Starting phenix.real_space_refine on Sun Jul 27 22:50:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pde_13335/07_2025/7pde_13335.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pde_13335/07_2025/7pde_13335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pde_13335/07_2025/7pde_13335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pde_13335/07_2025/7pde_13335.map" model { file = "/net/cci-nas-00/data/ceres_data/7pde_13335/07_2025/7pde_13335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pde_13335/07_2025/7pde_13335.cif" } resolution = 4.5 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= 0.002 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 69 5.16 5 C 6144 2.51 5 N 1604 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9553 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6711 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 825} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 5.51, per 1000 atoms: 0.58 Number of scatterers: 9553 At special positions: 0 Unit cell: (166.05, 103.68, 115.02, 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 69 16.00 P 3 15.00 Mg 1 11.99 O 1732 8.00 N 1604 7.00 C 6144 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: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 62.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 99 through 137 removed outlier: 3.552A pdb=" N MET A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.896A pdb=" N HIS A 137 " --> pdb=" O TYR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 163 Processing helix chain 'A' and resid 171 through 193 removed outlier: 4.528A pdb=" N GLN A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 238 removed outlier: 4.309A pdb=" N SER A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 261 Processing helix chain 'A' and resid 279 through 336 removed outlier: 4.254A pdb=" N VAL A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 434 removed outlier: 3.850A pdb=" N GLU A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 480 Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.549A 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 782 through 808 Processing helix chain 'A' and resid 817 through 843 removed outlier: 3.972A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 858 Processing helix chain 'A' and resid 862 through 881 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 882 through 884 No H-bonds generated for 'chain 'A' and resid 882 through 884' Processing helix chain 'A' and resid 891 through 907 Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.847A pdb=" N PHE A 912 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 936 Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 977 through 1037 removed outlier: 3.564A pdb=" N GLN A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 Processing helix chain 'A' and resid 1067 through 1072 Processing helix chain 'A' and resid 1079 through 1098 removed outlier: 3.797A pdb=" N TYR A1083 " --> pdb=" O GLY A1079 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A1096 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1105 removed outlier: 3.561A pdb=" N SER A1104 " --> pdb=" O ASP A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1156 removed outlier: 3.967A pdb=" N ASP A1151 " --> pdb=" O MET A1147 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A1152 " --> pdb=" O ARG A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1200 removed outlier: 3.718A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1220 removed outlier: 3.503A pdb=" N VAL A1216 " --> pdb=" O GLU A1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 89 through 111 removed outlier: 4.111A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 4.087A 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 Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.534A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 174 through 182 removed outlier: 3.509A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 228 through 238 removed outlier: 3.898A pdb=" N TRP B 234 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 313 through 316 Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.104A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 388 removed outlier: 4.389A pdb=" N LEU