Starting phenix.real_space_refine on Thu Jan 18 06:15:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/01_2024/7wy8_32887_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/01_2024/7wy8_32887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/01_2024/7wy8_32887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/01_2024/7wy8_32887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/01_2024/7wy8_32887_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/01_2024/7wy8_32887_neut.pdb" } resolution = 2.83 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= 0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5121 2.51 5 N 1393 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8049 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2123 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 3, 'TRANS': 258} Chain breaks: 1 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1926 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 331} Time building chain proxies: 4.68, per 1000 atoms: 0.58 Number of scatterers: 8049 At special positions: 0 Unit cell: (80.3, 97.9, 133.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1479 8.00 N 1393 7.00 C 5121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R1008 " - pdb=" SG CYS R1080 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 40.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'R' and resid 925 through 929 removed outlier: 3.805A pdb=" N LEU R 928 " --> pdb=" O PHE R 925 " (cutoff:3.500A) Processing helix chain 'R' and resid 940 through 956 removed outlier: 3.933A pdb=" N LEU R 944 " --> pdb=" O VAL R 940 " (cutoff:3.500A) Processing helix chain 'R' and resid 958 through 969 removed outlier: 3.643A pdb=" N ILE R 962 " --> pdb=" O VAL R 958 " (cutoff:3.500A) Processing helix chain 'R' and resid 970 through 974 removed outlier: 3.770A pdb=" N LEU R 973 " --> pdb=" O PHE R 970 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN R 974 " --> pdb=" O ARG R 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 970 through 974' Processing helix chain 'R' and resid 975 through 999 removed outlier: 3.578A pdb=" N ILE R 999 " --> pdb=" O PHE R 995 " (cutoff:3.500A) Processing helix chain 'R' and resid 1008 through 1038 removed outlier: 4.042A pdb=" N HIS R1016 " --> pdb=" O ALA R1012 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET R1036 " --> pdb=" O GLN R1032 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1056 Processing helix chain 'R' and resid 1056 through 1070 removed outlier: 3.574A pdb=" N ALA R1060 " --> pdb=" O TYR R1056 " (cutoff:3.500A) Processing helix chain 'R' and resid 1086 through 1088 No H-bonds generated for 'chain 'R' and resid 1086 through 1088' Processing helix chain 'R' and resid 1089 through 1113 Proline residue: R1095 - end of helix removed outlier: 3.736A pdb=" N LEU R1098 " --> pdb=" O GLY R1094 " (cutoff:3.500A) Processing helix chain 'R' and resid 1144 through 1152 Processing helix chain 'R' and resid 1155 through 1164 removed outlier: 3.745A pdb=" N TRP R1158 " --> pdb=" O GLY R1155 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA R1159 " --> pdb=" O LEU R1156 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR R1164 " --> pdb=" O GLY R1161 " (cutoff:3.500A) Processing helix chain 'R' and resid 1169 through 1181 removed outlier: 3.791A pdb=" N ALA R1173 " --> pdb=" O THR R1169 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER R1181 " --> pdb=" O THR R1177 " (cutoff:3.500A) Processing helix chain 'R' and resid 1182 through 1193 removed outlier: 3.625A pdb=" N PHE R1188 " --> pdb=" O GLY R1184 " (cutoff:3.500A) Processing helix chain 'R' and resid 1195 through 1207 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.779A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.508A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.824A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.735A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 No H-bonds generated for 'chain 'A' and resid 252 through 264' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.562A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.862A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.625A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.585A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.603A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.579A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.867A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.266A