REVERT: A 1066 TYR cc_start: 0.9539 (p90) cc_final: 0.9051 (p90) REVERT: A 1088 TYR cc_start: 0.7303 (t80) cc_final: 0.6982 (t80) REVERT: A 1221 VAL cc_start: 0.3456 (OUTLIER) cc_final: 0.2505 (p) REVERT: A 1237 MET cc_start: 0.6072 (OUTLIER) cc_final: 0.5490 (mmp) REVERT: A 1250 ILE cc_start: -0.1273 (OUTLIER) cc_final: -0.1997 (mp) outliers start: 31 outliers final: 15 residues processed: 151 average time/residue: 0.4812 time to fit residues: 79.4904 Evaluate side-chains 146 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1250 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 184 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.141609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096559 restraints weight = 24070.220| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.91 r_work: 0.3331 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10370 Z= 0.248 Angle : 0.692 15.070 14031 Z= 0.363 Chirality : 0.049 0.507 1545 Planarity : 0.004 0.040 1802 Dihedral : 4.892 19.549 1348 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.64 % Allowed : 18.85 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1227 helix: 0.73 (0.25), residues: 377 sheet: -0.08 (0.33), residues: 243 loop : -1.07 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.033 0.002 TYR A 751 PHE 0.019 0.002 PHE A 338 TRP 0.012 0.001 TRP A 946 HIS 0.010 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00576 (10370) covalent geometry : angle 0.69212 (14031) hydrogen bonds : bond 0.05613 ( 400) hydrogen bonds : angle 5.25379 ( 1179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8602 (t) cc_final: 0.8350 (p) REVERT: A 163 PHE cc_start: 0.7640 (m-10) cc_final: 0.7427 (m-10) REVERT: A 201 GLU cc_start: 0.8121 (tp30) cc_final: 0.7874 (tp30) REVERT: A 283 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8548 (ttp80) REVERT: A 800 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7352 (mtt) REVERT: A 826 ASN cc_start: 0.8310 (p0) cc_final: 0.8056 (p0) REVERT: A 946 TRP cc_start: 0.5848 (m100) cc_final: 0.5505 (m100) REVERT: A 962 TYR cc_start: 0.8524 (p90) cc_final: 0.8252 (p90) REVERT: A 1054 MET cc_start: 0.7835 (tpp) cc_final: 0.7143 (tmm) REVERT: A 1066 TYR cc_start: 0.9570 (p90) cc_final: 0.9104 (p90) REVERT: A 1088 TYR cc_start: 0.7237 (t80) cc_final: 0.6920 (t80) REVERT: A 1221 VAL cc_start: 0.3540 (OUTLIER) cc_final: 0.2554 (p) REVERT: A 1237 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5594 (mmp) REVERT: A 1250 ILE cc_start: -0.1176 (OUTLIER) cc_final: -0.1935 (mp) outliers start: 30 outliers final: 15 residues processed: 149 average time/residue: 0.4977 time to fit residues: 80.6827 Evaluate side-chains 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1250 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 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 = 0.4315 r_free = 0.4315 target = 0.143394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099737 restraints weight = 24364.966| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.57 r_work: 0.3397 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10370 Z= 0.165 Angle : 0.671 18.512 14031 Z= 0.346 Chirality : 0.048 0.509 1545 Planarity : 0.003 0.033 1802 Dihedral : 4.724 19.326 1348 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.29 % Allowed : 20.35 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1227 helix: 0.91 (0.25), residues: 377 sheet: 0.06 (0.34), residues: 233 loop : -1.03 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 113 TYR 0.040 0.002 TYR A 751 PHE 0.014 0.002 PHE A 425 TRP 0.014 0.001 TRP A 946 HIS 0.008 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00381 (10370) covalent geometry : angle 0.67109 (14031) hydrogen bonds : bond 0.04864 ( 400) hydrogen bonds : angle 5.03358 ( 1179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8336 (t) cc_final: 0.8063 (p) REVERT: A 201 GLU cc_start: 0.8112 (tp30) cc_final: 0.7885 (tp30) REVERT: A 606 TRP cc_start: 0.7984 (t60) cc_final: 0.7700 (t60) REVERT: A 632 ILE cc_start: 0.7792 (pp) cc_final: 0.7544 (pt) REVERT: A 800 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7298 (mtt) REVERT: A 962 TYR cc_start: 0.8461 (p90) cc_final: 0.8202 (p90) REVERT: A 1054 MET cc_start: 0.7776 (tpp) cc_final: 0.7083 (tmm) REVERT: A 1066 TYR cc_start: 0.9527 (p90) cc_final: 0.9038 (p90) REVERT: A 1088 TYR cc_start: 0.7346 (t80) cc_final: 0.7025 (t80) REVERT: A 1221 VAL cc_start: 0.3565 (OUTLIER) cc_final: 0.2582 (p) REVERT: A 1237 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5365 (mmp) REVERT: A 1250 ILE cc_start: -0.1289 (OUTLIER) cc_final: -0.2010 (mp) outliers start: 26 outliers final: 16 residues processed: 142 average time/residue: 0.5012 time to fit residues: 77.6425 Evaluate side-chains 143 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1250 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.144472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.100260 restraints weight = 24155.746| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.85 r_work: 0.3422 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10370 Z= 0.141 Angle : 0.663 17.003 14031 Z= 0.341 Chirality : 0.047 0.499 1545 Planarity : 0.003 0.033 1802 