B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.291A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 531 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 1106 through 1111 removed outlier: 4.821A pdb=" N LYS A1107 " --> pdb=" O ALA A1118 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A1118 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS A1170 " --> pdb=" O SER A1210 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 213 removed outlier: 6.036A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA B 243 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL B 247 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 46 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ALA B 249 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1686 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: 3.20 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3055 1.34 - 1.46: 2250 1.46 - 1.58: 4343 1.58 - 1.69: 5 1.69 - 1.81: 106 Bond restraints: 9759 Sorted by residual: bond pdb=" C HIS A 239 " pdb=" N LEU A 240 " ideal model delta sigma weight residual 1.331 1.238 0.093 2.07e-02 2.33e+03 2.03e+01 bond pdb=" CA TYR A 909 " pdb=" C TYR A 909 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.45e-02 4.76e+03 9.97e+00 bond pdb=" CA LEU B 43 " pdb=" CB LEU B 43 " ideal model delta sigma weight residual 1.526 1.503 0.024 1.53e-02 4.27e+03 2.39e+00 bond pdb=" CA GLY A1167 " pdb=" C GLY A1167 " ideal model delta sigma weight residual 1.520 1.509 0.011 7.30e-03 1.88e+04 2.29e+00 bond pdb=" CB PHE A1001 " pdb=" CG PHE A1001 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.27e+00 ... (remaining 9754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 13016 2.47 - 4.95: 166 4.95 - 7.42: 17 7.42 - 9.90: 2 9.90 - 12.37: 3 Bond angle restraints: 13204 Sorted by residual: angle pdb=" N VAL A 337 " pdb=" CA VAL A 337 " pdb=" C VAL A 337 " ideal model delta sigma weight residual 113.71 109.46 4.25 9.50e-01 1.11e+00 2.00e+01 angle pdb=" N VAL B 134 " pdb=" CA VAL B 134 " pdb=" C VAL B 134 " ideal model delta sigma weight residual 111.91 107.99 3.92 8.90e-01 1.26e+00 1.94e+01 angle pdb=" C SER A1130 " pdb=" N HIS A1131 " pdb=" CA HIS A1131 " ideal model delta sigma weight residual 120.65 114.79 5.86 1.36e+00 5.41e-01 1.86e+01 angle pdb=" C THR A 196 " pdb=" N PRO A 197 " pdb=" CD PRO A 197 " ideal model delta sigma weight residual 125.00 137.37 -12.37 4.10e+00 5.95e-02 9.11e+00 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 112.98 109.41 3.57 1.25e+00 6.40e-01 8.17e+00 ... (remaining 13199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5132 17.52 - 35.03: 547 35.03 - 52.55: 99 52.55 - 70.07: 10 70.07 - 87.58: 12 Dihedral angle restraints: 5800 sinusoidal: 2329 harmonic: 3471 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 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA CYS A 910 " pdb=" C CYS A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR A 236 " pdb=" C THR A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 5797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 880 0.033 - 0.067: 424 0.067 - 0.100: 146 0.100 - 0.133: 33 0.133 - 0.166: 5 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CA ASP B 215 " pdb=" N ASP B 215 " pdb=" C ASP B 215 " pdb=" CB ASP B 215 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" C3' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C4' GSP B 501 " pdb=" O3' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.63 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA HIS B 64 " pdb=" N HIS B 64 " pdb=" C HIS B 64 " pdb=" CB HIS B 64 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1485 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A1038 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 993 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C LEU A 993 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 993 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 994 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 815 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 816 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 816 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 816 " 0.020 5.00e-02 4.00e+02 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 152 2.47 - 3.08: 8059 3.08 - 3.69: 