Starting phenix.real_space_refine on Fri Jun 6 17:23:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wy5_32884/06_2025/7wy5_32884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wy5_32884/06_2025/7wy5_32884.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/cci-nas-00/data/ceres_data/7wy5_32884/06_2025/7wy5_32884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wy5_32884/06_2025/7wy5_32884.map" model { file = "/net/cci-nas-00/data/ceres_data/7wy5_32884/06_2025/7wy5_32884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wy5_32884/06_2025/7wy5_32884_neut.cif" } 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= 0.021 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 5097 2.51 5 N 1382 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8009 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1877 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} 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 Time building chain proxies: 4.82, per 1000 atoms: 0.60 Number of scatterers: 8009 At special positions: 0 Unit cell: (79.2, 100.1, 134.2, 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 1474 8.00 N 1382 7.00 C 5097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R1008 " - pdb=" SG CYS R1080 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.0 seconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 38.0% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.797A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.764A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 239' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.620A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.748A 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 317 removed outlier: 3.532A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.576A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.572A pdb=" N GLU A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.737A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.505A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 940 through 956 removed outlier: 3.877A pdb=" N LEU R 944 " --> pdb=" O VAL R 940 " (cutoff:3.500A) Processing helix chain 'R' and resid 958 through 970 removed outlier: 3.695A pdb=" N ILE R 962 " --> pdb=" O VAL R 958 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE R 970 " --> pdb=" O THR R 966 " (cutoff:3.500A) Processing helix chain 'R' and resid 971 through 974 removed outlier: 3.657A pdb=" N GLN R 974 " --> pdb=" O ARG R 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 971 through 974' Processing helix chain 'R' and resid 975 through 999 removed outlier: 3.725A pdb=" N ILE R 999 " --> pdb=" O PHE R 995 " (cutoff:3.500A) Processing helix chain 'R' and resid 1010 through 1035 removed outlier: 3.616A pdb=" N GLY R1030 " --> pdb=" O MET R1026 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1056 removed outlier: 3.650A pdb=" N TYR R1056 " --> pdb=" O TYR R1052 " (cutoff:3.500A) Processing helix chain 'R' and resid 1056 through 1070 removed outlier: 3.923A 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 1118 Proline residue: R1095 - end of helix removed outlier: 4.436A pdb=" N ILE R1105 " --> pdb=" O MET R1101 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR R1118 " --> pdb=" O MET R1114 " (cutoff:3.500A) Processing helix chain 'R' and resid 1144 through 1154 removed outlier: 3.674A pdb=" N LEU R1151 " --> pdb=" O ALA R1147 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS R1152 " --> pdb=" O ILE R1148 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU R1153 " --> pdb=" O ALA R1149 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU R1154 " --> pdb=" O LEU R1150 " (cutoff:3.500A) Processing helix chain 'R' and resid 1155 through 1163 removed outlier: 3.644A pdb=" N TRP R1158 " --> pdb=" O GLY R1155 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA R1159 " --> pdb=" O LEU R1156 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY R1161 " --> pdb=" O TRP R1158 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU R1162 " --> pdb=" O ALA R1159 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET R1163 " --> pdb=" O PHE R1160 " (cutoff:3.500A) Processing helix chain 'R' and resid 1169 through 1181 removed outlier: 4.170A pdb=" N ALA R1173 " --> pdb=" O THR