Starting phenix.real_space_refine on Thu Mar 13 20:12:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cr1_16801/03_2025/8cr1_16801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cr1_16801/03_2025/8cr1_16801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cr1_16801/03_2025/8cr1_16801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cr1_16801/03_2025/8cr1_16801.map" model { file = "/net/cci-nas-00/data/ceres_data/8cr1_16801/03_2025/8cr1_16801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cr1_16801/03_2025/8cr1_16801.cif" } resolution = 3.2 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= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 76 5.16 5 C 5978 2.51 5 N 1502 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9205 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2464 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain breaks: 1 Chain: "C" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2138 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 1 Chain: "B" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2464 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2138 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2009 SG CYS A 289 35.437 43.592 12.321 1.00 37.49 S ATOM 2032 SG CYS A 292 33.793 45.853 15.139 1.00 32.41 S ATOM 6611 SG CYS B 289 35.863 47.142 12.343 1.00 37.99 S ATOM 6634 SG CYS B 292 37.505 44.880 15.160 1.00 34.33 S Time building chain proxies: 6.04, per 1000 atoms: 0.66 Number of scatterers: 9205 At special positions: 0 Unit cell: (72.09, 91.53, 136.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 76 16.00 O 1648 8.00 N 1502 7.00 C 5978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C1157 " distance=1.99 Simple disulfide: pdb=" SG CYS D 208 " - pdb=" SG CYS D 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D1157 " distance=2.07 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: 2.35 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 289 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 289 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 292 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 292 " Number of angles added : 6 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 73.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.714A pdb=" N ILE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 removed outlier: 3.622A pdb=" N CYS A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 removed outlier: 3.820A pdb=" N ASP A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 removed outlier: 4.013A pdb=" N LEU A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.219A pdb=" N LYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 159 removed outlier: 3.630A pdb=" N GLU A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.644A pdb=" N LEU A 177 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.591A pdb=" N SER A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 215 through 238 removed outlier: 3.973A pdb=" N ALA A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 239 through 242 removed outlier: 4.029A pdb=" N THR A 242 " --> pdb=" O PRO A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'C' and resid 192 through 206 Processing helix chain 'C' and resid 214 through 231 Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.951A pdb=" N ALA C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 291 Processing helix chain 'C' and resid 1006 through 1027 Processing helix chain 'C' and resid 1027 through 1032 Processing helix chain 'C' and resid 1032 through 1063 removed outlier: 4.349A pdb=" N VAL C1038 " --> pdb=" O PHE C1034 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C1044 " --> pdb=" O GLN C1040 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN C1045 " --> pdb=" O LYS C1041 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C1053 " --> pdb=" O MET C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1124 Processing helix chain 'C' and resid 1132 through 1136 Processing helix chain 'C' and resid 1139 through 1144 Processing helix chain 'C' and resid 1151 through 1169 removed outlier: 3.769A pdb=" N THR C1156 " --> pdb=" O GLY C1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.714A pdb=" N ILE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 3.622A pdb=" N CYS B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.820A pdb=" N ASP B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 removed outlier: 4.013A pdb=" N LEU B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 125 through 138 removed outlier: 4.219A pdb=" N LYS B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 159 removed outlier: 3.629A pdb=" N GLU B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.644A pdb=" N LEU B 177 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.591A pdb=" N SER B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Proline residue: B 199 - end of helix Processing helix chain 'B' and resid 215 through 238 removed outlier: 3.973A pdb=" N ALA B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 239 through 242 removed outlier: 