Starting phenix.real_space_refine on Wed Feb 14 11:59:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr1_16801/02_2024/8cr1_16801.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr1_16801/02_2024/8cr1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr1_16801/02_2024/8cr1_16801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr1_16801/02_2024/8cr1_16801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr1_16801/02_2024/8cr1_16801.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr1_16801/02_2024/8cr1_16801.pdb" } 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 Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "C GLU 1052": "OE1" <-> "OE2" Residue "C ASP 1055": "OD1" <-> "OD2" Residue "C PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D GLU 1052": "OE1" <-> "OE2" Residue "D ASP 1055": "OD1" <-> "OD2" Residue "D PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.33, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.74 Conformation dependent library (CDL) restraints added in 1.7 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: 0.90 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: 2.90 Time building geometry restraints manager: 3.99 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: 98.63 - 105.71: 220 105.71 - 112.78: 5026 112.78 - 119.86: 3166 119.86 - 126.93: 4192 126.93 - 134.01: 108 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 2.440 nonbonded pdb=" OG SER B 80 " pdb=" OE2 GLU B 104 " model vdw 2.244 2.440 nonbonded pdb=" O ASP A 308 " pdb=" NH2 ARG C1074 " model vdw 2.262 2.520 nonbonded pdb=" NE1 TRP A 39 " pdb=" OE1 GLN A 235 " model vdw 2.296 2.520 nonbonded pdb=" NE1 TRP B 39 " pdb=" OE1 GLN B 235 " model vdw 2.296 2.520 ... (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 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: 2.170 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: 7.890 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.190 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.920 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.070 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: 0.2233 time to fit residues: 58.9081 Evaluate side-chains 135 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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: 0.6980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1022 ASN D1022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9400 Z= 0.277 Angle : 0.647 7.127 12712 Z= 0.329 Chirality : 0.045 0.151 1468 Planarity : 0.005 0.057 1582 Dihedral : 4.204 28.592 1230 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.17 % Allowed : 12.89 % Favored : 85.94 % 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: 0.41 (0.25), residues: 1142 helix: 1.30 (0.18), residues: 796 sheet: -2.33 (0.44), residues: 92 loop : -1.93 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C1158 HIS 0.003 0.001 HIS D 285 PHE 0.022 0.002 PHE C 214 TYR 0.011 0.001 TYR A 302 ARG 0.002 0.000 ARG D 204 *********************** 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 170 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.6492 (mp0) cc_final: 0.6149 (mp0) REVERT: B 293 GLU cc_start: 0.6479 (mp0) cc_final: 0.6136 (mp0) outliers start: 12 outliers final: 10 residues processed: 168 average time/residue: 0.2334 time to fit residues: 52.9457 Evaluate side-chains 150 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 166 ASP 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 B residue 166 ASP 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 57 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 0.0000 chunk 28 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 83 optimal weight: 1.9990 overall best weight: 0.6686 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9400 Z= 0.224 Angle : 0.613 6.635 12712 Z= 0.313 Chirality : 0.043 0.152 1468 Planarity : 0.005 0.057 1582 Dihedral : 4.031 14.432 1228 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.44 % Allowed : 16.99 % Favored : 80.57 % 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: 0.60 (0.25), residues: 1142 helix: 1.48 (0.18), residues: 796 sheet: -2.43 (0.43), residues: 92 loop : -1.91 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D1158 HIS 0.003 0.001 HIS C1008 PHE 0.014 0.001 PHE C 214 TYR 0.020 0.001 TYR A 342 ARG 0.003 0.000 ARG D 259 *********************** 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 175 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.6364 (mp0) cc_final: 0.6055 (mp0) outliers start: 25 outliers final: 14 residues processed: 165 average time/residue: 0.2153 time to fit residues: 49.0267 Evaluate side-chains 151 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 221 LYS 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 B residue 74 ASP Chi-restraints excluded: chain B residue 221 LYS 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 Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2290 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= 0.218 Angle : 0.600 8.607 12712 Z= 0.308 Chirality : 0.043 0.151 1468 Planarity : 0.005 0.061 1582 Dihedral : 3.966 13.299 1228 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.93 % Allowed : 19.14 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1142 helix: 1.54 (0.18), residues: 798 sheet: -2.75 (0.42), residues: 98 loop : -1.76 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D1158 HIS 0.011 0.001 HIS D1008 PHE 0.013 0.001 PHE D 214 TYR 0.014 0.001 TYR A 342 ARG 0.002 0.000 ARG D 259 *********************** 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 171 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.6367 (mp0) cc_final: 0.6092 (mp0) REVERT: D 1049 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6722 (tmm) REVERT: D 1050 ARG cc_start: 0.7378 (ttm170) cc_final: 0.7133 (ttm110) outliers start: 30 outliers final: 16 residues processed: 161 average time/residue: 0.2157 time to fit residues: 48.1247 Evaluate side-chains 148 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain C residue 1008 HIS 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 74 ASP Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 166 ASP 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 91 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 0.0770 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9400 Z= 0.210 Angle : 0.607 8.394 12712 Z= 0.312 Chirality : 0.042 0.155 1468 Planarity : 0.005 0.057 1582 Dihedral : 3.976 16.554 1228 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.73 % Allowed : 20.41 % 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: 0.73 (0.26), residues: 1142 helix: 1.58 (0.18), residues: 798 sheet: -2.56 (0.44), residues: 92 loop : -1.83 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D1158 HIS 0.010 0.001 HIS D1008 PHE 0.024 0.001 PHE D 283 TYR 0.033 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 177 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6123 (mp0) REVERT: B 293 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.6077 (mp0) REVERT: D 1049 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6743 (tmm) outliers start: 28 outliers final: 19 residues processed: 164 average time/residue: 0.2221 time to fit residues: 49.5445 Evaluate side-chains 156 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 1008 HIS 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 74 ASP Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 293 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS D1008 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9400 Z= 0.241 Angle : 0.632 7.316 12712 Z= 0.322 Chirality : 0.043 0.161 1468 Planarity : 0.005 0.068 1582 Dihedral : 4.006 17.177 1228 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.42 % Allowed : 20.21 % Favored : 76.37 % 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: 0.72 (0.26), residues: 1142 helix: 1.60 (0.18), residues: 796 sheet: -2.62 (0.44), residues: 92 loop : -1.87 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D1011 HIS 0.004 0.001 HIS C1008 PHE 0.020 0.001 PHE C 214 TYR 0.040 0.001 TYR C 230 ARG 0.008 0.000 ARG B 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 175 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8065 (mmp) cc_final: 0.7728 (mmp) REVERT: A 293 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: B 293 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: D 1049 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6761 (tmm) REVERT: D 1050 ARG cc_start: 0.7353 (ttm170) cc_final: 0.7075 (ttm110) outliers start: 35 outliers final: 24 residues processed: 163 average time/residue: 0.2082 time to fit residues: 47.5223 Evaluate side-chains 158 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 221 LYS 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 286 GLU Chi-restraints excluded: chain C residue 1022 ASN 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 74 ASP Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2769 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= 0.222 Angle : 0.620 8.300 12712 Z= 0.319 Chirality : 0.043 0.161 1468 Planarity : 0.005 0.056 1582 Dihedral : 3.999 15.625 1228 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.12 % Allowed : 20.80 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1142 helix: 1.62 (0.18), residues: 796 sheet: -2.59 (0.45), residues: 92 loop : -1.90 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D1158 HIS 0.002 0.001 HIS A 314 PHE 0.024 0.001 PHE D 283 TYR 0.037 0.001 TYR C 230 ARG 0.006 0.000 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 179 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7977 (mmp) cc_final: 0.7648 (mmp) REVERT: A 293 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: B 293 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: D 1050 ARG cc_start: 0.7338 (ttm170) cc_final: 0.7093 (ttm110) outliers start: 32 outliers final: 25 residues processed: 169 average time/residue: 0.2063 time to fit residues: 48.6886 Evaluate side-chains 164 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 ASP 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 286 GLU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 1022 ASN 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 54 SER Chi-restraints excluded: chain B residue 74 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1008 