16539 3.69 - 4.29: 23342 4.29 - 4.90: 34643 Nonbonded interactions: 82735 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.869 2.170 nonbonded pdb=" O3G GSP B 501 " pdb="MG MG B 502 " model vdw 2.027 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.097 3.040 nonbonded pdb=" OG SER B 54 " pdb=" OG1 THR B 204 " model vdw 2.125 3.040 nonbonded pdb=" O ARG A 503 " pdb=" NZ LYS A1107 " model vdw 2.131 3.120 ... (remaining 82730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.730 Find NCS groups from input model: 0.100 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.006 0.093 9759 Z= 0.300 Angle : 0.788 12.375 13204 Z= 0.459 Chirality : 0.043 0.166 1488 Planarity : 0.004 0.047 1660 Dihedral : 14.841 87.582 3554 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 29.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.19 % Allowed : 8.45 % Favored : 91.35 % 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: -3.63 (0.21), residues: 1169 helix: -2.14 (0.16), residues: 669 sheet: -2.59 (0.38), residues: 126 loop : -2.43 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 130 HIS 0.008 0.002 HIS A 319 PHE 0.023 0.002 PHE A 232 TYR 0.018 0.002 TYR A 445 ARG 0.007 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.15687 ( 583) hydrogen bonds : angle 6.86279 ( 1686) covalent geometry : bond 0.00571 ( 9759) covalent geometry : angle 0.78846 (13204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8591 (m100) cc_final: 0.8330 (m100) REVERT: A 229 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8525 (mt-10) REVERT: A 288 HIS cc_start: 0.9197 (m90) cc_final: 0.8955 (m90) REVERT: A 338 MET cc_start: 0.9000 (mtp) cc_final: 0.8620 (ttm) REVERT: A 502 MET cc_start: 0.8407 (mmm) cc_final: 0.8129 (mmm) REVERT: A 840 ARG cc_start: 0.5571 (mtt-85) cc_final: 0.4866 (ttp80) REVERT: A 849 MET cc_start: 0.8664 (ttt) cc_final: 0.8104 (tpp) REVERT: A 991 LEU cc_start: 0.9797 (mm) cc_final: 0.9513 (tt) REVERT: A 1002 GLU cc_start: 0.9194 (tp30) cc_final: 0.8810 (mt-10) REVERT: A 1022 ILE cc_start: 0.8276 (tp) cc_final: 0.7770 (tp) REVERT: A 1146 MET cc_start: 0.9504 (ptm) cc_final: 0.9187 (ppp) REVERT: A 1147 MET cc_start: 0.9401 (tpp) cc_final: 0.9170 (tpp) REVERT: B 65 VAL cc_start: 0.8254 (t) cc_final: 0.7620 (t) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.2384 time to fit residues: 50.6910 Evaluate side-chains 118 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS A 315 GLN A1040 HIS A1075 ASN A1156 ASN A1237 GLN ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 271 ASN B 362 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.053151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.042956 restraints weight = 75297.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044194 restraints weight = 46577.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045142 restraints weight = 33174.700| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9759 Z= 0.167 Angle : 0.685 12.032 13204 Z= 0.351 Chirality : 0.043 0.252 1488 Planarity : 0.004 0.058 1660 Dihedral : 5.189 48.715 1302 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.72 % 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: -1.56 (0.23), residues: 1169 helix: -0.38 (0.18), residues: 693 sheet: -1.94 (0.40), residues: 123 loop : -1.74 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 130 HIS 0.009 0.001 HIS A 292 PHE 0.028 0.002 PHE A 121 TYR 0.021 0.002 TYR A 252 ARG 0.006 0.001 ARG A 999 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 583) hydrogen bonds : angle 5.23155 ( 1686) covalent geometry : bond 0.00347 ( 9759) covalent geometry : angle 0.68491 (13204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8435 (m100) cc_final: 0.8135 (m100) REVERT: A 224 PHE cc_start: 0.9660 (t80) cc_final: 0.9301 (t80) REVERT: A 228 ILE cc_start: 0.9707 (mm) cc_final: 0.9486 (mm) REVERT: A 256 PHE cc_start: 0.8745 (t80) cc_final: 0.8413 (t80) REVERT: A 318 MET cc_start: 0.8983 (tmm) cc_final: 0.8633 (tmm) REVERT: A 338 MET cc_start: 0.9107 (mtp) cc_final: 0.8648 (ttm) REVERT: A 469 MET cc_start: 0.9561 (ptp) cc_final: 0.9074 (ptm) REVERT: A 502 MET cc_start: 0.8085 (mmm) cc_final: 0.7876 (mmm) REVERT: A 849 MET cc_start: 0.8491 (ttt) cc_final: 0.7932 (tpp) REVERT: A 925 THR cc_start: 0.9484 (m) cc_final: 0.9282 (m) REVERT: A 1092 ASP cc_start: 0.9084 (m-30) cc_final: 0.8798 (m-30) REVERT: A 1108 ILE cc_start: 0.9461 (mm) cc_final: 0.9199 (mt) REVERT: A 1220 MET cc_start: 0.9507 (mtm) cc_final: 0.9238 (mtm) REVERT: B 110 MET cc_start: 0.9348 (mtt) cc_final: 0.8900 (mmm) REVERT: B 289 LEU cc_start: 0.9445 (tt) cc_final: 0.9214 (tt) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.1924 time to fit residues: 44.3988 Evaluate side-chains 124 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.053650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043187 restraints weight = 75870.