Starting phenix.real_space_refine on Tue Feb 11 22:52:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r4p_4722/02_2025/6r4p_4722.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r4p_4722/02_2025/6r4p_4722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r4p_4722/02_2025/6r4p_4722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r4p_4722/02_2025/6r4p_4722.map" model { file = "/net/cci-nas-00/data/ceres_data/6r4p_4722/02_2025/6r4p_4722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r4p_4722/02_2025/6r4p_4722.cif" } resolution = 3.1 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= 0.003 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 81 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 4149 2.51 5 N 1139 2.21 5 O 1245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6583 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3741 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 465} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2809 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.39, per 1000 atoms: 0.67 Number of scatterers: 6583 At special positions: 0 Unit cell: (100.122, 106.634, 103.378, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 3 15.00 Mg 1 11.99 O 1245 8.00 N 1139 7.00 C 4149 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: 1.65 Conformation dependent library (CDL) restraints added in 937.6 milliseconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 5 sheets defined 50.2% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 320 through 336 removed outlier: 4.234A pdb=" N GLU A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.836A pdb=" N LYS A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.712A pdb=" N MET A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.742A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 1021 through 1037 Processing helix chain 'A' and resid 1038 through 1047 removed outlier: 3.822A pdb=" N VAL A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 3.528A pdb=" N GLU A1070 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1133 through 1154 removed outlier: 3.629A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 3.685A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1218 Processing helix chain 'A' and resid 1219 through 1221 No H-bonds generated for 'chain 'A' and resid 1219 through 1221' Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.646A pdb=" N ASP B 33 " --> pdb=" O GLN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 89 through 113 removed outlier: 4.214A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.776A pdb=" N ASP B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.529A pdb=" N ARG B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 4.023A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.680A pdb=" N ARG B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 236 " --> pdb=" O LYS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 293 through 304 removed outlier: 3.862A pdb=" N GLY B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.919A pdb=" N ALA B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.872A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 389 Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 441 removed outlier: 7.531A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 485 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 441 removed outlier: 7.531A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 485 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N HIS A 530 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 488 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.134A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 214 removed outlier: 5.980A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL B 247 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 46 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA B 249 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 287 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS B 362 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 289 " --> pdb=" O HIS B 362 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 987 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: 2.05 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1983 1.33 - 1.45: 1059 1.45 - 1.57: 3586 1.57 - 1.69: 5 1.69 - 1.81: 72 Bond restraints: 6705 Sorted by residual: bond pdb=" CB VAL A1041 " pdb=" CG1 VAL A1041 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.22e+00 bond pdb=" CG LEU A1139 " pdb=" CD1 LEU A1139 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB VAL A1166 " pdb=" CG2 VAL A1166 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" CD LYS A1107 " pdb=" CE LYS A1107 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.59e+00 bond pdb=" CG LEU A1164 " pdb=" CD2 LEU A1164 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.22e+00 ... (remaining 6700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 8771 2.53 - 5.07: 231 5.07 - 7.60: 24 7.60 - 10.14: 16 10.14 - 12.67: 3 Bond angle restraints: 9045 Sorted by residual: angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 131.67 -10.13 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta sigma weight residual 121.54 131.17 -9.63 