pdb=" N GLY D 10 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.053A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.082A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.964A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.969A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.945A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.759A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.973A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1041 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: 2.32 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2622 1.34 - 1.46: 1991 1.46 - 1.58: 3526 1.58 - 1.70: 0 1.70 - 1.83: 80 Bond restraints: 8219 Sorted by residual: bond pdb=" C LEU C 50 " pdb=" N LEU C 51 " ideal model delta sigma weight residual 1.332 1.277 0.055 1.35e-02 5.49e+03 1.68e+01 bond pdb=" N LYS R1113 " pdb=" CA LYS R1113 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.22e-02 6.72e+03 5.24e+00 bond pdb=" N MET R1114 " pdb=" CA MET R1114 " ideal model delta sigma weight residual 1.456 1.482 -0.025 1.28e-02 6.10e+03 3.95e+00 bond pdb=" CA PHE B 292 " pdb=" CB PHE B 292 " ideal model delta sigma weight residual 1.530 1.492 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" CB TRP D 36 " pdb=" CG TRP D 36 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.43e+00 ... (remaining 8214 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 165 106.52 - 113.39: 4411 113.39 - 120.27: 3187 120.27 - 127.14: 3279 127.14 - 134.01: 81 Bond angle restraints: 11123 Sorted by residual: angle pdb=" N VAL R 958 " pdb=" CA VAL R 958 " pdb=" C VAL R 958 " ideal model delta sigma weight residual 112.12 107.19 4.93 8.40e-01 1.42e+00 3.45e+01 angle pdb=" N CYS B 204 " pdb=" CA CYS B 204 " pdb=" C CYS B 204 " ideal model delta sigma weight residual 108.58 100.71 7.87 1.82e+00 3.02e-01 1.87e+01 angle pdb=" N MET R1114 " pdb=" CA MET R1114 " pdb=" C MET R1114 " ideal model delta sigma weight residual 113.88 108.74 5.14 1.23e+00 6.61e-01 1.75e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 114.31 119.54 -5.23 1.29e+00 6.01e-01 1.64e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.70 128.88 -7.18 1.80e+00 3.09e-01 1.59e+01 ... (remaining 11118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 4472 15.05 - 30.11: 296 30.11 - 45.16: 57 45.16 - 60.22: 30 60.22 - 75.27: 10 Dihedral angle restraints: 4865 sinusoidal: 1915 harmonic: 2950 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.64 42.36 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CA PHE D 108 " pdb=" C PHE D 108 " pdb=" N ASP D 109 " pdb=" CA ASP D 109 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR B 65 " pdb=" C THR B 65 " pdb=" N ASP B 66 " pdb=" CA ASP B 66 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1033 0.064 - 0.129: 195 0.129 - 0.193: 15 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CA GLN B 75 " pdb=" N GLN B 75 " pdb=" C GLN B 75 " pdb=" CB GLN B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ASP B 163 " pdb=" N ASP B 163 " pdb=" C ASP B 163 " pdb=" CB ASP B 163 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASN R1166 " pdb=" N ASN R1166 " pdb=" C ASN R1166 " pdb=" CB ASN R1166 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1243 not shown) Planarity restraints: 1414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 40 " 0.050 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO D 41 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN R1004 " -0.037 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO R1005 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO R1005 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R1005 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.030 5.00e-02 4.00e+02 ... (remaining 1411 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1193 2.76 - 3.29: 7080 3.29 - 3.83: 12083 3.83 - 4.36: 14045 4.36 - 4.90: 25419 Nonbonded interactions: 59820 Sorted by model distance: nonbonded pdb=" O ASN R1166 " pdb=" OG1 THR R1169 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR R 966 " pdb=" OH TYR R1202 " model vdw 2.237 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.307 2.440 nonbonded pdb=" O PRO D 100 " pdb=" OG SER B 227 " model vdw 2.330 2.440 