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044453 restraints weight = 46489.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.045274 restraints weight = 32989.758| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9759 Z= 0.155 Angle : 0.644 12.012 13204 Z= 0.329 Chirality : 0.042 0.222 1488 Planarity : 0.004 0.058 1660 Dihedral : 4.984 43.883 1302 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: -0.66 (0.24), residues: 1169 helix: 0.38 (0.19), residues: 692 sheet: -1.47 (0.45), residues: 117 loop : -1.51 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 130 HIS 0.010 0.001 HIS A1170 PHE 0.021 0.002 PHE A 397 TYR 0.016 0.002 TYR A 446 ARG 0.007 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 583) hydrogen bonds : angle 4.85200 ( 1686) covalent geometry : bond 0.00320 ( 9759) covalent geometry : angle 0.64447 (13204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8404 (m100) cc_final: 0.8139 (m100) REVERT: A 224 PHE cc_start: 0.9626 (t80) cc_final: 0.9245 (t80) REVERT: A 228 ILE cc_start: 0.9699 (mm) cc_final: 0.9479 (mm) REVERT: A 256 PHE cc_start: 0.8636 (t80) cc_final: 0.8314 (t80) REVERT: A 300 ILE cc_start: 0.9700 (pt) cc_final: 0.9494 (pt) REVERT: A 318 MET cc_start: 0.9065 (tmm) cc_final: 0.8802 (tmm) REVERT: A 469 MET cc_start: 0.9342 (ptp) cc_final: 0.9072 (ptm) REVERT: A 1092 ASP cc_start: 0.9125 (m-30) cc_final: 0.8904 (m-30) REVERT: A 1108 ILE cc_start: 0.9448 (mm) cc_final: 0.9041 (mt) REVERT: A 1145 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9119 (mm-30) REVERT: A 1183 LEU cc_start: 0.9668 (mt) cc_final: 0.9376 (mt) REVERT: A 1184 LEU cc_start: 0.9572 (tt) cc_final: 0.8657 (mt) REVERT: A 1220 MET cc_start: 0.9539 (mtm) cc_final: 0.9003 (mtp) REVERT: B 255 MET cc_start: 0.9445 (mmt) cc_final: 0.9158 (mmm) REVERT: B 289 LEU cc_start: 0.9395 (tt) cc_final: 0.9102 (tt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1891 time to fit residues: 40.7662 Evaluate side-chains 121 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.042987 restraints weight = 76087.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.044235 restraints weight = 46917.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045202 restraints weight = 33392.014| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9759 Z= 0.173 Angle : 0.645 12.018 13204 Z= 0.329 Chirality : 0.041 0.203 1488 Planarity : 0.004 0.057 1660 Dihedral : 4.878 40.945 1302 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: -0.46 (0.25), residues: 1169 helix: 0.55 (0.19), residues: 692 sheet: -1.54 (0.44), residues: 121 loop : -1.40 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 130 HIS 0.005 0.001 HIS A 319 PHE 0.026 0.002 PHE A 397 TYR 0.020 0.002 TYR A 122 ARG 0.005 0.001 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 583) hydrogen bonds : angle 4.75007 ( 1686) covalent geometry : bond 0.00359 ( 9759) covalent geometry : angle 0.64476 (13204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.9658 (t80) cc_final: 0.9281 (t80) REVERT: A 238 MET cc_start: 0.8595 (mmp) cc_final: 0.8383 (mmm) REVERT: A 338 MET cc_start: 0.9177 (mtp) cc_final: 0.8122 (ttm) REVERT: A 429 LEU cc_start: 0.9781 (mt) cc_final: 0.9434 (tp) REVERT: A 465 MET cc_start: 0.8979 (tpp) cc_final: 0.8382 (tpt) REVERT: A 849 MET cc_start: 0.7836 (ttm) cc_final: 0.7246 (tpp) REVERT: A 1001 PHE cc_start: 0.9305 (m-80) cc_final: 0.9104 (m-80) REVERT: A 1145 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8969 (mm-30) REVERT: A 1184 LEU cc_start: 0.9580 (tt) cc_final: 0.8711 (mt) REVERT: A 1220 MET cc_start: 0.9505 (mtm) cc_final: 0.8881 (mtp) REVERT: B 255 MET cc_start: 0.9482 (mmt) cc_final: 0.9206 (mmm) REVERT: B 289 LEU cc_start: 0.9395 (tt) cc_final: 0.9072 (tt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1925 time to fit residues: 41.2525 Evaluate side-chains 121 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 97 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.053994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.043461 restraints weight = 75319.