4.028A pdb=" N THR B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 289 through 310 Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 214 through 231 Processing helix chain 'D' and resid 242 through 249 removed outlier: 3.952A pdb=" N ALA D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 291 Processing helix chain 'D' and resid 1006 through 1027 Processing helix chain 'D' and resid 1027 through 1032 Processing helix chain 'D' and resid 1032 through 1063 removed outlier: 4.349A pdb=" N VAL D1038 " --> pdb=" O PHE D1034 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU D1044 " --> pdb=" O GLN D1040 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN D1045 " --> pdb=" O LYS D1041 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D1053 " --> pdb=" O MET D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1124 Processing helix chain 'D' and resid 1132 through 1136 Processing helix chain 'D' and resid 1139 through 1144 Processing helix chain 'D' and resid 1151 through 1169 removed outlier: 3.769A pdb=" N THR D1156 " --> pdb=" O GLY D1152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 6.267A pdb=" N VAL A 68 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N MET A 103 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 70 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 69 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP A 166 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE A 71 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 274 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 275 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 318 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 277 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 6.267A pdb=" N VAL B 68 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET B 103 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE B 70 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 69 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP B 166 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE B 71 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN B 274 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 318 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL B 277 " --> pdb=" O LEU B 318 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2178 1.33 - 1.45: 1803 1.45 - 1.58: 5297 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 9400 Sorted by residual: bond pdb=" C PHE D1145 " pdb=" N PRO D1146 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.20e-02 6.94e+03 2.40e+00 bond pdb=" C PHE C1145 " pdb=" N PRO C1146 " ideal model delta sigma weight residual 1.333 1.351 -0.018 1.20e-02 6.94e+03 2.32e+00 bond pdb=" CA GLU B 251 " pdb=" CB GLU B 251 " ideal model delta sigma weight residual 1.534 1.511 0.023 1.65e-02 3.67e+03 2.00e+00 bond pdb=" CG GLU B 251 " pdb=" CD GLU B 251 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" CA GLU A 251 " pdb=" CB GLU A 251 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.65e-02 3.67e+03 1.84e+00 ... (remaining 9395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 12508 2.37 - 4.75: 161 4.75 - 7.12: 32 7.12 - 9.50: 7 9.50 - 11.87: 4 Bond angle restraints: 12712 Sorted by residual: angle pdb=" CB MET B 127 " pdb=" CG MET B 127 " pdb=" SD MET B 127 " ideal model delta sigma weight residual 112.70 124.57 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB MET A 127 " pdb=" CG MET A 127 " pdb=" SD MET A 127 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" C ALA A 135 " pdb=" N MET A 136 " pdb=" CA MET A 136 " ideal model delta sigma weight residual 122.38 115.86 6.52 1.81e+00 3.05e-01 1.30e+01 angle pdb=" C ALA B 135 " pdb=" N MET B 136 " pdb=" CA MET B 136 " ideal model delta sigma weight residual 122.38 115.87 6.51 1.81e+00 3.05e-01 1.29e+01 angle pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " pdb=" CD LYS A 290 " ideal model delta sigma weight residual 111.30 118.90 -7.60 2.30e+00 1.89e-01 1.09e+01 ... (remaining 12707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5154 17.86 - 35.71: 462 35.71 - 53.57: 84 53.57 - 71.42: 14 71.42 - 89.28: 6 Dihedral angle restraints: 5720 sinusoidal: 2316 harmonic: 3404 Sorted by residual: dihedral pdb=" CB CYS C 208 " pdb=" SG CYS C 208 " pdb=" SG CYS C 284 " pdb=" CB CYS C 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.72 53.28 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CB CYS D 208 " pdb=" SG CYS D 208 " pdb=" SG CYS D 284 " pdb=" CB CYS D 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.74 53.26 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" SG CYS C 275 " pdb=" CB CYS C1157 " pdb=" SG CYS C1157 " pdb=" CA CYS C1157 " ideal model delta sinusoidal sigma weight residual -73.00 -9.64 -63.36 1 2.00e+01 2.50e-03 1.32e+01 ... (remaining 5717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 936 0.036 - 0.071: 361 0.071 - 0.107: 119 0.107 - 0.143: 44 0.143 - 0.178: 8 Chirality restraints: 1468 Sorted by residual: chirality pdb=" CA GLU D 286 " pdb=" N GLU D 286 " pdb=" C GLU D 286 " pdb=" CB GLU D 286 