R1169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER R1181 " --> pdb=" O THR R1177 " (cutoff:3.500A) Processing helix chain 'R' and resid 1182 through 1193 Processing helix chain 'R' and resid 1195 through 1207 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.470A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.826A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.066A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.877A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.180A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.055A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.844A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.194A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 987 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: 2.21 Time building geometry restraints manager: 2.12 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: 2498 1.34 - 1.45: 1232 1.45 - 1.57: 4362 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8172 Sorted by residual: bond pdb=" C ASP B 291 " pdb=" N PHE B 292 " ideal model delta sigma weight residual 1.331 1.373 -0.043 1.35e-02 5.49e+03 1.00e+01 bond pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 1.525 1.493 0.032 1.38e-02 5.25e+03 5.38e+00 bond pdb=" CA ASP B 291 " pdb=" CB ASP B 291 " ideal model delta sigma weight residual 1.528 1.559 -0.031 1.37e-02 5.33e+03 5.10e+00 bond pdb=" N THR R1169 " pdb=" CA THR R1169 " ideal model delta sigma weight residual 1.458 1.438 0.020 9.00e-03 1.23e+04 4.84e+00 bond pdb=" CA THR R1169 " pdb=" C THR R1169 " ideal model delta sigma weight residual 1.525 1.547 -0.023 1.11e-02 8.12e+03 4.12e+00 ... (remaining 8167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 10719 1.83 - 3.66: 277 3.66 - 5.48: 46 5.48 - 7.31: 13 7.31 - 9.14: 3 Bond angle restraints: 11058 Sorted by residual: angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.41 117.51 -7.10 1.18e+00 7.18e-01 3.62e+01 angle pdb=" N ILE R1165 " pdb=" CA ILE R1165 " pdb=" C ILE R1165 " ideal model delta sigma weight residual 111.62 116.00 -4.38 7.90e-01 1.60e+00 3.08e+01 angle pdb=" N TYR N 94 " pdb=" CA TYR N 94 " pdb=" C TYR N 94 " ideal model delta sigma weight residual 108.90 115.18 -6.28 1.63e+00 3.76e-01 1.48e+01 angle pdb=" N MET R1163 " pdb=" CA MET R1163 " pdb=" C MET R1163 " ideal model delta sigma weight residual 110.68 115.87 -5.19 1.39e+00 5.18e-01 1.40e+01 angle pdb=" C ILE R1165 " pdb=" CA ILE R1165 " pdb=" CB ILE R1165 " ideal model delta sigma weight residual 111.05 107.76 3.29 8.90e-01 1.26e+00 1.37e+01 ... (remaining 11053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4444 17.66 - 35.33: 336 35.33 - 52.99: 49 52.99 - 70.65: 7 70.65 - 88.31: 7 Dihedral angle restraints: 4843 sinusoidal: 1903 harmonic: 2940 Sorted by residual: dihedral pdb=" CB CYS R1008 " pdb=" SG CYS R1008 " pdb=" SG CYS R1080 " pdb=" CB CYS R1080 " ideal model delta sinusoidal sigma weight residual -86.00 -133.09 47.09 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual 180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ILE R 997 " pdb=" C ILE R 997 " pdb=" N GLY R 998 " pdb=" CA GLY R 998 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 4840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 992 0.055 - 0.110: 213 0.110 - 0.165: 36 0.165 - 0.219: 1 0.219 - 0.274: 7 Chirality restraints: 1249 Sorted by residual: chirality pdb=" CA CYS R1008 " pdb=" N CYS R1008 " pdb=" C CYS R1008 " pdb=" CB CYS R1008 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA MET R1163 " pdb=" N MET R1163 " pdb=" C MET R1163 " pdb=" CB MET R1163 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1246 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.021 2.00e-02 2.50e+03 1.74e-02 6.06e+00 pdb=" CG TYR B 59 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO B 236 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO G 60 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.027 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 47 2.57 - 3.15: 6069 3.15 - 3.73: 10982 3.73 - 4.32: 15324 4.32 - 4.90: 26433 Nonbonded interactions: 58855 Sorted by model distance: nonbonded pdb=" OG1 THR R1076 " pdb=" O VAL R1079 " model vdw 1.986 3.040 nonbonded pdb=" OG1 THR R 966 " pdb=" OH TYR R1202 " model vdw 2.175 3.040 nonbonded pdb=" NH1 ARG N 67 " pdb=" O SER N 85 " model vdw 