nonbonded pdb=" O VAL D 110 " pdb=" NH1 ARG D 118 " model vdw 2.331 2.520 ... (remaining 59815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 3.800 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.380 Find NCS groups from input model: 0.230 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 : 0.007 0.055 8219 Z= 0.439 Angle : 0.814 8.893 11123 Z= 0.489 Chirality : 0.050 0.322 1246 Planarity : 0.006 0.077 1414 Dihedral : 12.025 75.273 2953 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.39 (0.25), residues: 1001 helix: 0.49 (0.28), residues: 361 sheet: 1.01 (0.36), residues: 209 loop : -1.58 (0.25), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 PHE 0.034 0.003 PHE A 376 TYR 0.019 0.002 TYR R1034 ARG 0.006 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.943 Fit side-chains REVERT: R 1088 PHE cc_start: 0.7386 (t80) cc_final: 0.7086 (t80) REVERT: R 1172 MET cc_start: 0.5424 (mmm) cc_final: 0.5170 (mmm) REVERT: A 314 GLU cc_start: 0.6745 (mp0) cc_final: 0.6476 (mp0) REVERT: B 156 GLN cc_start: 0.7993 (mt0) cc_final: 0.7687 (mt0) REVERT: B 304 ARG cc_start: 0.7324 (mtm180) cc_final: 0.7075 (ttm110) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 1.1734 time to fit residues: 234.7628 Evaluate side-chains 168 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0040 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1183 GLN A 236 GLN A 292 ASN D 31 ASN B 75 GLN B 155 ASN B 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8219 Z= 0.177 Angle : 0.555 8.715 11123 Z= 0.305 Chirality : 0.042 0.159 1246 Planarity : 0.005 0.069 1414 Dihedral : 4.690 21.715 1106 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.07 % Allowed : 8.86 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.39 (0.26), residues: 1001 helix: 1.72 (0.29), residues: 352 sheet: 1.10 (0.35), residues: 207 loop : -1.45 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.002 PHE A 376 TYR 0.013 0.001 TYR D 95 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 0.945 Fit side-chains REVERT: R 1082 LEU cc_start: 0.8290 (mt) cc_final: 0.7975 (mm) REVERT: R 1092 PHE cc_start: 0.6608 (t80) cc_final: 0.6106 (t80) REVERT: C 42 GLU cc_start: 0.7349 (tp30) cc_final: 0.7069 (tp30) REVERT: A 314 GLU cc_start: 0.6666 (mp0) cc_final: 0.6353 (mp0) REVERT: B 59 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7766 (t80) outliers start: 18 outliers final: 10 residues processed: 174 average time/residue: 1.3175 time to fit residues: 241.7888 Evaluate side-chains 179 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 168 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8219 Z= 0.240 Angle : 0.575 7.454 11123 Z= 0.313 Chirality : 0.042 0.156 1246 Planarity : 0.004 0.055 1414 Dihedral : 4.602 22.626 1106 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 10.47 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.57 (0.26), residues: 1001 helix: 1.96 (0.29), residues: 352 sheet: 1.42 (0.36), residues: 194 loop : -1.47 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE A 376 TYR 0.015 0.002 TYR D 95 ARG 0.008 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 0.931 Fit side-chains REVERT: R 1082 LEU cc_start: 0.8290 (mt) cc_final: 0.7982 (mm) REVERT: A 236 GLN cc_start: 0.7979 (mt0) cc_final: 0.7756 (mt0) REVERT: A 314 GLU cc_start: 0.6650 (mp0) cc_final: 0.6364 (mp0) REVERT: A 319 THR cc_start: 0.8379 (t) cc_final: 0.8121 (m) REVERT: B 59 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7804 (t80) REVERT: B 156 GLN cc_start: 0.7923 (mt0) cc_final: 0.7647 (mt0) outliers start: 26 outliers final: 19 residues processed: 173 average time/residue: 1.3102 time to fit residues: 239.0920 Evaluate side-chains 182 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 292 ASN D 31 ASN B 75 GLN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8219 Z= 0.248 Angle : 0.571 7.983 11123 Z= 0.312 Chirality : 0.042 0.180 1246 Planarity : 0.004 0.052 1414 Dihedral : 4.565 22.340 1106 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.34 % Allowed : 11.05 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1001 helix: 2.10 (0.29), residues: 352 sheet: 1.30 (0.36), residues: 199 loop : -1.41 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 PHE 0.020 0.002 PHE B 151 TYR 0.016 0.002 TYR B 289 ARG 0.005 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 0.929 Fit side-chains