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C VAL B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 angle pdb=" CA CYS A 451 " pdb=" CB CYS A 451 " pdb=" SG CYS A 451 " ideal model delta sigma weight residual 114.40 124.15 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CB MET A 469 " pdb=" CG MET A 469 " pdb=" SD MET A 469 " ideal model delta sigma weight residual 112.70 100.03 12.67 3.00e+00 1.11e-01 1.78e+01 ... (remaining 9040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 3754 15.46 - 30.91: 210 30.91 - 46.37: 76 46.37 - 61.82: 6 61.82 - 77.28: 8 Dihedral angle restraints: 4054 sinusoidal: 1669 harmonic: 2385 Sorted by residual: dihedral pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 144.60 35.40 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual -180.00 -145.07 -34.93 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ILE B 182 " pdb=" C ILE B 182 " pdb=" N ASP B 183 " pdb=" CA ASP B 183 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 764 0.071 - 0.141: 197 0.141 - 0.211: 17 0.211 - 0.282: 6 0.282 - 0.352: 2 Chirality restraints: 986 Sorted by residual: chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB ILE A1061 " pdb=" CA ILE A1061 " pdb=" CG1 ILE A1061 " pdb=" CG2 ILE A1061 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR A1243 " pdb=" N TYR A1243 " pdb=" C TYR A1243 " pdb=" CB TYR A1243 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 983 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO B 115 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1087 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" CG ASN A1087 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A1087 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A1087 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO A1038 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.037 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 78 2.64 - 3.21: 5784 3.21 - 3.77: 10224 3.77 - 4.34: 13969 4.34 - 4.90: 22734 Nonbonded interactions: 52789 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 2.080 2.170 nonbonded pdb=" OG SER B 54 " pdb="MG MG B 502 " model vdw 2.121 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.129 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.132 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.210 3.040 ... (remaining 52784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 0.075 6705 Z= 0.538 Angle : 1.043 12.673 9045 Z= 0.552 Chirality : 0.063 0.352 986 Planarity : 0.007 0.078 1170 Dihedral : 11.941 77.280 2514 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.57 % Allowed : 6.51 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.13 % 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: -3.18 (0.25), residues: 807 helix: -1.99 (0.21), residues: 356 sheet: -1.76 (0.41), residues: 143 loop : -2.18 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A1159 HIS 0.015 0.003 HIS B 149 PHE 0.042 0.004 PHE A 397 TYR 0.036 0.003 TYR A 446 ARG 0.015 0.001 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 333 MET cc_start: 0.8845 (mmt) cc_final: 0.8507 (mmp) REVERT: A 1220 MET cc_start: 0.8294 (mtm) cc_final: 0.8080 (mtp) outliers start: 4 outliers final: 0 residues processed: 93 average time/residue: 0.2830 time to fit residues: 32.4504 Evaluate side-chains 51 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1055 HIS A1154 ASN A1193 ASN A1231 ASN B 98 ASN B 213 GLN B 239 ASN B 264 ASN B 362 HIS B 371 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.098669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076233 restraints weight = 13755.576| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.73 r_work: 0.3023 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6705 Z= 0.191 Angle : 0.606 7.700 9045 Z= 0.317 Chirality : 0.045 0.170 986 Planarity : 0.004 0.068 1170 Dihedral : 5.477 33.475 908 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.84 % Allowed : 8.77 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.28), residues: 807 helix: -0.11 (0.26), residues: 371 sheet: -1.27 (0.40), residues: 137 loop : -1.89 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1159 HIS 0.005 0.001 HIS B 149 PHE 0.014 0.001 PHE A1093 TYR 0.020 0.002 TYR A 446 ARG 0.004 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.795 Fit side-chains REVERT: A 465 MET cc_start: 0.8921 (tmt) cc_final: 0.8112 (tmt) REVERT: A 1027 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: B 188 ASP cc_start: 0.7911 (p0) cc_final: 0.7334 (t0) outliers start: 13 outliers final: 2 residues processed: 72 average time/residue: 0.1974 time to fit residues: 19.4070 Evaluate side-chains 50 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074601 restraints weight = 13961.743| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.76 r_work: 0.2987 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6705 Z= 0.213 Angle : 0.582 7.789 9045 Z= 0.302 Chirality : 0.045 0.162 986 Planarity : 0.004 0.059 1170 Dihedral : 5.060 32.577 908 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.11 % Allowed : 10.04 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.29), residues: 807 helix: 0.69 (0.27), residues: 370 sheet: -0.85 (0.42), residues: 120 loop : -1.75 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.003 0.001 HIS B 149 PHE 0.013 0.001 PHE A 385 TYR 0.020 0.002 TYR A 446 ARG 0.003 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 348 LYS cc_start: 0.6977 (mmtp) cc_final: 0.6705 (mmtt) REVERT: A 385 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6286 (p90) REVERT: A 465 MET cc_start: 0.8985 (tmt) cc_final: 0.8122 (tmt) REVERT: A 1027 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: B 188 ASP cc_start: 0.7919 (p0) cc_final: 0.7344 (t0) outliers start: 22 outliers final: 7 residues processed: 66 average time/residue: 0.1662 time to fit residues: 15.7677 Evaluate side-chains 55 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.0170 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 0.0470 chunk 55 optimal weight: 6.