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA GLU C 286 " pdb=" N GLU C 286 " pdb=" C GLU C 286 " pdb=" CB GLU C 286 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA GLU C 269 " pdb=" N GLU C 269 " pdb=" C GLU C 269 " pdb=" CB GLU C 269 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1465 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 106 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO B 107 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 106 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A 107 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 217 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C PHE D 217 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE D 217 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU D 218 " 0.012 2.00e-02 2.50e+03 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1817 2.77 - 3.31: 9587 3.31 - 3.84: 15649 3.84 - 4.37: 17043 4.37 - 4.90: 29045 Nonbonded interactions: 73141 Sorted by model distance: nonbonded pdb=" OG SER A 80 " pdb=" OE2 GLU A 104 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 80 " pdb=" OE2 GLU B 104 " model vdw 2.244 3.040 nonbonded pdb=" O ASP A 308 " pdb=" NH2 ARG C1074 " model vdw 2.262 3.120 nonbonded pdb=" NE1 TRP A 39 " pdb=" OE1 GLN A 235 " model vdw 2.296 3.120 nonbonded pdb=" NE1 TRP B 39 " pdb=" OE1 GLN B 235 " model vdw 2.296 3.120 ... (remaining 73136 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 344) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.420 Find NCS groups from input model: 0.310 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 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 : 0.003 0.037 9400 Z= 0.216 Angle : 0.723 11.871 12712 Z= 0.365 Chirality : 0.045 0.178 1468 Planarity : 0.005 0.058 1582 Dihedral : 14.007 89.275 3488 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % 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: 0.14 (0.25), residues: 1142 helix: 1.01 (0.18), residues: 794 sheet: -2.23 (0.45), residues: 92 loop : -1.75 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D1158 HIS 0.004 0.001 HIS B 323 PHE 0.036 0.002 PHE D1019 TYR 0.012 0.001 TYR D 277 ARG 0.005 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.3999 (pmm) cc_final: 0.1398 (mmt) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.2162 time to fit residues: 57.1208 Evaluate side-chains 135 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1008 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN C1022 ASN D1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.246848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.194075 restraints weight = 10477.802| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.01 r_work: 0.3807 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9400 Z= 0.232 Angle : 0.643 7.266 12712 Z= 0.329 Chirality : 0.045 0.153 1468 Planarity : 0.005 0.057 1582 Dihedral : 4.121 26.043 1230 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.98 % Allowed : 12.40 % Favored : 86.62 % 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: 0.43 (0.25), residues: 1142 helix: 1.31 (0.18), residues: 796 sheet: -2.25 (0.46), residues: 92 loop : -1.91 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C1158 HIS 0.003 0.001 HIS D 285 PHE 0.021 0.002 PHE C 214 TYR 0.009 0.001 TYR A 302 ARG 0.004 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7320 (mp0) cc_final: 0.6848 (mp0) REVERT: A 326 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6921 (ptm160) REVERT: C 286 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5627 (mp0) REVERT: C 1066 MET cc_start: 0.8232 (mmt) cc_final: 0.8001 (mmm) REVERT: B 293 GLU cc_start: 0.7352 (mp0) cc_final: 0.6772 (mp0) REVERT: B 326 ARG cc_start: 0.7202 (ttp80) cc_final: 0.6892 (ptm160) outliers start: 10 outliers final: 7 residues processed: 166 average time/residue: 0.2277 time to fit residues: 51.2619 Evaluate side-chains 152 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 24 optimal weight: 0.0970 chunk 111 optimal weight: 20.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1008 HIS D1008 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.245944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.188030 restraints weight = 10463.059| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.81 r_work: 0.3805 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9400 Z= 0.231 Angle : 0.620 6.849 12712 Z= 0.317 Chirality : 0.044 0.152 1468 Planarity : 0.005 0.060 1582 Dihedral : 3.973 14.073 1228 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.86 % Allowed : 16.80 % Favored : 81.35 % 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: 0.61 (0.25), residues: 1142 helix: 1.47 (0.18), residues: 796 sheet: -2.43 (0.43), residues: 92 loop : -1.88 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D1158 HIS 0.002 0.001 HIS D 285 PHE 0.014 0.001 PHE D 214 TYR 0.009 0.001 TYR B 302 ARG 0.004 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7511 (mp0) cc_final: 0.7022 (mp0) REVERT: A 326 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6976 (ptm160) REVERT: C 258 ASN cc_start: 0.8092 (m110) cc_final: 0.7853 (m110) REVERT: C 1066 MET cc_start: 0.8361 (mmt) cc_final: 0.8141 (mmm) REVERT: B 293 GLU cc_start: 0.7523 (mp0) cc_final: 0.7024 (mp0) REVERT: B 326 ARG cc_start: 0.7328 (ttp80) cc_final: 0.6995 (ptm160) REVERT: D 1116 MET cc_start: 0.9070 (mmm) cc_final: 0.8694 (ttt) outliers start: 19 outliers final: 11 residues processed: 165 average time/residue: 0.2300 time to fit residues: 51.6771 Evaluate side-chains 153 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1008 HIS Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 0.0040 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 73 optimal weight: 8.9990 chunk 35 optimal weight: 0.0970 chunk 88 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1008 HIS C1022 ASN B 263 GLN D1008 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.247553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166499 restraints weight = 10354.233| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.80 r_work: 0.3610 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9400 Z= 0.195 Angle : 0.606 8.259 12712 Z= 0.310 Chirality : 0.043 0.150 1468 Planarity : 0.005 0.062 1582 Dihedral : 3.904 12.852 1228 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.64 % Allowed : 18.07 % Favored : 79.30 % 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: 0.67 (0.26), residues: 1142 helix: 1.54 (0.18), residues: 796 sheet: -2.73 (0.42), residues: 98 loop : -1.75 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D1158 HIS 0.003 0.001 HIS D1008 PHE 0.014 0.001 PHE D 214 TYR 0.009 0.001 TYR D 230 ARG 0.006 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 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 293 GLU cc_start: 0.7103 (mp0) cc_final: 0.6554 (mp0) REVERT: A 326 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6931 (ptm160) REVERT: C 258 ASN cc_start: 0.8151 (m110) cc_final: 0.7942 (m110) REVERT: C 1022 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8206 (m110) REVERT: C 1049 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6820 (tmm) REVERT: C 1066 MET cc_start: 0.8284 (mmt) cc_final: 0.8033 (mmm) REVERT: B 326 ARG cc_start: 0.7308 (ttp80) cc_final: 0.6950 (ptm160) REVERT: D 1049 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6841 (tmm) outliers start: 27 outliers final: 14 residues processed: 165 average time/residue: 0.2638 time to fit residues: 60.0283 Evaluate side-chains 156 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1008 HIS Chi-restraints excluded: chain C residue 1022 ASN Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 63 optimal weight: 0.0050 chunk 43 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1022 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.247213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.179430 restraints weight = 10377.916| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.31 r_work: 0.3702 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9400 Z= 0.199 Angle : 0.614 8.329 12712 Z= 0.313 Chirality : 0.043 0.155 1468 Planarity : 0.005 0.056 1582 Dihedral : 3.895 12.878 1228 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.83 % Allowed : 19.34 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.26), residues: 1142 helix: 1.56 (0.18), residues: 798 sheet: -2.78 (0.42), residues: 98 loop : -1.72 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D1158 HIS 0.006 0.001 HIS C1008 PHE 0.012 0.001 PHE D 214 TYR 0.032 0.001 TYR C 230 ARG 0.004 0.000 ARG C1050 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.035 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 293 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: A 326 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7048 (ptm160) REVERT: C 218 LEU cc_start: 0.8722 (tp) cc_final: 0.8512 (mt) REVERT: C 1049 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6872 (tmm) REVERT: C 1066 MET cc_start: 0.8341 (mmt) cc_final: 0.8102 (mmm) REVERT: C 1116 MET cc_start: 0.9159 (mmm) cc_final: 0.8709 (mtp) REVERT: B 326 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7032 (ptm160) REVERT: D 283 PHE cc_start: 0.8193 (t80) cc_final: 0.7889 (t80) REVERT: D 286 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6440 (pm20) REVERT: D 1049 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6922 (tmm) REVERT: D 1116 MET cc_start: 0.9125 (mmm) cc_final: 0.8701 (mtp) outliers start: 29 outliers final: 13 residues processed: 170 average time/residue: 0.2872 time to fit residues: 65.3410 Evaluate side-chains 161 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 82 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 ASN D1008 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.246999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164194 restraints weight = 10320.856| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.64 r_work: 0.3560 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9400 Z= 0.210 Angle : 0.618 7.438 12712 Z= 0.319 Chirality : 0.043 0.164 1468 Planarity : 0.005 0.070 1582 Dihedral : 3.929 16.158 1228 