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.044743 restraints weight = 47287.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045707 restraints weight = 33996.092| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9759 Z= 0.135 Angle : 0.631 11.870 13204 Z= 0.317 Chirality : 0.041 0.163 1488 Planarity : 0.004 0.056 1660 Dihedral : 4.722 37.518 1302 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.41 % 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 (0.25), residues: 1169 helix: 0.78 (0.19), residues: 697 sheet: -1.41 (0.46), residues: 121 loop : -1.33 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 130 HIS 0.008 0.001 HIS A 292 PHE 0.047 0.002 PHE A 184 TYR 0.021 0.001 TYR A 446 ARG 0.004 0.000 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 583) hydrogen bonds : angle 4.55437 ( 1686) covalent geometry : bond 0.00283 ( 9759) covalent geometry : angle 0.63083 (13204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.9615 (t80) cc_final: 0.9278 (t80) REVERT: A 338 MET cc_start: 0.9122 (mtp) cc_final: 0.8079 (ttm) REVERT: A 849 MET cc_start: 0.7811 (ttm) cc_final: 0.7196 (tpp) REVERT: A 992 LEU cc_start: 0.9535 (mm) cc_final: 0.9297 (mm) REVERT: A 1001 PHE cc_start: 0.9261 (m-80) cc_final: 0.9053 (m-80) REVERT: A 1146 MET cc_start: 0.9592 (ttm) cc_final: 0.9297 (mmm) REVERT: A 1182 LYS cc_start: 0.8983 (tppt) cc_final: 0.8754 (mmmt) REVERT: A 1220 MET cc_start: 0.9463 (mtm) cc_final: 0.8818 (mtp) REVERT: B 255 MET cc_start: 0.9462 (mmt) cc_final: 0.9203 (mmm) REVERT: B 289 LEU cc_start: 0.9345 (tt) cc_final: 0.8989 (tt) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1909 time to fit residues: 44.2297 Evaluate side-chains 122 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.053593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.043103 restraints weight = 76534.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.044339 restraints weight = 47360.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045354 restraints weight = 33992.582| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9759 Z= 0.165 Angle : 0.642 11.933 13204 Z= 0.326 Chirality : 0.041 0.184 1488 Planarity : 0.004 0.055 1660 Dihedral : 4.734 36.814 1302 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: -0.10 (0.25), residues: 1169 helix: 0.78 (0.19), residues: 695 sheet: -1.20 (0.51), residues: 102 loop : -1.24 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 995 HIS 0.012 0.001 HIS A 530 PHE 0.048 0.002 PHE A 184 TYR 0.022 0.002 TYR A 446 ARG 0.004 0.000 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 583) hydrogen bonds : angle 4.59679 ( 1686) covalent geometry : bond 0.00340 ( 9759) covalent geometry : angle 0.64209 (13204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.9599 (m-80) cc_final: 0.9351 (m-80) REVERT: A 229 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8824 (mp0) REVERT: A 238 MET cc_start: 0.8663 (mmp) cc_final: 0.8379 (mmm) REVERT: A 849 MET cc_start: 0.7901 (ttm) cc_final: 0.7280 (tpp) REVERT: A 987 PHE cc_start: 0.9135 (t80) cc_final: 0.8675 (t80) REVERT: A 992 LEU cc_start: 0.9580 (mm) cc_final: 0.9371 (mm) REVERT: A 1001 PHE cc_start: 0.9286 (m-80) cc_final: 0.9059 (m-80) REVERT: A 1092 ASP cc_start: 0.9097 (m-30) cc_final: 0.8825 (m-30) REVERT: A 1220 MET cc_start: 0.9479 (mtm) cc_final: 0.9163 (mtp) REVERT: B 60 MET cc_start: 0.8949 (tpt) cc_final: 0.8549 (tpt) REVERT: B 255 MET cc_start: 0.9515 (mmt) cc_final: 0.9287 (mmm) REVERT: B 289 LEU cc_start: 0.9369 (tt) cc_final: 0.9031 (tt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1943 time to fit residues: 42.0728 Evaluate side-chains 122 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 94 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.052477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042259 restraints weight = 80267.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043496 restraints weight = 50375.