Starting phenix.real_space_refine on Fri Feb 14 04:52:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pde_13335/02_2025/7pde_13335.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pde_13335/02_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_13335/02_2025/7pde_13335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pde_13335/02_2025/7pde_13335.map" model { file = "/net/cci-nas-00/data/ceres_data/7pde_13335/02_2025/7pde_13335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pde_13335/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.99, per 1000 atoms: 0.63 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: 2.79 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: 0.94 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: 3.09 Time building geometry restraints manager: 3.13 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: 1.790 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- 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= 0.367 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 *********************** 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 : 1.106 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: 0.2392 time to fit residues: 50.8109 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 : 1.192 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.053060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.042760 restraints weight = 74970.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.043861 restraints weight = 46013.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044895 restraints weight = 33494.202| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- 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= 0.226 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 *********************** 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 : 1.032 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: 0.8434 (m100) cc_final: 0.8132 (m100) REVERT: A 224 PHE cc_start: 0.9669 (t80) cc_final: 0.9307 (t80) REVERT: A 228 ILE cc_start: 0.9712 (mm) cc_final: 0.9488 (mm) REVERT: A 238 MET cc_start: 0.8666 (mmp) cc_final: 0.8448 (mmm) REVERT: A 256 PHE cc_start: 0.8753 (t80) cc_final: 0.8425 (t80) REVERT: A 318 MET cc_start: 0.8981 (tmm) cc_final: 0.8635 (tmm) REVERT: A 338 MET cc_start: 0.9106 (mtp) cc_final: 0.8650 (ttm) REVERT: A 469 MET cc_start: 0.9566 (ptp) cc_final: 0.9081 (ptm) REVERT: A 502 MET cc_start: 0.8091 (mmm) cc_final: 0.7886 (mmm) REVERT: A 849 MET cc_start: 0.8489 (ttt) cc_final: 0.7931 (tpp) REVERT: A 925 THR cc_start: 0.9484 (m) cc_final: 0.9283 (m) REVERT: A 1092 ASP cc_start: 0.9087 (m-30) cc_final: 0.8802 (m-30) REVERT: A 1108 ILE cc_start: 0.9464 (mm) cc_final: 0.9198 (mt) REVERT: A 1220 MET cc_start: 0.9507 (mtm) cc_final: 0.9240 (mtm) REVERT: B 110 MET cc_start: 0.9352 (mtt) cc_final: 0.8902 (mmm) REVERT: B 289 LEU cc_start: 0.9448 (tt) cc_final: 0.9214 (tt) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.2007 time to fit residues: 45.9425 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 : 1.175 ------------------------------------------------------------------------------- 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: 8.9990 chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.053571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043078 restraints weight = 75694.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.044394 restraints weight = 46405.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.045376 restraints weight = 33033.675| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9759 Z= 0.207 Angle : 0.645 12.025 13204 Z= 0.329 Chirality : 0.042 0.219 1488 Planarity : 0.004 0.058 1660 Dihedral : 4.990 44.068 1302 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -0.68 (0.24), residues: 1169 helix: 0.36 (0.19), residues: 692 sheet: -1.48 (0.45), residues: 117 loop : -1.51 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 130 HIS 0.011 0.001 HIS A1170 PHE 0.017 0.002 PHE A 397 TYR 0.016 0.002 TYR A 446 ARG 0.007 0.001 ARG A 305 *********************** 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 146 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8387 (m100) cc_final: 0.8122 (m100) REVERT: A 224 PHE cc_start: 0.9641 (t80) cc_final: 0.9256 (t80) REVERT: A 228 ILE cc_start: 0.9702 (mm) cc_final: 0.9479 (mm) REVERT: A 256 PHE cc_start: 0.8639 (t80) cc_final: 0.8322 (t80) REVERT: A 300 ILE cc_start: 0.9717 (pt) cc_final: 0.9510 (pt) REVERT: A 318 MET