2.183 3.120 nonbonded pdb=" OD1 ASP A 229 " pdb=" OG1 THR N 113 " model vdw 2.233 3.040 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.241 3.040 ... (remaining 58850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.150 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.580 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.005 0.043 8173 Z= 0.235 Angle : 0.746 9.138 11060 Z= 0.441 Chirality : 0.049 0.274 1249 Planarity : 0.004 0.056 1403 Dihedral : 12.829 88.312 2938 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.28 (0.26), residues: 997 helix: 0.77 (0.28), residues: 361 sheet: 0.91 (0.35), residues: 217 loop : -1.68 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.043 0.002 TYR B 59 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.15210 ( 348) hydrogen bonds : angle 5.82233 ( 987) SS BOND : bond 0.00787 ( 1) SS BOND : angle 2.44162 ( 2) covalent geometry : bond 0.00517 ( 8172) covalent geometry : angle 0.74560 (11058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.849 Fit side-chains REVERT: A 299 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6208 (mm-30) REVERT: R 947 VAL cc_start: 0.8045 (t) cc_final: 0.7806 (m) REVERT: R 954 LEU cc_start: 0.7756 (mt) cc_final: 0.7329 (mt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 1.1838 time to fit residues: 206.7889 Evaluate side-chains 148 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 392 ASN B 75 GLN B 268 ASN G 44 HIS R 981 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121911 restraints weight = 11023.141| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.08 r_work: 0.3476 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8173 Z= 0.187 Angle : 0.646 9.562 11060 Z= 0.350 Chirality : 0.044 0.166 1249 Planarity : 0.004 0.054 1403 Dihedral : 5.104 26.301 1098 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.38 % Allowed : 8.29 % Favored : 90.32 % 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 (0.27), residues: 997 helix: 1.31 (0.28), residues: 354 sheet: 0.77 (0.35), residues: 223 loop : -1.39 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE B 241 TYR 0.028 0.002 TYR B 59 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.07023 ( 348) hydrogen bonds : angle 4.61001 ( 987) SS BOND : bond 0.00625 ( 1) SS BOND : angle 2.56372 ( 2) covalent geometry : bond 0.00433 ( 8172) covalent geometry : angle 0.64517 (11058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.788 Fit side-chains REVERT: A 32 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7792 (mttm) REVERT: A 299 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6868 (mm-30) REVERT: B 270 ILE cc_start: 0.8520 (pt) cc_final: 0.8040 (mt) REVERT: B 312 ASP cc_start: 0.7806 (t0) cc_final: 0.7560 (t0) REVERT: R 947 VAL cc_start: 0.8191 (t) cc_final: 0.7988 (m) outliers start: 12 outliers final: 6 residues processed: 160 average time/residue: 1.2166 time to fit residues: 206.5561 Evaluate side-chains 154 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 91 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.143568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124086 restraints weight = 11284.666| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.11 r_work: 0.3506 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8173 Z= 0.124 Angle : 0.561 10.096 11060 Z= 0.301 Chirality : 0.042 0.142 1249 Planarity : 0.004 0.051 1403 Dihedral : 4.639 22.953 1098 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.96 % Allowed : 11.52 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.27), residues: 997 helix: 1.71 (0.29), residues: 354 sheet: 0.77 (0.34), residues: 223 loop : -1.26 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.017 0.001 TYR N 95 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05362 ( 348) hydrogen bonds : angle 4.23852 ( 987) SS BOND : bond 0.00395 ( 1) SS BOND : angle 2.08332 ( 2) covalent geometry : bond 0.00270 ( 8172) covalent geometry : angle 0.56041 (11058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7634 (mtm110) REVERT: A 285 ILE cc_start: 0.8640 (mt) cc_final: 0.8427 (mp) REVERT: A 300 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7234 (ttmp) REVERT: B 270 ILE cc_start: 0.8494 (pt) cc_final: 0.8043 (mt) REVERT: B 312 ASP cc_start: 0.7804 (t0) cc_final: 0.7454 (t0) outliers start: 