Starting phenix.real_space_refine on Tue Mar 3 15:48:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r4p_4722/03_2026/6r4p_4722.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r4p_4722/03_2026/6r4p_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_4722/03_2026/6r4p_4722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r4p_4722/03_2026/6r4p_4722.map" model { file = "/net/cci-nas-00/data/ceres_data/6r4p_4722/03_2026/6r4p_4722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r4p_4722/03_2026/6r4p_4722.cif" } resolution = 3.1 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= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1} 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: 1.65, per 1000 atoms: 0.25 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: 0.68 Conformation dependent library (CDL) restraints added in 250.7 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: 0.23 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: 1.12 Time building geometry restraints manager: 0.88 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.210 Find NCS groups from input model: 0.030 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.440 ------------------------------------------------------------------------------- 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= 0.348 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 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: -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 ARG 0.015 0.001 ARG B 342 TYR 0.036 0.003 TYR A 446 PHE 0.042 0.004 PHE A 397 TRP 0.022 0.004 TRP A1159 HIS 0.015 0.003 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00829 ( 6705) covalent geometry : angle 1.04253 ( 9045) hydrogen bonds : bond 0.17399 ( 333) hydrogen bonds : angle 7.55404 ( 987) *********************** 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 : 0.215 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: 0.1249 time to fit residues: 14.1552 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 : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.098652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076129 restraints weight = 14017.436| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.75 r_work: 0.3021 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6705 Z= 0.135 Angle : 0.604 7.634 9045 Z= 0.317 Chirality : 0.044 0.169 986 Planarity : 0.004 0.067 1170 Dihedral : 5.459 33.244 908 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.98 % Allowed : 8.77 % Favored : 89.25 % 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: -1.47 (0.28), residues: 807 helix: -0.07 (0.26), residues: 371 sheet: -1.27 (0.40), residues: 136 loop : -1.88 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1215 TYR 0.020 0.002 TYR A 446 PHE 0.013 0.001 PHE A1093 TRP 0.014 0.001 TRP A1159 HIS 0.004 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6705) covalent geometry : angle 0.60413 ( 9045) hydrogen bonds : bond 0.04625 ( 333) hydrogen bonds : angle 5.07869 ( 987) *********************** 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: 14 poor density : 61 time to evaluate : 0.227 Fit side-chains REVERT: A 465 MET cc_start: 0.8915 (tmt) cc_final: 0.8134 (tmt) REVERT: A 1027 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: B 188 ASP cc_start: 0.7910 (p0) cc_final: 0.7333 (t0) outliers start: 14 outliers final: 4 residues processed: 72 average time/residue: 0.0881 time to fit residues: 8.4919 Evaluate side-chains 53 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 333 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.096725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073855 restraints weight = 13913.204| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.74 r_work: 0.2972 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6705 Z= 0.162 Angle : 0.587 7.822 9045 Z= 0.306 Chirality : 0.045 0.164 986 Planarity : 0.004 0.058 1170 Dihedral : 5.088 33.062 908 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.25 % Allowed : 9.76 % Favored : 86.99 % 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: -0.71 (0.29), residues: 807 helix: 0.71 (0.27), residues: 370 sheet: -0.74 (0.43), residues: 117 loop : -1.76 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 374 TYR 0.020 0.002 TYR A 446 PHE 0.015 0.002 PHE A 385 TRP 0.013 0.001 TRP A1159 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6705) covalent geometry : angle 0.58734 ( 9045) hydrogen bonds : bond 0.04541 ( 333) hydrogen bonds : angle 4.70996 ( 987) *********************** 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 70 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.201 Fit side-chains REVERT: A 385 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.6243 (p90) REVERT: A 465 MET cc_start: 0.8989 (tmt) cc_final: 0.8130 (tmt) REVERT: A 537 LYS cc_start: 0.8721 (pttp) cc_final: 0.8494 (ptmm) REVERT: A 1027 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: A 1147 MET cc_start: 0.9314 (tpp) cc_final: 0.9113 (mmm) REVERT: B 188 ASP cc_start: 0.7895 (p0) cc_final: 0.7326 (t0) outliers start: 23 outliers final: 9 residues processed: 66 average time/residue: 0.0780 time to fit residues: 7.1170 Evaluate side-chains 53 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 VAL 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 Chi-restraints excluded: chain B residue 333 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.098397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076382 restraints weight = 13865.820| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.68 r_work: 0.3011 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6705 Z= 0.119 Angle : 0.556 7.639 9045 Z= 0.285 Chirality : 0.043 0.157 986 Planarity : 0.003 0.056 1170 Dihedral : 4.815 30.765 908 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.69 % Allowed : 11.03 % 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 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: -0.19 (0.29), residues: 807 helix: 1.31 (0.27), residues: 363 sheet: -0.76 (0.40), residues: 127 loop : -1.55 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.018 