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.044198 restraints weight = 36454.547| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9759 Z= 0.243 Angle : 0.723 13.360 13204 Z= 0.371 Chirality : 0.043 0.166 1488 Planarity : 0.005 0.068 1660 Dihedral : 5.015 40.639 1302 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: -0.35 (0.25), residues: 1169 helix: 0.55 (0.19), residues: 697 sheet: -1.58 (0.48), residues: 108 loop : -1.15 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 130 HIS 0.009 0.002 HIS B 220 PHE 0.043 0.002 PHE A 184 TYR 0.029 0.002 TYR A 252 ARG 0.010 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 583) hydrogen bonds : angle 4.90496 ( 1686) covalent geometry : bond 0.00496 ( 9759) covalent geometry : angle 0.72295 (13204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8746 (mp0) REVERT: A 238 MET cc_start: 0.8698 (mmp) cc_final: 0.8407 (mmm) REVERT: A 300 ILE cc_start: 0.9681 (pt) cc_final: 0.9476 (pt) REVERT: A 469 MET cc_start: 0.9357 (ppp) cc_final: 0.9085 (ppp) REVERT: A 849 MET cc_start: 0.8008 (ttm) cc_final: 0.7377 (tpp) REVERT: A 1092 ASP cc_start: 0.9169 (m-30) cc_final: 0.8910 (m-30) REVERT: A 1220 MET cc_start: 0.9491 (mtm) cc_final: 0.9163 (mtp) REVERT: B 60 MET cc_start: 0.9041 (tpt) cc_final: 0.8789 (tpt) REVERT: B 255 MET cc_start: 0.9504 (mmt) cc_final: 0.9237 (mmm) REVERT: B 289 LEU cc_start: 0.9379 (tt) cc_final: 0.9050 (tt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2225 time to fit residues: 46.0812 Evaluate side-chains 116 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.055311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.044305 restraints weight = 75649.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.045675 restraints weight = 47225.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046685 restraints weight = 33927.902| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9759 Z= 0.130 Angle : 0.666 11.881 13204 Z= 0.333 Chirality : 0.042 0.162 1488 Planarity : 0.004 0.068 1660 Dihedral : 4.709 35.254 1302 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 0.04 (0.25), residues: 1169 helix: 0.87 (0.20), residues: 695 sheet: -1.44 (0.48), residues: 110 loop : -1.00 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 995 HIS 0.006 0.001 HIS A 530 PHE 0.033 0.002 PHE A1001 TYR 0.028 0.001 TYR A 446 ARG 0.014 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 583) hydrogen bonds : angle 4.49237 ( 1686) covalent geometry : bond 0.00266 ( 9759) covalent geometry : angle 0.66561 (13204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.9668 (t80) cc_final: 0.9355 (t80) REVERT: A 238 MET cc_start: 0.8660 (mmp) cc_final: 0.8398 (mmm) REVERT: A 469 MET cc_start: 0.9369 (ppp) cc_final: 0.9089 (ppp) REVERT: A 486 MET cc_start: 0.7898 (tmm) cc_final: 0.7566 (tmm) REVERT: A 849 MET cc_start: 0.7688 (ttm) cc_final: 0.7133 (tpp) REVERT: A 896 MET cc_start: 0.9645 (ttm) cc_final: 0.9225 (tpp) REVERT: A 1092 ASP cc_start: 0.8944 (m-30) cc_final: 0.8692 (m-30) REVERT: A 1220 MET cc_start: 0.9469 (mtm) cc_final: 0.8580 (mtp) REVERT: B 60 MET cc_start: 0.8982 (tpt) cc_final: 0.8755 (tpp) REVERT: B 110 MET cc_start: 0.9114 (mtt) cc_final: 0.8644 (mmm) REVERT: B 255 MET cc_start: 0.9434 (mmt) cc_final: 0.9190 (mmm) REVERT: B 289 LEU cc_start: 0.9373 (tt) cc_final: 0.9023 (tt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2556 time to fit residues: 56.7712 Evaluate side-chains 122 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 56 optimal weight: 0.0670 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042709 restraints weight = 78279.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.043951 restraints weight = 49232.