cc_start: 0.9063 (tmm) cc_final: 0.8796 (tmm) REVERT: A 469 MET cc_start: 0.9359 (ptp) cc_final: 0.9096 (ptm) REVERT: A 1092 ASP cc_start: 0.9122 (m-30) cc_final: 0.8828 (m-30) REVERT: A 1108 ILE cc_start: 0.9446 (mm) cc_final: 0.9047 (mt) REVERT: A 1145 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9118 (mm-30) REVERT: A 1183 LEU cc_start: 0.9670 (mt) cc_final: 0.9374 (mt) REVERT: A 1184 LEU cc_start: 0.9570 (tt) cc_final: 0.8647 (mt) REVERT: A 1220 MET cc_start: 0.9537 (mtm) cc_final: 0.9000 (mtp) REVERT: B 255 MET cc_start: 0.9437 (mmt) cc_final: 0.9141 (mmm) REVERT: B 289 LEU cc_start: 0.9400 (tt) cc_final: 0.9108 (tt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2014 time to fit residues: 42.3413 Evaluate side-chains 123 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 4 optimal weight: 0.2980 overall best weight: 2.0764 ------------------------------------------------------------------------------- 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 97 ASN ** B 124 ASN ** 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 = 0.3371 r_free = 0.3371 target = 0.054402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043782 restraints weight = 74567.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.045050 restraints weight = 46200.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.046074 restraints weight = 32766.926| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9759 Z= 0.178 Angle : 0.616 11.845 13204 Z= 0.311 Chirality : 0.041 0.172 1488 Planarity : 0.004 0.057 1660 Dihedral : 4.741 38.340 1302 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: -0.33 (0.25), residues: 1169 helix: 0.66 (0.19), residues: 697 sheet: -1.44 (0.45), residues: 121 loop : -1.40 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 130 HIS 0.005 0.001 HIS A 319 PHE 0.026 0.001 PHE A 397 TYR 0.020 0.002 TYR A 252 ARG 0.006 0.000 ARG B 61 *********************** 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 155 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.142 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: 0.9650 (t80) cc_final: 0.9258 (t80) REVERT: A 338 MET cc_start: 0.9184 (mtp) cc_final: 0.8156 (ttm) REVERT: A 429 LEU cc_start: 0.9779 (mt) cc_final: 0.9451 (tp) REVERT: A 465 MET cc_start: 0.8947 (tpp) cc_final: 0.8402 (tpt) REVERT: A 849 MET cc_start: 0.7807 (ttm) cc_final: 0.7232 (tpp) REVERT: A 1001 PHE cc_start: 0.9299 (m-80) cc_final: 0.9085 (m-80) REVERT: A 1092 ASP cc_start: 0.9097 (m-30) cc_final: 0.8829 (m-30) REVERT: A 1145 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8974 (mm-30) REVERT: A 1183 LEU cc_start: 0.9642 (mt) cc_final: 0.9352 (mt) REVERT: A 1184 LEU cc_start: 0.9535 (tt) cc_final: 0.8603 (mt) REVERT: A 1220 MET cc_start: 0.9485 (mtm) cc_final: 0.8885 (mtp) REVERT: B 255 MET cc_start: 0.9477 (mmt) cc_final: 0.9177 (mmm) REVERT: B 289 LEU cc_start: 0.9375 (tt) cc_final: 0.9015 (tt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1987 time to fit residues: 44.7859 Evaluate side-chains 124 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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: 5.9990 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 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 = 0.3367 r_free = 0.3367 target = 0.054296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043815 restraints weight = 75509.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.045070 restraints weight = 47383.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.046006 restraints weight = 34539.576| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9759 Z= 0.190 Angle : 0.627 11.858 13204 Z= 0.316 Chirality : 0.041 0.157 1488 Planarity : 0.004 0.055 1660 Dihedral : 4.622 35.572 1302 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.02 % 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: -0.13 (0.25), residues: 1169 helix: 0.78 (0.19), residues: 702 sheet: -1.22 (0.50), residues: 102 loop : -1.35 (0.35), residues: 365 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 0.051 0.002 PHE A 184 TYR 0.021 0.002 TYR A 446 ARG 0.004 0.000 ARG B 61 *********************** 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 150 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.9618 (t80) cc_final: 0.9269 (t80) REVERT: A 338 MET cc_start: 0.9142 (mtp) cc_final: 0.8099 (ttm) REVERT: A 397 PHE cc_start: 0.9055 (m-10) cc_final: 0.8781 (m-10) REVERT: A 849 MET cc_start: 0.7851 (ttm) cc_final: 0.7235 (tpp) REVERT: A 992 