0.001 TYR A 446 PHE 0.010 0.001 PHE A 385 TRP 0.012 0.001 TRP A1159 HIS 0.004 0.001 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6705) covalent geometry : angle 0.55596 ( 9045) hydrogen bonds : bond 0.04078 ( 333) hydrogen bonds : angle 4.48867 ( 987) *********************** 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 68 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.273 Fit side-chains REVERT: A 385 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.6632 (p90) REVERT: A 465 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8085 (tmt) REVERT: A 1027 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: B 188 ASP cc_start: 0.7901 (p0) cc_final: 0.7354 (t0) outliers start: 19 outliers final: 9 residues processed: 64 average time/residue: 0.0772 time to fit residues: 6.8754 Evaluate side-chains 56 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 221 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 20 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.097852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.075029 restraints weight = 14219.877| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.73 r_work: 0.2994 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6705 Z= 0.138 Angle : 0.565 7.612 9045 Z= 0.289 Chirality : 0.044 0.160 986 Planarity : 0.003 0.055 1170 Dihedral : 4.730 30.853 908 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.11 % Allowed : 11.88 % Favored : 85.01 % 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: 0.07 (0.29), residues: 807 helix: 1.44 (0.27), residues: 365 sheet: -0.58 (0.42), residues: 127 loop : -1.35 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1165 TYR 0.018 0.001 TYR A 446 PHE 0.014 0.001 PHE A 385 TRP 0.012 0.001 TRP A1159 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6705) covalent geometry : angle 0.56454 ( 9045) hydrogen bonds : bond 0.04171 ( 333) hydrogen bonds : angle 4.38764 ( 987) *********************** 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 67 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.267 Fit side-chains REVERT: A 385 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.6572 (p90) REVERT: A 465 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8103 (tmt) REVERT: A 1027 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: A 1116 MET cc_start: 0.9298 (ttt) cc_final: 0.9081 (ttm) REVERT: B 188 ASP cc_start: 0.7973 (p0) cc_final: 0.7412 (t0) outliers start: 22 outliers final: 10 residues processed: 63 average time/residue: 0.0649 time to fit residues: 5.9866 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 : 0.217 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.099195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077017 restraints weight = 14157.361| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.69 r_work: 0.3035 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6705 Z= 0.112 Angle : 0.544 7.693 9045 Z= 0.275 Chirality : 0.042 0.154 986 Planarity : 0.003 0.056 1170 Dihedral : 4.522 28.471 908 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.70 % Allowed : 13.01 % 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 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: 0.30 (0.30), residues: 807 helix: 1.60 (0.27), residues: 370 sheet: -0.45 (0.43), residues: 121 loop : -1.23 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1165 TYR 0.016 0.001 TYR A 446 PHE 0.009 0.001 PHE A1168 TRP 0.010 0.001 TRP A1159 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6705) covalent geometry : angle 0.54413 ( 9045) hydrogen bonds : bond 0.03817 ( 333) hydrogen bonds : angle 4.26863 ( 987) *********************** 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: 12 poor density : 50 time to evaluate : 0.241 Fit side-chains REVERT: A 465 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8087 (tmt) REVERT: A 537 LYS cc_start: 0.8616 (ptmm) cc_final: 0.8362 (ptmm) REVERT: A 1027 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: A 1116 MET cc_start: 0.9239 (ttt) cc_final: 0.9035 (ttm) REVERT: B 188 ASP cc_start: 0.7946 (p0) cc_final: 0.7446 (t0) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.0697 time to fit residues: 5.9987 Evaluate side-chains 54 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 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 = 0.098114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.075729 restraints weight = 14037.393| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.68 r_work: 0.3005 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6705 Z= 0.132 Angle : 0.547 8.217 9045 Z= 0.278 Chirality : 0.043 0.158 986 Planarity : 0.003 0.054 1170 Dihedral : 4.511 29.345 908 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.40 % Allowed : 12.31 % 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 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: 0.43 (0.30), residues: 807 helix: 1.68 (0.27), residues: 370 sheet: -0.37 (0.44), residues: 121 loop : -1.13 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1165 TYR 0.017 0.001 TYR A 446 PHE 0.013 0.001 PHE A 385 TRP 0.010 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6705) covalent geometry : angle 0.54678 ( 9045) hydrogen bonds : bond 0.03978 ( 333) hydrogen bonds : angle 4.23662 ( 987) *********************** 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 63 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.221 Fit side-chains REVERT: A 385 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.6479 (p90) REVERT: A 465 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8107 (tmt) REVERT: A 1027 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: A 1158 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.9004 (pp) REVERT: B 188 ASP cc_start: 0.7963 (p0) cc_final: 0.7436 (t0) outliers start: 17 outliers final: 9 residues processed: 60 average time/residue: 0.0626 time to fit residues: 5.6124 Evaluate side-chains 58 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 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 = 0.3557 r_free = 0.3557 target = 0.098169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075770 