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9400 Z= 0.218 Angle : 0.639 8.798 12712 Z= 0.328 Chirality : 0.043 0.167 1468 Planarity : 0.005 0.055 1582 Dihedral : 4.025 17.879 1228 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.22 % Allowed : 21.58 % Favored : 75.20 % 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: 0.76 (0.26), residues: 1142 helix: 1.63 (0.19), residues: 798 sheet: -2.59 (0.45), residues: 92 loop : -1.92 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP D1011 HIS 0.003 0.001 HIS C 285 PHE 0.019 0.001 PHE D 283 TYR 0.036 0.001 TYR C 230 ARG 0.005 0.000 ARG B 185 *********************** 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 180 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7958 (mmp) cc_final: 0.7637 (mmp) REVERT: A 293 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: B 293 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6084 (mp0) outliers start: 33 outliers final: 23 residues processed: 168 average time/residue: 0.2094 time to fit residues: 49.0696 Evaluate side-chains 162 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 92 THR 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 230 TYR 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 24 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 74 ASP 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 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 96 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 67 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9400 Z= 0.219 Angle : 0.684 10.977 12712 Z= 0.353 Chirality : 0.043 0.169 1468 Planarity : 0.005 0.055 1582 Dihedral : 4.043 16.727 1228 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.83 % Allowed : 22.36 % Favored : 74.80 % 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: 1.59 (0.19), residues: 796 sheet: -2.58 (0.46), residues: 92 loop : -1.95 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP D1158 HIS 0.012 0.001 HIS D1008 PHE 0.024 0.001 PHE D 283 TYR 0.035 0.001 TYR C 230 ARG 0.005 0.000 ARG B 185 *********************** 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 170 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7942 (mmp) cc_final: 0.7626 (mmp) REVERT: A 293 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: B 293 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6101 (mp0) outliers start: 29 outliers final: 26 residues processed: 160 average time/residue: 0.2016 time to fit residues: 45.2135 Evaluate side-chains 163 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 ASP 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 289 ASP Chi-restraints excluded: chain C residue 1022 ASN 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 24 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 30.0000 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 285 HIS D1008 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9400 Z= 0.256 Angle : 0.744 15.241 12712 Z= 0.380 Chirality : 0.045 0.178 1468 Planarity : 0.005 0.055 1582 Dihedral : 4.073 16.430 1228 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.73 % Allowed : 22.66 % Favored : 74.61 % 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: 1.60 (0.19), residues: 794 sheet: -2.80 (0.44), residues: 96 loop : -1.91 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.004 TRP D1011 HIS 0.003 0.001 HIS A 314 PHE 0.014 0.001 PHE C 214 TYR 0.043 0.002 TYR D 210 ARG 0.004 0.000 ARG B 185 ********************** 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 167 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7955 (mmp) cc_final: 0.7677 (mmp) REVERT: A 293 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: B 293 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: D 1050 ARG cc_start: 0.7342 (ttm170) cc_final: 0.7016 (ttm110) outliers start: 28 outliers final: 24 residues processed: 156 average time/residue: 0.2081 time to fit residues: 45.4474 Evaluate side-chains 160 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 92 THR 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 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 24 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 74 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.4741 r_free = 0.4741 target = 0.245323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3831 r_free = 0.3831 target = 0.154536 restraints weight = 10370.188| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.03 r_work: 0.3563 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9400 Z= 0.213 Angle : 0.718 11.415 12712 Z= 0.378 Chirality : 0.044 0.223 1468 Planarity : 0.005 0.055 1582 Dihedral : 3.990 16.182 1228 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.34 % Allowed : 23.14 % Favored : 74.51 % 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: 0.76 (0.26), residues: 1142 helix: 1.65 (0.19), residues: 796 sheet: -2.54 (0.46), residues: 92 loop : -1.95 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.004 TRP D1158 HIS 0.010 0.001 HIS D1008 PHE 0.029 0.001 PHE D 283 TYR 0.035 0.001 TYR C 230 ARG 0.005 0.000 ARG A 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.65 seconds wall clock time: 42 minutes 32.30 seconds (2552.30 seconds total)