LEU cc_start: 0.9530 (mm) cc_final: 0.9303 (mm) REVERT: A 1001 PHE cc_start: 0.9254 (m-80) cc_final: 0.9029 (m-80) REVERT: A 1092 ASP cc_start: 0.9144 (m-30) cc_final: 0.8855 (m-30) REVERT: A 1146 MET cc_start: 0.9547 (ttm) cc_final: 0.9254 (mmm) REVERT: A 1220 MET cc_start: 0.9464 (mtm) cc_final: 0.8829 (mtp) REVERT: B 61 ARG cc_start: 0.9136 (mmp-170) cc_final: 0.8923 (tpt90) REVERT: B 65 VAL cc_start: 0.8435 (t) cc_final: 0.7217 (t) REVERT: B 255 MET cc_start: 0.9465 (mmt) cc_final: 0.9204 (mmm) REVERT: B 289 LEU cc_start: 0.9318 (tt) cc_final: 0.8967 (tt) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1836 time to fit residues: 40.9142 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 : 1.059 ------------------------------------------------------------------------------- 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: 0.9980 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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** ** B 124 ASN ** 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 = 0.3347 r_free = 0.3347 target = 0.053749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043376 restraints weight = 77911.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.044620 restraints weight = 47954.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045610 restraints weight = 34863.798| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9759 Z= 0.220 Angle : 0.637 11.902 13204 Z= 0.324 Chirality : 0.041 0.184 1488 Planarity : 0.004 0.053 1660 Dihedral : 4.690 34.996 1302 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % 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: -0.19 (0.25), residues: 1169 helix: 0.74 (0.19), residues: 702 sheet: -1.29 (0.51), residues: 102 loop : -1.35 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 995 HIS 0.011 0.001 HIS A 530 PHE 0.020 0.002 PHE A 256 TYR 0.024 0.002 TYR A 446 ARG 0.003 0.000 ARG A 487 *********************** 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 146 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.9614 (t80) cc_final: 0.9255 (t80) REVERT: A 229 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8834 (mp0) REVERT: A 238 MET cc_start: 0.8648 (mmp) cc_final: 0.8364 (mmm) REVERT: A 397 PHE cc_start: 0.9101 (m-10) cc_final: 0.8813 (m-10) REVERT: A 849 MET cc_start: 0.7917 (ttm) cc_final: 0.7295 (tpp) REVERT: A 1001 PHE cc_start: 0.9284 (m-80) cc_final: 0.9044 (m-80) REVERT: A 1092 ASP cc_start: 0.9162 (m-30) cc_final: 0.8871 (m-30) REVERT: A 1220 MET cc_start: 0.9482 (mtm) cc_final: 0.9173 (mtp) REVERT: B 65 VAL cc_start: 0.8436 (t) cc_final: 0.7136 (t) REVERT: B 255 MET cc_start: 0.9513 (mmt) cc_final: 0.9273 (mmm) REVERT: B 289 LEU cc_start: 0.9380 (tt) cc_final: 0.8992 (tt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2018 time to fit residues: 43.9891 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 : 1.188 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 41 optimal weight: 0.0670 chunk 72 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** 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 = 0.3383 r_free = 0.3383 target = 0.055232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.044392 restraints weight = 75017.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.045715 restraints weight = 46577.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046764 restraints weight = 33246.947| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9759 Z= 0.169 Angle : 0.640 11.822 13204 Z= 0.319 Chirality : 0.041 0.152 1488 Planarity : 0.004 0.052 1660 Dihedral : 4.624 31.516 1302 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.11 (0.25), residues: 1169 helix: 0.94 (0.19), residues: 702 sheet: -1.00 (0.50), residues: 101 loop : -1.21 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 995 HIS 0.007 0.001 HIS A 530 PHE 0.039 0.002 PHE A 184 TYR 0.024 0.001 TYR A 446 ARG 0.010 0.000 ARG A 305 *********************** 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 157 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.076 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 238 MET cc_start: 0.8669 (mmp) cc_final: 0.8415 (mmm) REVERT: A 397 PHE cc_start: 0.9001 (m-10) cc_final: 0.8681 (m-10) REVERT: A 465 MET cc_start: 0.9543 (mtt) cc_final: 0.9121 (mtt) REVERT: A 849 MET cc_start: 0.7883 (ttm) cc_final: 0.7285 (tpp) REVERT: A 992 LEU cc_start: 0.9549 (mm) cc_final: 0.9318 (mm) REVERT: A 1001 PHE cc_start: 0.9234 (m-80) cc_final: 0.9009 (m-80) REVERT: A 1033 