restraints weight = 13941.925| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.68 r_work: 0.3006 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3070 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= 0.130 Angle : 0.552 8.764 9045 Z= 0.281 Chirality : 0.043 0.158 986 Planarity : 0.003 0.054 1170 Dihedral : 4.522 29.234 908 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.12 % Allowed : 13.44 % 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 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: 0.54 (0.30), residues: 807 helix: 1.72 (0.27), residues: 369 sheet: -0.35 (0.44), residues: 121 loop : -0.98 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1165 TYR 0.017 0.001 TYR A 446 PHE 0.010 0.001 PHE A 385 TRP 0.010 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6705) covalent geometry : angle 0.55220 ( 9045) hydrogen bonds : bond 0.03933 ( 333) hydrogen bonds : angle 4.20474 ( 987) *********************** 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 60 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.247 Fit side-chains REVERT: A 385 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.6465 (p90) REVERT: A 465 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8132 (tmt) REVERT: A 1027 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: B 188 ASP cc_start: 0.7937 (p0) cc_final: 0.7449 (t0) outliers start: 15 outliers final: 9 residues processed: 57 average time/residue: 0.0581 time to fit residues: 5.1041 Evaluate side-chains 57 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.095065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.072461 restraints weight = 14112.654| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.64 r_work: 0.2935 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6705 Z= 0.232 Angle : 0.635 9.158 9045 Z= 0.324 Chirality : 0.047 0.176 986 Planarity : 0.004 0.049 1170 Dihedral : 4.931 34.408 908 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.26 % Allowed : 13.01 % 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 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: 0.41 (0.30), residues: 807 helix: 1.56 (0.26), residues: 371 sheet: -0.53 (0.41), residues: 140 loop : -0.93 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 425 TYR 0.020 0.002 TYR A 446 PHE 0.015 0.002 PHE A 385 TRP 0.010 0.001 TRP A1159 HIS 0.009 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 6705) covalent geometry : angle 0.63523 ( 9045) hydrogen bonds : bond 0.04697 ( 333) hydrogen bonds : angle 4.46520 ( 987) *********************** 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 61 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.222 Fit side-chains REVERT: A 385 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.6655 (p90) REVERT: A 1027 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: B 188 ASP cc_start: 0.7954 (p0) cc_final: 0.7393 (t0) outliers start: 16 outliers final: 9 residues processed: 58 average time/residue: 0.0636 time to fit residues: 5.5047 Evaluate side-chains 56 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 1027 ASP 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 Chi-restraints excluded: chain B residue 276 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.096934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074467 restraints weight = 14011.962| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.67 r_work: 0.2975 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3072 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= 0.147 Angle : 0.583 11.923 9045 Z= 0.294 Chirality : 0.044 0.161 986 Planarity : 0.003 0.053 1170 Dihedral : 4.763 31.450 908 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.70 % Allowed : 13.01 % 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 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: 0.59 (0.30), residues: 807 helix: 1.68 (0.27), residues: 369 sheet: -0.41 (0.42), residues: 140 loop : -0.78 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1206 TYR 0.018 0.002 TYR A 446 PHE 0.014 0.001 PHE A 385 TRP 0.010 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6705) covalent geometry : angle 0.58350 ( 9045) hydrogen bonds : bond 0.04182 ( 333) hydrogen bonds : angle 4.30422 ( 987) ********************** 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 57 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.255 Fit side-chains REVERT: A 385 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.6649 (p90) REVERT: A 1027 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: B 188 ASP cc_start: 0.7903 (p0) cc_final: 0.7325 (t0) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.0579 time to fit residues: 4.7664 Evaluate side-chains 56 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 1027 ASP Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 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 26 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 5 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 = 0.3552 r_free = 0.3552 target = 0.098162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076063 restraints weight = 13861.246| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.65 r_work: 0.2997 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6705 Z= 0.132 Angle : 0.563 11.597 9045 Z= 0.284 Chirality : 0.043 0.159 986 Planarity : 0.003 0.052 1170 Dihedral : 4.607 29.960 908 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.84 % Allowed : 13.30 % 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 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: 0.73 (0.30), residues: 807 helix: 1.81 (0.27), residues: 369 sheet: -0.34 (0.42), residues: 140 loop : -0.74 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 42 TYR 0.017 0.001 TYR A 446 PHE 0.009 0.001 PHE A1093 TRP 0.010 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6705) covalent geometry : angle 0.56267 ( 9045) hydrogen bonds : bond 0.04001 ( 333) hydrogen bonds : angle 4.21314 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1552.86 seconds wall clock time: 27 minutes 22.71 seconds (1642.71 seconds total)