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.044974 restraints weight = 35194.877| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9759 Z= 0.204 Angle : 0.713 12.205 13204 Z= 0.365 Chirality : 0.043 0.168 1488 Planarity : 0.004 0.052 1660 Dihedral : 4.879 36.550 1302 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.10 (0.25), residues: 1169 helix: 0.76 (0.19), residues: 699 sheet: -1.47 (0.48), residues: 109 loop : -1.09 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 995 HIS 0.007 0.001 HIS B 220 PHE 0.027 0.002 PHE A 987 TYR 0.039 0.002 TYR A 446 ARG 0.013 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 583) hydrogen bonds : angle 4.72395 ( 1686) covalent geometry : bond 0.00423 ( 9759) covalent geometry : angle 0.71305 (13204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.9013 (mtt180) cc_final: 0.8307 (mtp85) REVERT: A 238 MET cc_start: 0.8739 (mmp) cc_final: 0.8393 (mmm) REVERT: A 469 MET cc_start: 0.9402 (ppp) cc_final: 0.9161 (ppp) REVERT: A 486 MET cc_start: 0.7896 (tmm) cc_final: 0.7428 (tmm) REVERT: A 849 MET cc_start: 0.7822 (ttm) cc_final: 0.7242 (tpp) REVERT: A 1001 PHE cc_start: 0.9293 (m-80) cc_final: 0.8939 (m-80) REVERT: A 1006 ARG cc_start: 0.3175 (ttm170) cc_final: 0.2944 (ttt180) REVERT: A 1092 ASP cc_start: 0.9070 (m-30) cc_final: 0.8803 (m-30) REVERT: A 1220 MET cc_start: 0.9489 (mtm) cc_final: 0.8561 (mtp) REVERT: B 60 MET cc_start: 0.9045 (tpt) cc_final: 0.8843 (tpp) REVERT: B 110 MET cc_start: 0.9160 (mtt) cc_final: 0.8689 (mmm) REVERT: B 255 MET cc_start: 0.9527 (mmt) cc_final: 0.9299 (mmm) REVERT: B 289 LEU cc_start: 0.9397 (tt) cc_final: 0.9135 (tt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2148 time to fit residues: 46.4466 Evaluate side-chains 119 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 0.4980 chunk 31 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.053916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043406 restraints weight = 78431.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.044702 restraints weight = 49965.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045625 restraints weight = 36145.457| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9759 Z= 0.172 Angle : 0.719 15.615 13204 Z= 0.363 Chirality : 0.042 0.183 1488 Planarity : 0.004 0.053 1660 Dihedral : 4.860 36.078 1302 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.07 (0.25), residues: 1169 helix: 0.75 (0.19), residues: 701 sheet: -1.37 (0.45), residues: 122 loop : -1.01 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 995 HIS 0.014 0.001 HIS A 288 PHE 0.028 0.002 PHE A 987 TYR 0.035 0.002 TYR A 446 ARG 0.013 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 583) hydrogen bonds : angle 4.67338 ( 1686) covalent geometry : bond 0.00363 ( 9759) covalent geometry : angle 0.71943 (13204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8297 (mtp85) REVERT: A 184 PHE cc_start: 0.9411 (m-80) cc_final: 0.9119 (m-10) REVERT: A 238 MET cc_start: 0.8651 (mmp) cc_final: 0.8348 (mmm) REVERT: A 469 MET cc_start: 0.9365 (ppp) cc_final: 0.9102 (ppp) REVERT: A 486 MET cc_start: 0.7896 (tmm) cc_final: 0.7369 (tmm) REVERT: A 849 MET cc_start: 0.7740 (ttm) cc_final: 0.7173 (tpp) REVERT: A 1001 PHE cc_start: 0.9245 (m-80) cc_final: 0.8913 (m-80) REVERT: A 1220 MET cc_start: 0.9463 (mtm) cc_final: 0.8529 (mtp) REVERT: B 60 MET cc_start: 0.9043 (tpt) cc_final: 0.8836 (tpp) REVERT: B 110 MET cc_start: 0.9132 (mtt) cc_final: 0.8669 (mmm) REVERT: B 255 MET cc_start: 0.9463 (mmt) cc_final: 0.9220 (mmm) REVERT: B 289 LEU cc_start: 0.9362 (tt) cc_final: 0.9090 (tt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2442 time to fit residues: 51.6612 Evaluate side-chains 118 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 overall best weight: 1.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.054940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044177 restraints weight = 76949.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.045484 restraints weight = 49276.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.046403 restraints weight = 35739.673| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9759 Z= 0.138 Angle : 0.679 11.948 13204 Z= 0.343 Chirality : 0.042 0.183 1488 Planarity : 0.004 0.053 1660 Dihedral : 4.683 32.955 1302 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.03 (0.25), residues: 1169 helix: 0.82 (0.20), residues: 701 sheet: -1.24 (0.48), residues: 116 loop : -1.00 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 995 HIS 0.003 0.001 HIS B 357 PHE 0.028 0.002 PHE A 987 TYR 0.033 0.002 TYR A 446 ARG 0.010 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 583) hydrogen bonds : angle 4.57812 ( 1686) covalent geometry : bond 0.00294 ( 9759) covalent geometry : angle 0.67858 (13204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.29 seconds wall clock time: 59 minutes 12.95 seconds (3552.95 seconds total)