Dihedral : 4.620 19.220 1348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.67 % Allowed : 20.79 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.23), residues: 1227 helix: 1.17 (0.26), residues: 371 sheet: -0.07 (0.33), residues: 243 loop : -0.98 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 827 TYR 0.038 0.002 TYR A 751 PHE 0.015 0.001 PHE A 425 TRP 0.014 0.001 TRP A 946 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00324 (10370) covalent geometry : angle 0.66258 (14031) hydrogen bonds : bond 0.04543 ( 400) hydrogen bonds : angle 4.85639 ( 1179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 TYR cc_start: 0.5549 (m-80) cc_final: 0.5285 (m-80) REVERT: A 201 GLU cc_start: 0.8168 (tp30) cc_final: 0.7952 (tp30) REVERT: A 632 ILE cc_start: 0.7715 (pp) cc_final: 0.7489 (pt) REVERT: A 684 TYR cc_start: 0.6729 (m-10) cc_final: 0.5730 (m-10) REVERT: A 690 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7715 (tp) REVERT: A 946 TRP cc_start: 0.5960 (m100) cc_final: 0.5505 (m100) REVERT: A 962 TYR cc_start: 0.8425 (p90) cc_final: 0.8172 (p90) REVERT: A 1054 MET cc_start: 0.7845 (tpp) cc_final: 0.7253 (tmm) REVERT: A 1066 TYR cc_start: 0.9550 (p90) cc_final: 0.9066 (p90) REVERT: A 1088 TYR cc_start: 0.7354 (t80) cc_final: 0.7003 (t80) REVERT: A 1221 VAL cc_start: 0.3546 (OUTLIER) cc_final: 0.2583 (p) REVERT: A 1237 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.5643 (mmp) REVERT: A 1250 ILE cc_start: -0.1302 (OUTLIER) cc_final: -0.2034 (mp) outliers start: 19 outliers final: 8 residues processed: 136 average time/residue: 0.4679 time to fit residues: 69.7636 Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 105 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.0670 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** 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 = 0.4337 r_free = 0.4337 target = 0.144778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.101836 restraints weight = 24204.294| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.76 r_work: 0.3434 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10370 Z= 0.140 Angle : 0.682 16.525 14031 Z= 0.351 Chirality : 0.047 0.482 1545 Planarity : 0.003 0.041 1802 Dihedral : 4.593 20.950 1348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.32 % Allowed : 22.03 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.23), residues: 1227 helix: 1.32 (0.26), residues: 364 sheet: 0.06 (0.34), residues: 233 loop : -0.98 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 827 TYR 0.031 0.001 TYR A 250 PHE 0.015 0.001 PHE A1100 TRP 0.014 0.001 TRP A 606 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00322 (10370) covalent geometry : angle 0.68185 (14031) hydrogen bonds : bond 0.04474 ( 400) hydrogen bonds : angle 4.80958 ( 1179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.7575 (t0) cc_final: 0.6776 (t0) REVERT: A 73 TYR cc_start: 0.5381 (m-80) cc_final: 0.5162 (m-80) REVERT: A 301 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7716 (pttm) REVERT: A 606 TRP cc_start: 0.7806 (t60) cc_final: 0.7593 (t60) REVERT: A 632 ILE cc_start: 0.7692 (pp) cc_final: 0.7484 (pt) REVERT: A 684 TYR cc_start: 0.6844 (m-10) cc_final: 0.5787 (m-10) REVERT: A 690 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7781 (tp) REVERT: A 826 ASN cc_start: 0.8324 (p0) cc_final: 0.7937 (p0) REVERT: A 946 TRP cc_start: 0.6148 (m100) cc_final: 0.5642 (m100) REVERT: A 962 TYR cc_start: 0.8388 (p90) cc_final: 0.8145 (p90) REVERT: A 1054 MET cc_start: 0.7862 (tpp) cc_final: 0.7253 (tmm) REVERT: A 1066 TYR cc_start: 0.9516 (p90) cc_final: 0.9046 (p90) REVERT: A 1088 TYR cc_start: 0.7402 (t80) cc_final: 0.7029 (t80) outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 0.4878 time to fit residues: 69.8291 Evaluate side-chains 125 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1237 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 3 optimal weight: 0.0370 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 205 ASN A 311 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A 859 ASN ** 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 = 0.4341 r_free = 0.4341 target = 0.145031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.102022 restraints weight = 24626.092| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.58 r_work: 0.3450 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10370 Z= 0.147 Angle : 0.692 16.290 14031 Z= 0.357 Chirality : 0.048 0.478 1545 Planarity : 0.004 0.039 1802 Dihedral : 4.609 21.062 1348 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.15 % Allowed : 22.03 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.23), residues: 1227 helix: 1.26 (0.26), residues: 364 sheet: 0.11 (0.35), residues: 224 loop : -0.94 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 145 TYR 0.032 0.002 TYR A 250 PHE 0.035 0.002 PHE A 266 TRP 0.012 0.001 TRP A 946 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00341 (10370) covalent geometry : angle 0.69203 (14031) hydrogen bonds : bond 0.04531 ( 400) hydrogen bonds : angle 4.82054 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4251.68 seconds wall clock time: 73 minutes 18.13 seconds (4398.13 seconds total)