LEU cc_start: 0.9670 (tt) cc_final: 0.9206 (pp) REVERT: A 1073 GLU cc_start: 0.7294 (mp0) cc_final: 0.7091 (mp0) REVERT: A 1092 ASP cc_start: 0.9103 (m-30) cc_final: 0.8823 (m-30) REVERT: A 1146 MET cc_start: 0.9607 (ttm) cc_final: 0.9230 (mmm) REVERT: A 1220 MET cc_start: 0.9469 (mtm) cc_final: 0.9187 (mtp) REVERT: B 255 MET cc_start: 0.9456 (mmt) cc_final: 0.9217 (mmm) REVERT: B 289 LEU cc_start: 0.9287 (tt) cc_final: 0.9033 (tt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2038 time to fit residues: 45.9599 Evaluate side-chains 127 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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: 0.9980 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 51 optimal weight: 0.0040 chunk 17 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** 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 = 0.3369 r_free = 0.3369 target = 0.054656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043919 restraints weight = 76793.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.045266 restraints weight = 47652.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.045997 restraints weight = 34127.081| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9759 Z= 0.200 Angle : 0.653 12.071 13204 Z= 0.329 Chirality : 0.041 0.145 1488 Planarity : 0.004 0.050 1660 Dihedral : 4.645 30.607 1302 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 0.92 (0.19), residues: 704 sheet: -1.10 (0.49), residues: 101 loop : -1.15 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 995 HIS 0.005 0.001 HIS A 530 PHE 0.054 0.002 PHE A 184 TYR 0.046 0.002 TYR A 252 ARG 0.007 0.000 ARG A 305 *********************** 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 153 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.032 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: 0.9554 (m-80) cc_final: 0.9321 (m-80) REVERT: A 238 MET cc_start: 0.8659 (mmp) cc_final: 0.8413 (mmm) REVERT: A 465 MET cc_start: 0.9552 (mtt) cc_final: 0.9254 (mtt) REVERT: A 469 MET cc_start: 0.9384 (ppp) cc_final: 0.9141 (ppp) REVERT: A 486 MET cc_start: 0.8059 (tmm) cc_final: 0.7521 (tmm) REVERT: A 849 MET cc_start: 0.7958 (ttm) cc_final: 0.7370 (tpp) REVERT: A 992 LEU cc_start: 0.9500 (mm) cc_final: 0.9258 (mm) REVERT: A 1001 PHE cc_start: 0.9272 (m-80) cc_final: 0.9014 (m-80) REVERT: A 1033 LEU cc_start: 0.9651 (tt) cc_final: 0.9199 (pp) REVERT: A 1092 ASP cc_start: 0.9127 (m-30) cc_final: 0.8838 (m-30) REVERT: A 1146 MET cc_start: 0.9609 (ttm) cc_final: 0.9127 (mmm) REVERT: A 1220 MET cc_start: 0.9466 (mtm) cc_final: 0.9166 (mtp) REVERT: B 110 MET cc_start: 0.9115 (mtt) cc_final: 0.8659 (mmm) REVERT: B 255 MET cc_start: 0.9491 (mmt) cc_final: 0.9265 (mmm) REVERT: B 289 LEU cc_start: 0.9322 (tt) cc_final: 0.9018 (tt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1959 time to fit residues: 44.2032 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 : 1.021 ------------------------------------------------------------------------------- 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: 20.0000 chunk 84 optimal weight: 0.0570 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 883 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.056786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.045689 restraints weight = 74431.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.047099 restraints weight = 47280.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.047881 restraints weight = 34130.707| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9759 Z= 0.163 Angle : 0.662 11.752 13204 Z= 0.329 Chirality : 0.042 0.197 1488 Planarity : 0.003 0.050 1660 Dihedral : 4.480 26.029 1302 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 0.24 (0.25), residues: 1169 helix: 0.98 (0.19), residues: 701 sheet: -0.99 (0.46), residues: 121 loop : -0.97 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 995 HIS 0.006 0.001 HIS A 893 PHE 0.050 0.002 PHE A 184 TYR 0.030 0.001 TYR A 446 ARG 0.005 0.000 ARG A 305 *********************** 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 167 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.160 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 153 LEU cc_start: 0.9057 (tt) cc_final: 0.8792 (mt) REVERT: A 184 PHE cc_start: 0.9558 (m-80) cc_final: 0.9198 (m-80) REVERT: A 238 MET cc_start: 0.8602 (mmp) cc_final: 0.8295 (mmp) REVERT: A 252 TYR cc_start: 0.7612 (t80) cc_final: 0.7348 (t80) REVERT: A 465 MET cc_start: 0.9540 (mtt) cc_final: 