17 outliers final: 7 residues processed: 163 average time/residue: 1.1445 time to fit residues: 198.5037 Evaluate side-chains 155 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain R residue 1091 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 11 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123267 restraints weight = 10966.912| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.09 r_work: 0.3504 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8173 Z= 0.149 Angle : 0.582 9.148 11060 Z= 0.313 Chirality : 0.043 0.150 1249 Planarity : 0.004 0.053 1403 Dihedral : 4.669 24.546 1098 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.42 % Allowed : 13.59 % Favored : 83.99 % 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: 0.39 (0.27), residues: 997 helix: 1.58 (0.28), residues: 361 sheet: 0.83 (0.34), residues: 221 loop : -1.29 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.002 PHE A 340 TYR 0.019 0.001 TYR N 95 ARG 0.003 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05934 ( 348) hydrogen bonds : angle 4.25871 ( 987) SS BOND : bond 0.00444 ( 1) SS BOND : angle 2.26985 ( 2) covalent geometry : bond 0.00337 ( 8172) covalent geometry : angle 0.58170 (11058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 231 ARG cc_start: 0.8506 (ptp-170) cc_final: 0.8296 (ptm-80) REVERT: A 283 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7654 (mtm110) REVERT: A 285 ILE cc_start: 0.8692 (mt) cc_final: 0.8485 (mp) REVERT: A 299 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6990 (mm-30) REVERT: B 270 ILE cc_start: 0.8500 (pt) cc_final: 0.8042 (mt) REVERT: B 312 ASP cc_start: 0.7880 (t0) cc_final: 0.7532 (t0) outliers start: 21 outliers final: 17 residues processed: 159 average time/residue: 1.1477 time to fit residues: 194.3026 Evaluate side-chains 162 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 1091 SER Chi-restraints excluded: chain R residue 1157 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 30 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 66 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.124457 restraints weight = 10870.817| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.05 r_work: 0.3520 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8173 Z= 0.125 Angle : 0.550 8.880 11060 Z= 0.295 Chirality : 0.042 0.141 1249 Planarity : 0.004 0.050 1403 Dihedral : 4.494 23.138 1098 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.42 % Allowed : 13.94 % Favored : 83.64 % 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: 0.53 (0.27), residues: 997 helix: 1.68 (0.28), residues: 364 sheet: 0.83 (0.34), residues: 221 loop : -1.16 (0.29), residues: 412 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 0.017 0.001 PHE A 340 TYR 0.020 0.001 TYR A 37 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05180 ( 348) hydrogen bonds : angle 4.09602 ( 987) SS BOND : bond 0.00483 ( 1) SS BOND : angle 2.10296 ( 2) covalent geometry : bond 0.00274 ( 8172) covalent geometry : angle 0.54919 (11058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.823 Fit side-chains REVERT: A 283 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7633 (mtm110) REVERT: A 299 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7013 (mm-30) REVERT: A 300 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7168 (ttmp) REVERT: B 270 ILE cc_start: 0.8471 (pt) cc_final: 0.8036 (mt) REVERT: B 312 ASP cc_start: 0.7853 (t0) cc_final: 0.7537 (t0) outliers start: 21 outliers final: 14 residues processed: 162 average time/residue: 1.2470 time to fit residues: 214.5304 Evaluate side-chains 163 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 1091 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 56 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.144481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124089 restraints weight = 10918.883| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.09 r_work: 0.3518 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8173 Z= 0.129 Angle : 0.561 9.978 11060 Z= 0.299 Chirality : 0.042 0.143 1249 Planarity : 0.004 0.050 1403 Dihedral : 4.464 23.518 1098 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.96 % Allowed : 15.90 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 997 helix: 1.72 (0.29), residues: 364 sheet: 0.87 (0.34), residues: 221 loop : -1.10 (0.30), residues: 412 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 0.021 0.001 PHE A 340 TYR 0.018 0.001 TYR A 37 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05261 ( 348) hydrogen bonds : angle 4.09177 ( 987) SS BOND : bond 0.00467 ( 1) SS BOND : angle 2.16739 ( 2) covalent geometry : bond 0.00285 ( 8172) covalent geometry : angle 0.56073 (11058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.053 Fit side-chains REVERT: A 299 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 300 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7193 (ttmp) REVERT: B 270 ILE cc_start: 0.8482 (pt) cc_final: 0.8043 (mt) REVERT: B 312 ASP cc_start: 0.7841 (t0) cc_final: 0.7536 (t0) outliers start: 17 outliers final: 13 residues processed: 153 average time/residue: 1.2960 time to fit residues: 210.5193 Evaluate side-chains 160 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 1091 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 0.0070 chunk 86 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126054 restraints weight = 10969.744| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.10 r_work: 0.3546 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8173 Z= 0.107 Angle : 0.530 10.106 11060 Z= 0.282 Chirality : 0.041 0.146 1249 Planarity : 0.003 0.049 1403 Dihedral : 4.272 21.454 1098 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.07 % Allowed : 17.05 % Favored : 80.88 % 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: 0.83 (0.27), residues: 997 helix: 2.00 (0.29), residues: 357 sheet: 0.93 (0.34), residues: 221 loop : -0.98 (0.30), residues: 419 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 0.019 0.001 PHE A 340 TYR 0.018 0.001 TYR A 37 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 348) hydrogen bonds : angle 3.95213 ( 987) SS BOND : bond 0.00453 ( 1) SS BOND : angle 2.00343 ( 2) covalent geometry : bond 0.00229 ( 8172) covalent geometry : angle 0.52917 (11058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.843 Fit side-chains REVERT: A 299 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7032 (mm-30) REVERT: A 300 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7169 (ttmp) REVERT: B 270 ILE cc_start: 0.8437 (pt) cc_final: 0.7997 (mt) REVERT: B 312 ASP cc_start: 0.7795 (t0) cc_final: 0.7519 (t0) REVERT: N 60 TYR cc_start: 0.7183 (m-80) cc_final: 0.6857 (m-80) REVERT: R 1114 MET cc_start: 0.6124 (tpp) cc_final: 0.5813 (tpp) outliers start: 18 outliers final: 11 residues processed: 160 average time/residue: 1.2381 time to fit residues: 210.6981 Evaluate side-chains 157 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 1091 SER Chi-restraints excluded: chain R residue 1160 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122950 restraints weight = 11051.514| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.11 r_work: 0.3499 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8173 Z= 0.168 Angle : 0.597 9.063 11060 Z= 0.320 Chirality : 0.043 0.147 1249 Planarity : 0.004 0.050 1403 Dihedral : 4.560 25.041 1098 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.76 % Allowed : 16.94 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 997 helix: 1.67 (0.29), residues: 365 sheet: 1.05 (0.34), residues: 219 loop : -1.11 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.024 0.002 PHE A 340 TYR 0.020 0.001 TYR N 95 ARG 0.002 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.06064 ( 348) hydrogen bonds : angle 4.17416 ( 987) SS BOND : bond 0.00501 ( 1) SS BOND : angle 2.33818 ( 2) covalent geometry : bond 0.00391 ( 8172) covalent geometry : angle 0.59586 (11058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.891 Fit side-chains REVERT: A 299 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7114 (mm-30) REVERT: B 270 ILE cc_start: 0.8491 (pt) cc_final: 0.8050 (mt) REVERT: B 312 ASP cc_start: 0.7773 (t0) cc_final: 0.7478 (t0) REVERT: R 1114 MET cc_start: 0.6282 (tpp) cc_final: 0.5998 (tpp) REVERT: R 1160 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7184 (t80) outliers start: 24 outliers final: 19 residues processed: 160 average time/residue: 1.0688 time to fit residues: 182.4346 Evaluate side-chains 166 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 1006 ILE Chi-restraints excluded: chain R