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.098553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.076021 restraints weight = 14107.015| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.75 r_work: 0.3016 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6705 Z= 0.164 Angle : 0.558 7.676 9045 Z= 0.284 Chirality : 0.043 0.157 986 Planarity : 0.003 0.056 1170 Dihedral : 4.735 30.344 908 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.70 % Allowed : 12.02 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.29), residues: 807 helix: 1.27 (0.27), residues: 368 sheet: -0.69 (0.41), residues: 121 loop : -1.55 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.003 0.001 HIS B 149 PHE 0.009 0.001 PHE A 385 TYR 0.018 0.001 TYR A 446 ARG 0.002 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.850 Fit side-chains REVERT: A 385 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.6866 (p90) REVERT: A 465 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8092 (tmt) REVERT: A 1027 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: B 188 ASP cc_start: 0.7879 (p0) cc_final: 0.7337 (t0) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 0.2008 time to fit residues: 16.1603 Evaluate side-chains 54 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 2 optimal weight: 0.6980 chunk 70 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.098634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076045 restraints weight = 13936.677| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.74 r_work: 0.3013 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6705 Z= 0.169 Angle : 0.544 7.622 9045 Z= 0.278 Chirality : 0.043 0.156 986 Planarity : 0.003 0.055 1170 Dihedral : 4.591 29.619 908 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.97 % Allowed : 11.60 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 807 helix: 1.43 (0.27), residues: 370 sheet: -0.52 (0.42), residues: 121 loop : -1.36 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.003 0.001 HIS B 149 PHE 0.010 0.001 PHE A 385 TYR 0.018 0.001 TYR A 446 ARG 0.003 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.785 Fit side-chains REVERT: A 385 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.6798 (p90) REVERT: A 465 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8093 (tmt) REVERT: A 1027 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: A 1116 MET cc_start: 0.9266 (ttt) cc_final: 0.9051 (ttm) REVERT: A 1220 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8165 (mtp) REVERT: B 188 ASP cc_start: 0.7945 (p0) cc_final: 0.7400 (t0) outliers start: 21 outliers final: 10 residues processed: 68 average time/residue: 0.1620 time to fit residues: 15.9528 Evaluate side-chains 60 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075546 restraints weight = 13859.605| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.69 r_work: 0.3007 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6705 Z= 0.197 Angle : 0.560 8.095 9045 Z= 0.284 Chirality : 0.044 0.159 986 Planarity : 0.003 0.054 1170 Dihedral : 4.583 29.903 908 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.55 % Allowed : 12.73 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 807 helix: 1.53 (0.27), residues: 370 sheet: -0.41 (0.43), residues: 121 loop : -1.23 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.011 0.001 PHE A 385 TYR 0.018 0.001 TYR A 446 ARG 0.002 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.622 Fit side-chains REVERT: A 385 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.6830 (p90) REVERT: A 465 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8119 (tmt) REVERT: A 1027 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: B 188 ASP cc_start: 0.7983 (p0) cc_final: 0.7434 (t0) outliers start: 18 outliers final: 10 residues processed: 58 average time/residue: 0.1338 time to fit residues: 11.7253 Evaluate side-chains 56 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 8 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.075865 restraints weight = 13925.321| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.67 r_work: 0.3008 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6705 Z= 0.192 Angle : 0.545 8.160 9045 Z= 0.279 Chirality : 0.043 0.158 986 Planarity : 0.003 0.055 1170 Dihedral : 4.540 29.656 908 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.97 % Allowed : 11.74 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 807 helix: 1.60 (0.27), residues: 371 sheet: -0.34 (0.44), residues: 121 loop : -1.11 