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.64 % Allowed : 19.53 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.26), residues: 1142 helix: 1.62 (0.18), residues: 798 sheet: -2.81 (0.42), residues: 96 loop : -1.73 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP D1158 HIS 0.002 0.001 HIS A 314 PHE 0.012 0.001 PHE A 139 TYR 0.032 0.001 TYR C 230 ARG 0.008 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 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: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: A 326 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6975 (ptm160) REVERT: C 218 LEU cc_start: 0.8743 (tp) cc_final: 0.8510 (mt) REVERT: C 1049 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6798 (tmm) REVERT: C 1066 MET cc_start: 0.8294 (mmt) cc_final: 0.8044 (mmm) REVERT: B 152 MET cc_start: 0.8456 (mmp) cc_final: 0.8254 (mmp) REVERT: B 293 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: B 326 ARG cc_start: 0.7332 (ttp80) cc_final: 0.6946 (ptm160) REVERT: D 283 PHE cc_start: 0.8260 (t80) cc_final: 0.7954 (t80) REVERT: D 1049 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6918 (tmm) outliers start: 27 outliers final: 16 residues processed: 166 average time/residue: 0.2249 time to fit residues: 51.2764 Evaluate side-chains 160 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.243243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3915 r_free = 0.3915 target = 0.157707 restraints weight = 10458.648| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.32 r_work: 0.3581 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9400 Z= 0.374 Angle : 0.691 8.197 12712 Z= 0.357 Chirality : 0.047 0.166 1468 Planarity : 0.005 0.058 1582 Dihedral : 4.126 15.080 1228 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.22 % Allowed : 19.34 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1142 helix: 1.50 (0.18), residues: 798 sheet: -3.10 (0.40), residues: 96 loop : -1.88 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP D1158 HIS 0.011 0.001 HIS D1008 PHE 0.020 0.002 PHE A 41 TYR 0.034 0.001 TYR C 230 ARG 0.006 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5268 (ppp) cc_final: 0.4687 (mtm) REVERT: A 293 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: A 326 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7015 (ptm160) REVERT: C 218 LEU cc_start: 0.8708 (tp) cc_final: 0.8495 (mt) REVERT: C 225 MET cc_start: 0.6834 (mtp) cc_final: 0.5794 (mmp) REVERT: C 1116 MET cc_start: 0.9177 (mmm) cc_final: 0.8701 (mtp) REVERT: B 204 MET cc_start: 0.5254 (ppp) cc_final: 0.4650 (mtm) REVERT: B 293 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: B 326 ARG cc_start: 0.7368 (ttp80) cc_final: 0.6992 (ptm160) REVERT: D 1049 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7068 (tmm) REVERT: D 1116 MET cc_start: 0.9127 (mmm) cc_final: 0.8747 (mtp) outliers start: 33 outliers final: 18 residues processed: 170 average time/residue: 0.2231 time to fit residues: 52.5308 Evaluate side-chains 164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 85 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1008 HIS D1022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.245860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.167592 restraints weight = 10518.810| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.65 r_work: 0.3559 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9400 Z= 0.202 Angle : 0.654 9.371 12712 Z= 0.341 Chirality : 0.044 0.168 1468 Planarity : 0.005 0.056 1582 Dihedral : 4.073 18.108 1228 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.05 % Allowed : 20.41 % Favored : 77.54 % 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: 0.62 (0.26), residues: 1142 helix: 1.57 (0.18), residues: 798 sheet: -3.04 (0.42), residues: 96 loop : -1.92 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.004 TRP D1158 HIS 0.004 0.001 HIS C 285 PHE 0.044 0.001 PHE D 283 TYR 0.036 0.001 TYR C 230 ARG 0.006 0.000 ARG D1050 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.069 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 293 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: A 326 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7028 (ptm160) REVERT: A 342 TYR cc_start: 0.7781 (t80) cc_final: 0.7550 (t80) REVERT: C 218 LEU cc_start: 0.8630 (tp) cc_final: 0.8429 (mt) REVERT: C 225 MET cc_start: 0.6945 (mtp) cc_final: 0.5890 (mmp) REVERT: C 1048 GLN cc_start: 0.8121 (pp30) cc_final: 0.7817 (tp40) REVERT: C 1116 MET cc_start: 0.9167 (mmm) cc_final: 0.8696 (mtp) REVERT: B 204 MET cc_start: 0.5135 (ppp) cc_final: 0.4525 (mtm) REVERT: B 293 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: B 326 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7044 (ptm160) REVERT: B 342 TYR cc_start: 0.7760 (t80) cc_final: 0.7539 (t80) REVERT: D 1049 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6998 (tmm) outliers start: 21 outliers final: 18 residues processed: 152 average time/residue: 0.2153 time to fit residues: 45.1610 Evaluate side-chains 162 