REVERT: R 1082 LEU cc_start: 0.8241 (mt) cc_final: 0.7956 (mm) REVERT: R 1114 MET cc_start: 0.4893 (mtt) cc_final: 0.4334 (ttm) REVERT: C 21 MET cc_start: 0.7189 (tpp) cc_final: 0.6845 (ttt) REVERT: A 314 GLU cc_start: 0.6628 (mp0) cc_final: 0.6360 (mp0) REVERT: B 59 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7803 (t80) REVERT: B 156 GLN cc_start: 0.7958 (mt0) cc_final: 0.7645 (mt0) outliers start: 29 outliers final: 23 residues processed: 176 average time/residue: 1.3827 time to fit residues: 256.2058 Evaluate side-chains 192 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1093 ILE Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.0060 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8219 Z= 0.248 Angle : 0.570 9.431 11123 Z= 0.309 Chirality : 0.042 0.154 1246 Planarity : 0.004 0.051 1414 Dihedral : 4.531 22.235 1106 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.45 % Allowed : 12.54 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1001 helix: 2.19 (0.29), residues: 352 sheet: 1.31 (0.37), residues: 199 loop : -1.37 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 PHE 0.018 0.002 PHE B 151 TYR 0.015 0.001 TYR D 95 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.006 Fit side-chains REVERT: R 1114 MET cc_start: 0.4850 (mtt) cc_final: 0.4378 (ttm) REVERT: C 21 MET cc_start: 0.7186 (tpp) cc_final: 0.6836 (ttt) REVERT: A 307 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7728 (mmtm) REVERT: A 314 GLU cc_start: 0.6510 (mp0) cc_final: 0.6263 (mp0) REVERT: B 59 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7811 (t80) outliers start: 30 outliers final: 24 residues processed: 174 average time/residue: 1.3548 time to fit residues: 248.5800 Evaluate side-chains 192 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1093 ILE Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 50 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 35 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8219 Z= 0.222 Angle : 0.544 6.748 11123 Z= 0.296 Chirality : 0.041 0.150 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.428 21.467 1106 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.45 % Allowed : 12.54 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.86 (0.26), residues: 1001 helix: 2.32 (0.29), residues: 351 sheet: 1.38 (0.36), residues: 199 loop : -1.32 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS C 44 PHE 0.016 0.002 PHE B 151 TYR 0.015 0.001 TYR D 95 ARG 0.003 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 0.913 Fit side-chains REVERT: R 1114 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.4338 (ttm) REVERT: C 21 MET cc_start: 0.7190 (tpp) cc_final: 0.6844 (ttt) REVERT: A 314 GLU cc_start: 0.6506 (mp0) cc_final: 0.6283 (mp0) outliers start: 30 outliers final: 22 residues processed: 181 average time/residue: 1.2809 time to fit residues: 245.1505 Evaluate side-chains 186 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1006 ILE Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1114 MET Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.0070 chunk 69 optimal weight: 0.0070 chunk 80 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1032 GLN A 35 GLN A 50 ASN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8219 Z= 0.136 Angle : 0.482 6.699 11123 Z= 0.262 Chirality : 0.040 0.137 1246 Planarity : 0.003 0.049 1414 Dihedral : 4.070 18.437 1106 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.99 % Allowed : 13.23 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 1001 helix: 2.56 (0.29), residues: 352 sheet: 1.50 (0.37), residues: 196 loop : -1.23 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.016 0.001 TYR B 289 ARG 0.003 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 0.936 Fit side-chains REVERT: C 21 MET cc_start: 0.7173 (tpp) cc_final: 0.6846 (ttt) REVERT: A 314 GLU cc_start: 0.6472 (mp0) cc_final: 0.6249 (mp0) REVERT: A 317 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6864 (ptm-80) REVERT: B 156 GLN cc_start: 0.7896 (mt0) cc_final: 0.7581 (mt0) outliers start: 26 outliers final: 12 residues processed: 175 average time/residue: 1.2726 time to fit residues: 235.4194 Evaluate side-chains 174 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 overall best weight: 0.1970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 213 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8219 