residue 1091 SER Chi-restraints excluded: chain R residue 1160 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 924 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122868 restraints weight = 11082.564| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.10 r_work: 0.3496 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8173 Z= 0.168 Angle : 0.605 11.980 11060 Z= 0.323 Chirality : 0.043 0.148 1249 Planarity : 0.004 0.050 1403 Dihedral : 4.616 24.350 1098 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.42 % Allowed : 17.51 % Favored : 80.07 % 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: 0.60 (0.27), residues: 997 helix: 1.63 (0.29), residues: 365 sheet: 1.03 (0.34), residues: 219 loop : -1.13 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.002 PHE A 340 TYR 0.020 0.002 TYR N 95 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.06075 ( 348) hydrogen bonds : angle 4.20800 ( 987) SS BOND : bond 0.00526 ( 1) SS BOND : angle 2.24270 ( 2) covalent geometry : bond 0.00390 ( 8172) covalent geometry : angle 0.60437 (11058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.900 Fit side-chains REVERT: A 299 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 270 ILE cc_start: 0.8500 (pt) cc_final: 0.8070 (mt) REVERT: B 312 ASP cc_start: 0.7812 (t0) cc_final: 0.7505 (t0) REVERT: R 1114 MET cc_start: 0.6126 (tpp) cc_final: 0.5849 (tpp) outliers start: 21 outliers final: 16 residues processed: 158 average time/residue: 1.3732 time to fit residues: 230.6762 Evaluate side-chains 163 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 1091 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123330 restraints weight = 10920.466| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.06 r_work: 0.3504 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8173 Z= 0.156 Angle : 0.595 10.485 11060 Z= 0.318 Chirality : 0.042 0.144 1249 Planarity : 0.004 0.050 1403 Dihedral : 4.596 24.850 1098 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.84 % Allowed : 18.66 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.27), residues: 997 helix: 1.66 (0.29), residues: 365 sheet: 1.02 (0.34), residues: 219 loop : -1.12 (0.30), residues: 413 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 0.021 0.002 PHE A 340 TYR 0.023 0.002 TYR N 80 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05850 ( 348) hydrogen bonds : angle 4.17105 ( 987) SS BOND : bond 0.00595 ( 1) SS BOND : angle 2.13509 ( 2) covalent geometry : bond 0.00359 ( 8172) covalent geometry : angle 0.59458 (11058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.830 Fit side-chains REVERT: A 60 MET cc_start: 0.7428 (mtm) cc_final: 0.7182 (mtp) REVERT: A 299 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 270 ILE cc_start: 0.8490 (pt) cc_final: 0.8057 (mt) REVERT: B 312 ASP cc_start: 0.7772 (t0) cc_final: 0.7477 (t0) REVERT: R 1114 MET cc_start: 0.6117 (tpp) cc_final: 0.5838 (tpp) outliers start: 16 outliers final: 16 residues processed: 155 average time/residue: 1.1108 time to fit residues: 183.2381 Evaluate side-chains 160 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 1091 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 5 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.147303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127469 restraints weight = 11067.135| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.05 r_work: 0.3564 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8173 Z= 0.099 Angle : 0.527 12.522 11060 Z= 0.279 Chirality : 0.041 0.162 1249 Planarity : 0.003 0.049 1403 Dihedral : 4.181 20.762 1098 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.04 % Allowed : 19.35 % Favored : 79.61 % 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: 0.96 (0.28), residues: 997 helix: 2.12 (0.29), residues: 357 sheet: 1.18 (0.34), residues: 212 loop : -0.98 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE A 340 TYR 0.015 0.001 TYR N 95 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 348) hydrogen bonds : angle 3.85519 ( 987) SS BOND : bond 0.00473 ( 1) SS BOND : angle 1.79045 ( 2) covalent geometry : bond 0.00207 ( 8172) covalent geometry : angle 0.52647 (11058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6631.43 seconds wall clock time: 115 minutes 35.08 seconds (6935.08 seconds total)