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.244287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.162291 restraints weight = 10314.491| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.39 r_work: 0.3561 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9400 Z= 0.277 Angle : 0.683 10.022 12712 Z= 0.355 Chirality : 0.045 0.170 1468 Planarity : 0.005 0.056 1582 Dihedral : 4.114 17.347 1228 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.15 % Allowed : 20.61 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.26), residues: 1142 helix: 1.55 (0.18), residues: 798 sheet: -3.11 (0.41), residues: 96 loop : -1.92 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.004 TRP D1158 HIS 0.007 0.001 HIS D1008 PHE 0.041 0.002 PHE D 283 TYR 0.036 0.001 TYR C 230 ARG 0.005 0.000 ARG C1050 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.227 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 204 MET cc_start: 0.5220 (ppp) cc_final: 0.4707 (mtm) REVERT: A 293 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: A 326 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7066 (ptm160) REVERT: C 218 LEU cc_start: 0.8686 (tp) cc_final: 0.8460 (mt) REVERT: C 225 MET cc_start: 0.6922 (mtp) cc_final: 0.5928 (mmp) REVERT: C 1048 GLN cc_start: 0.8106 (pp30) cc_final: 0.7892 (tp40) REVERT: C 1116 MET cc_start: 0.9184 (mmm) cc_final: 0.8712 (mtp) REVERT: B 293 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: B 326 ARG cc_start: 0.7409 (ttp80) cc_final: 0.7056 (ptm160) REVERT: D 261 MET cc_start: 0.7413 (ppp) cc_final: 0.7093 (pmm) REVERT: D 1049 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7019 (tmm) REVERT: D 1116 MET cc_start: 0.9116 (mmm) cc_final: 0.8761 (mtp) outliers start: 22 outliers final: 18 residues processed: 156 average time/residue: 0.2473 time to fit residues: 53.9121 Evaluate side-chains 164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1109 TYR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 45 optimal weight: 0.2980 chunk 11 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1008 HIS D1022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.245754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3996 r_free = 0.3996 target = 0.164022 restraints weight = 10502.990| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.21 r_work: 0.3600 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9400 Z= 0.206 Angle : 0.674 10.671 12712 Z= 0.353 Chirality : 0.044 0.179 1468 Planarity : 0.005 0.056 1582 Dihedral : 4.051 16.097 1228 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.34 % Allowed : 20.80 % Favored : 76.86 % 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 (0.26), residues: 1142 helix: 1.61 (0.18), residues: 796 sheet: -2.91 (0.42), residues: 100 loop : -1.94 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.005 TRP D1158 HIS 0.002 0.000 HIS D1008 PHE 0.040 0.001 PHE D 283 TYR 0.035 0.001 TYR C 230 ARG 0.007 0.000 ARG C1050 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.100 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 204 MET cc_start: 0.5212 (ppp) cc_final: 0.4763 (mtm) REVERT: A 293 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: A 326 ARG cc_start: 0.7415 (ttp80) cc_final: 0.7062 (ptm160) REVERT: C 218 LEU cc_start: 0.8695 (tp) cc_final: 0.8462 (mt) REVERT: C 225 MET cc_start: 0.6899 (mtp) cc_final: 0.5947 (mmp) REVERT: C 1048 GLN cc_start: 0.8117 (pp30) cc_final: 0.7829 (tp40) REVERT: C 1116 MET cc_start: 0.9194 (mmm) cc_final: 0.8787 (mtp) REVERT: B 204 MET cc_start: 0.5246 (ppp) cc_final: 0.4742 (mtm) REVERT: B 293 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: B 326 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7128 (ptm160) REVERT: D 1116 MET cc_start: 0.9128 (mmm) cc_final: 0.8750 (mtp) outliers start: 24 outliers final: 20 residues processed: 155 average time/residue: 0.2176 time to fit residues: 46.9241 Evaluate side-chains 159 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1109 TYR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 chunk 32 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1008 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.245564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3984 r_free = 0.3984 target = 0.162146 restraints weight = 10459.664| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.21 r_work: 0.3659 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9400 Z= 0.228 Angle : 0.694 11.332 12712 Z= 0.365 Chirality : 0.045 0.224 1468 Planarity : 0.005 0.055 1582 Dihedral : 4.033 16.103 1228 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.44 % Allowed : 21.39 % Favored : 76.17 % 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: 0.69 (0.26), residues: 1142 helix: 1.63 (0.18), residues: 796 sheet: -2.89 (0.42), residues: 100 loop : -1.91 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.005 TRP D1158 HIS 0.013 0.001 HIS D1008 PHE 0.038 0.001 PHE D 283 TYR 0.035 0.001 TYR C 230 ARG 0.007 0.000 ARG C1050 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6613.61 seconds wall clock time: 116 minutes 14.73 seconds (6974.73 seconds total)