Z= 0.123 Angle : 0.472 6.532 11123 Z= 0.258 Chirality : 0.040 0.166 1246 Planarity : 0.003 0.048 1414 Dihedral : 3.889 16.767 1106 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.30 % Allowed : 15.30 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.27), residues: 1001 helix: 2.68 (0.29), residues: 353 sheet: 1.54 (0.36), residues: 211 loop : -1.17 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.011 0.001 TYR B 289 ARG 0.003 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 0.936 Fit side-chains REVERT: C 21 MET cc_start: 0.7175 (tpp) cc_final: 0.6849 (ttt) REVERT: B 156 GLN cc_start: 0.7873 (mt0) cc_final: 0.7568 (mt0) outliers start: 20 outliers final: 11 residues processed: 178 average time/residue: 1.2319 time to fit residues: 232.1487 Evaluate side-chains 174 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 53 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 213 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8219 Z= 0.176 Angle : 0.508 6.476 11123 Z= 0.279 Chirality : 0.040 0.160 1246 Planarity : 0.004 0.048 1414 Dihedral : 4.039 18.785 1106 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.84 % Allowed : 17.03 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.27), residues: 1001 helix: 2.69 (0.28), residues: 353 sheet: 1.36 (0.35), residues: 216 loop : -1.09 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE B 241 TYR 0.025 0.001 TYR A 37 ARG 0.003 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 0.892 Fit side-chains REVERT: C 21 MET cc_start: 0.7188 (tpp) cc_final: 0.6887 (ttt) REVERT: A 317 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6881 (ptm-80) REVERT: B 156 GLN cc_start: 0.7918 (mt0) cc_final: 0.7585 (mt0) outliers start: 16 outliers final: 12 residues processed: 172 average time/residue: 1.2242 time to fit residues: 222.9485 Evaluate side-chains 173 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1088 PHE Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7393 > 50: distance: 20 - 158: 35.153 distance: 23 - 155: 29.974 distance: 38 - 141: 32.391 distance: 41 - 138: 35.102 distance: 83 - 149: 35.796 distance: 86 - 146: 32.824 distance: 97 - 129: 35.018 distance: 100 - 126: 32.818 distance: 121 - 126: 30.493 distance: 127 - 128: 4.416 distance: 127 - 130: 41.899 distance: 128 - 129: 54.233 distance: 128 - 138: 34.056 distance: 130 - 131: 29.834 distance: 131 - 132: 40.369 distance: 131 - 133: 8.700 distance: 132 - 134: 16.100 distance: 133 - 135: 52.967 distance: 134 - 136: 51.879 distance: 135 - 136: 3.583 distance: 136 - 137: 16.524 distance: 139 - 140: 12.491 distance: 139 - 142: 11.925 distance: 140 - 141: 43.114 distance: 140 - 146: 27.759 distance: 142 - 143: 27.999 distance: 146 - 147: 41.033 distance: 147 - 148: 57.504 distance: 148 - 149: 38.992 distance: 148 - 155: 51.840 distance: 152 - 153: 56.533 distance: 152 - 154: 44.297 distance: 155 - 156: 40.160 distance: 156 - 157: 39.777 distance: 156 - 159: 16.318 distance: 157 - 158: 39.357 distance: 157 - 163: 40.081 distance: 159 - 160: 26.265 distance: 160 - 161: 21.830 distance: 161 - 162: 28.142 distance: 163 - 164: 21.966 distance: 164 - 165: 35.529 distance: 164 - 167: 24.196 distance: 165 - 166: 15.448 distance: 165 - 171: 29.254 distance: 167 - 168: 19.457 distance: 168 - 169: 31.771 distance: 168 - 170: 39.188 distance: 171 - 172: 42.820 distance: 172 - 173: 56.128 distance: 172 - 175: 20.334 distance: 173 - 174: 38.524 distance: 173 - 177: 51.671 distance: 175 - 176: 24.740 distance: 177 - 178: 23.981 distance: 178 - 179: 59.543 distance: 178 - 181: 44.273 distance: 179 - 180: 39.380 distance: 181 - 182: 50.167 distance: 182 - 183: 40.577 distance: 182 - 184: 42.585 distance: 185 - 186: 28.416 distance: 186 - 187: 41.856 distance: 186 - 189: 42.381 distance: 187 - 188: 40.553 distance: 187 - 194: 39.671 distance: 188 - 210: 32.017 distance: 189 - 190: 40.481 distance: 191 - 192: 48.703 distance: 192 - 193: 55.129 distance: 194 - 195: 65.848 distance: 194 - 200: 39.675 distance: 195 - 196: 52.522 distance: 195 - 198: 39.777 distance: 196 - 197: 55.831 distance: 199 - 200: 40.199 distance: 201 - 202: 57.255 distance: 202 - 203: 39.248 distance: 202 - 205: 41.215 distance: 203 - 204: 57.008 distance: 203 - 210: 33.430 distance: 206 - 207: 40.913 distance: 207 - 208: 39.929 distance: 207 - 209: 34.236