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.011 0.001 PHE A 385 TYR 0.018 0.001 TYR A 446 ARG 0.002 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.748 Fit side-chains REVERT: A 385 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.6807 (p90) REVERT: A 465 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8108 (tmt) REVERT: A 1027 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: A 1158 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8970 (pp) REVERT: B 188 ASP cc_start: 0.7979 (p0) cc_final: 0.7437 (t0) outliers start: 21 outliers final: 10 residues processed: 65 average time/residue: 0.1435 time to fit residues: 13.9077 Evaluate side-chains 59 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 67 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075713 restraints weight = 13897.090| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.66 r_work: 0.3007 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6705 Z= 0.194 Angle : 0.562 9.025 9045 Z= 0.283 Chirality : 0.043 0.158 986 Planarity : 0.003 0.055 1170 Dihedral : 4.511 29.459 908 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.26 % Allowed : 12.87 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 807 helix: 1.65 (0.27), residues: 371 sheet: -0.29 (0.44), residues: 121 loop : -1.02 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.011 0.001 PHE A 385 TYR 0.017 0.001 TYR A 446 ARG 0.002 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.746 Fit side-chains REVERT: A 385 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.6806 (p90) REVERT: A 465 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8126 (tmt) REVERT: A 1027 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: A 1158 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8972 (pp) REVERT: B 188 ASP cc_start: 0.7908 (p0) cc_final: 0.7427 (t0) outliers start: 16 outliers final: 11 residues processed: 61 average time/residue: 0.1511 time to fit residues: 13.8521 Evaluate side-chains 60 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 1 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.099376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.076633 restraints weight = 14073.239| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.74 r_work: 0.3024 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6705 Z= 0.162 Angle : 0.537 8.150 9045 Z= 0.272 Chirality : 0.043 0.154 986 Planarity : 0.003 0.056 1170 Dihedral : 4.416 28.166 908 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.84 % Allowed : 13.44 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 807 helix: 1.75 (0.27), residues: 369 sheet: -0.17 (0.45), residues: 121 loop : -0.89 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.009 0.001 PHE A 385 TYR 0.016 0.001 TYR A 446 ARG 0.001 0.000 ARG A1206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.815 Fit side-chains REVERT: A 465 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8102 (tmt) REVERT: A 1027 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: A 1158 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8956 (pp) REVERT: B 188 ASP cc_start: 0.7944 (p0) cc_final: 0.7487 (t0) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.1574 time to fit residues: 13.3455 Evaluate side-chains 58 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076467 restraints weight = 14138.372| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.74 r_work: 0.3022 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6705 Z= 0.168 Angle : 0.531 7.934 9045 Z= 0.271 Chirality : 0.043 0.155 986 Planarity : 0.003 0.055 1170 Dihedral : 4.393 28.100 908 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.70 % Allowed : 13.86 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 807 helix: 1.81 (0.27), residues: 369 sheet: -0.14 (0.45), residues: 121 loop : -0.85 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.010 0.001 PHE A 385 TYR 0.017 0.001 TYR A 446 ARG 0.002 0.000 ARG A 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.748 Fit side-chains REVERT: A 465 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8090 (tmt) REVERT: A 1027 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: B 188 ASP cc_start: 0.7926 (p0) cc_final: 0.7464 (t0) outliers start: 12 outliers final: 9 residues processed: 58 average time/residue: 0.1521 time to fit residues: 13.2331 Evaluate side-chains 58 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 18 optimal weight: 0.0470 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076483 restraints weight = 14232.614| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.76 r_work: 0.3020 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6705 Z= 0.168 Angle : 0.527 7.818 9045 Z= 0.268 Chirality : 0.043 0.155 986 Planarity : 0.003 0.055 1170 Dihedral : 4.369 27.969 908 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.98 % Allowed : 13.44 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.30), residues: 807 helix: 1.89 (0.27), residues: 369 sheet: -0.10 (0.45), residues: 121 loop : -0.79 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.010 0.001 PHE A 385 TYR 0.017 0.001 TYR A 446 ARG 0.001 0.000 ARG A1206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3118.13 seconds wall clock time: 56 minutes 3.70 seconds (3363.70 seconds total)