0.9208 (mtt) REVERT: A 469 MET cc_start: 0.9338 (ppp) cc_final: 0.9123 (ppp) REVERT: A 849 MET cc_start: 0.7853 (ttm) cc_final: 0.7297 (tpp) REVERT: A 925 THR cc_start: 0.9525 (m) cc_final: 0.9105 (m) REVERT: A 988 PHE cc_start: 0.9348 (t80) cc_final: 0.9125 (t80) REVERT: A 992 LEU cc_start: 0.9496 (mm) cc_final: 0.8931 (mm) REVERT: A 995 TRP cc_start: 0.8288 (m100) cc_final: 0.7448 (m100) REVERT: A 1001 PHE cc_start: 0.9261 (m-80) cc_final: 0.8995 (m-80) REVERT: A 1092 ASP cc_start: 0.9063 (m-30) cc_final: 0.8765 (m-30) REVERT: A 1108 ILE cc_start: 0.9237 (mt) cc_final: 0.8779 (mm) REVERT: A 1146 MET cc_start: 0.9577 (ttm) cc_final: 0.9098 (mmm) REVERT: A 1220 MET cc_start: 0.9409 (mtm) cc_final: 0.8564 (mtp) REVERT: B 110 MET cc_start: 0.9056 (mtt) cc_final: 0.8656 (mmm) REVERT: B 255 MET cc_start: 0.9423 (mmt) cc_final: 0.9179 (mmm) REVERT: B 289 LEU cc_start: 0.9279 (tt) cc_final: 0.9037 (tt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2004 time to fit residues: 48.6988 Evaluate side-chains 131 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 883 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN A1193 ASN ** B 93 GLN ** 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 278 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.054983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044369 restraints weight = 78014.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045673 restraints weight = 50439.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.046419 restraints weight = 36888.472| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9759 Z= 0.229 Angle : 0.678 12.031 13204 Z= 0.341 Chirality : 0.042 0.173 1488 Planarity : 0.004 0.049 1660 Dihedral : 4.564 29.089 1302 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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: 0.26 (0.25), residues: 1169 helix: 1.00 (0.20), residues: 698 sheet: -1.17 (0.45), residues: 122 loop : -0.85 (0.37), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 995 HIS 0.013 0.001 HIS A 288 PHE 0.038 0.002 PHE A 184 TYR 0.032 0.002 TYR A 446 ARG 0.007 0.001 ARG A 305 ********************** 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 151 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.9560 (m-80) cc_final: 0.9186 (m-80) REVERT: A 238 MET cc_start: 0.8649 (mmp) cc_final: 0.8350 (mmm) REVERT: A 252 TYR cc_start: 0.7520 (t80) cc_final: 0.6777 (t80) REVERT: A 256 PHE cc_start: 0.8276 (t80) cc_final: 0.8021 (t80) REVERT: A 465 MET cc_start: 0.9500 (mtt) cc_final: 0.9161 (mtt) REVERT: A 849 MET cc_start: 0.7983 (ttm) cc_final: 0.7405 (tpp) REVERT: A 896 MET cc_start: 0.9634 (ttm) cc_final: 0.9362 (tpp) REVERT: A 925 THR cc_start: 0.9579 (m) cc_final: 0.9042 (m) REVERT: A 992 LEU cc_start: 0.9434 (mm) cc_final: 0.9120 (mm) REVERT: A 995 TRP cc_start: 0.8232 (m100) cc_final: 0.7410 (m100) REVERT: A 1001 PHE cc_start: 0.9286 (m-80) cc_final: 0.9035 (m-80) REVERT: A 1092 ASP cc_start: 0.9100 (m-30) cc_final: 0.8876 (m-30) REVERT: A 1220 MET cc_start: 0.9444 (mtm) cc_final: 0.9141 (mtp) REVERT: B 110 MET cc_start: 0.9059 (mtt) cc_final: 0.8638 (mmm) REVERT: B 255 MET cc_start: 0.9483 (mmt) cc_final: 0.9276 (mmm) REVERT: B 289 LEU cc_start: 0.9312 (tt) cc_final: 0.9084 (tt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1874 time to fit residues: 41.9814 Evaluate side-chains 115 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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: 0.8980 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3420 r_free = 0.3420 target = 0.056583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045714 restraints weight = 75330.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.047092 restraints weight = 48594.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048043 restraints weight = 35265.754| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9759 Z= 0.170 Angle : 0.672 11.821 13204 Z= 0.331 Chirality : 0.041 0.184 1488 Planarity : 0.003 0.049 1660 Dihedral : 4.455 26.701 1302 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: 0.31 (0.25), residues: 1169 helix: 1.02 (0.20), residues: 699 sheet: -1.10 (0.45), residues: 127 loop : -0.81 (0.37), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 995 HIS 0.004 0.001 HIS A 530 PHE 0.037 0.002 PHE A 184 TYR 0.035 0.002 TYR A 909 ARG 0.006 0.000 ARG A 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2705.90 seconds wall clock time: 49 minutes 44.97 seconds (2984.97 seconds total)