Starting phenix.real_space_refine on Sat Apr 6 17:29:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/04_2024/7x10_32932_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/04_2024/7x10_32932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/04_2024/7x10_32932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/04_2024/7x10_32932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/04_2024/7x10_32932_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/04_2024/7x10_32932_neut.pdb" } resolution = 2.93 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 61 5.16 5 C 5546 2.51 5 N 1486 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8674 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1744 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 3 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: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 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: "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: 4.38, per 1000 atoms: 0.50 Number of scatterers: 8674 At special positions: 0 Unit cell: (90.2, 124.3, 132, 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 61 16.00 O 1581 8.00 N 1486 7.00 C 5546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 231 " distance=2.05 Simple disulfide: pdb=" SG CYS R1008 " - pdb=" SG CYS R1080 " distance=2.03 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: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.6% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 17 through 39 removed outlier: 3.948A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 66 Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.000A pdb=" N TRP A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.537A pdb=" N ASN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.778A pdb=" N PHE A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.752A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.742A pdb=" N ASN A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.782A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.876A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.601A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.072A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 925 through 930 removed outlier: 3.866A pdb=" N ALA R 930 " --> pdb=" O VAL R 927 " (cutoff:3.500A) Processing helix chain 'R' and resid 940 through 956 removed outlier: 3.990A pdb=" N LEU R 944 " --> pdb=" O VAL R 940 " (cutoff:3.500A) Processing helix chain 'R' and resid 958 through 967 Processing helix chain 'R' and resid 970 through 974 removed outlier: 3.930A pdb=" N LEU R 973 " --> pdb=" O PHE R 970 " (cutoff:3.500A) removed outlier: 3.946A 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 998 Processing helix chain 'R' and resid 1010 through 1038 removed outlier: 4.732A pdb=" N HIS R1016 " --> pdb=" O ALA R1012 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY R1030 " --> pdb=" O MET R1026 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1070 Proline residue: R1059 - end of helix Processing helix chain 'R' and resid 1086 through 1091 removed outlier: 4.403A pdb=" N ILE R1089 " --> pdb=" O THR R1086 " (cutoff:3.500A) Processing helix chain 'R' and resid 1092 through 1117 removed outlier: 3.735A pdb=" N HIS R1117 " --> pdb=" O LYS R1113 " (cutoff:3.500A) Processing helix chain 'R' and resid 1144 through 1154 removed outlier: 4.002A pdb=" N LEU R1151 " --> pdb=" O ALA R1147 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS R1152 " --> pdb=" O ILE R1148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU R1153 " --> pdb=" O ALA R1149 " (cutoff:3.500A) Processing helix chain 'R' and resid 1159 through 1164 removed outlier: 3.738A pdb=" N LEU R1162 " --> pdb=" O ALA R1159 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR R1164 " --> pdb=" O GLY R1161 " (cutoff:3.500A) Processing helix chain 'R' and resid 1166 through 1168 No H-bonds generated for 'chain 'R' and resid 1166 through 1168' Processing helix chain 'R' and resid 1169 through 1181 removed outlier: 3.874A pdb=" N ALA R1173 " --> pdb=" O THR R1169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR R1177 " --> pdb=" O ALA R1173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER R1181 " --> pdb=" O THR R1177 " (cutoff:3.500A) Processing helix chain 'R' and resid 1182 through 1191 removed outlier: 3.536A pdb=" N PHE R1188 " --> pdb=" O GLY R1184 " (cutoff:3.500A) Processing helix chain 'R' and resid 1195 through 1204 removed outlier: 3.758A pdb=" N LYS R1204 " --> pdb=" O LYS R1200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.807A pdb=" N SER A 243 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 343 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.871A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.943A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.890A 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: 6.881A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 149 removed outlier: 7.056A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.634A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.063A 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: 3.579A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.806A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.845A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.246A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 144 Processing sheet with id=AB3, first strand: chain 'E' and resid 148 through 150 removed outlier: 3.517A pdb=" N VAL E 149 " --> pdb=" O LYS E 246 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 248 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU E 180 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU E 189 " --> pdb=" O LEU E 180 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1077 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: 2.53 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2093 1.33 - 1.46: 2466 1.46 - 1.59: 4205 1.59 - 1.71: 0 1.71 - 1.84: 92 Bond restraints: 8856 Sorted by residual: bond pdb=" CA GLN E 113 " pdb=" C GLN E 113 " ideal model delta sigma weight residual 1.521 1.560 -0.039 1.29e-02 6.01e+03 9.08e+00 bond pdb=" CA GLY E 16 " pdb=" C GLY E 16 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.67e-02 3.59e+03 9.06e+00 bond pdb=" CA SER E 186 " pdb=" CB SER E 186 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.58e-02 4.01e+03 8.93e+00 bond pdb=" C LEU E 216 " pdb=" N THR E 217 " ideal model delta sigma weight residual 1.330 1.369 -0.039 1.32e-02 5.74e+03 8.90e+00 bond pdb=" C GLU E 236 " pdb=" O GLU E 236 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.26e-02 6.30e+03 6.55e+00 ... (remaining 8851 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.77: 131 105.77 - 112.84: 4695 112.84 - 119.91: 2957 119.91 - 126.97: 4092 126.97 - 134.04: 101 Bond angle restraints: 11976 Sorted by residual: angle pdb=" N ALA R1009 " pdb=" CA ALA R1009 " pdb=" C ALA R1009 " ideal model delta sigma weight residual 113.51 99.88 13.63 1.52e+00 4.33e-01 8.04e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.61 116.81 -6.20 1.25e+00 6.40e-01 2.46e+01 angle pdb=" C CYS R1008 " pdb=" N ALA R1009 " pdb=" CA ALA R1009 " ideal model delta sigma weight residual 126.86 119.08 7.78 1.57e+00 4.06e-01 2.46e+01 angle pdb=" C GLU E 224 " pdb=" CA GLU E 224 " pdb=" CB GLU E 224 " ideal model delta sigma weight residual 111.26 103.81 7.45 1.67e+00 3.59e-01 1.99e+01 angle pdb=" C PRO E 14 " pdb=" CA PRO E 14 " pdb=" CB PRO E 14 " ideal model delta sigma weight residual 111.39 116.57 -5.18 1.28e+00 6.10e-01 1.64e+01 ... (remaining 11971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4811 17.99 - 35.98: 367 35.98 - 53.97: 47 53.97 - 71.96: 8 71.96 - 89.95: 4 Dihedral angle restraints: 5237 sinusoidal: 2058 harmonic: 3179 Sorted by residual: dihedral pdb=" C CYS R1008 " pdb=" N CYS R1008 " pdb=" CA CYS R1008 " pdb=" CB CYS R1008 " ideal model delta harmonic sigma weight residual -122.60 -132.77 10.17 0 2.50e+00 1.60e-01 1.65e+01 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 -119.62 33.62 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CA ASP R1085 " pdb=" C ASP R1085 " pdb=" N THR R1086 " pdb=" CA THR R1086 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1188 0.075 - 0.150: 158 0.150 - 0.225: 9 0.225 - 0.299: 2 0.299 - 0.374: 1 Chirality restraints: 1358 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 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA SER R1073 " pdb=" N SER R1073 " pdb=" C SER R1073 " pdb=" CB SER R1073 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+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 1.38e+00 ... (remaining 1355 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.044 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO B 236 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 178 " -0.021 2.00e-02 2.50e+03 1.49e-02 5.56e+00 pdb=" CG TRP E 178 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP E 178 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP E 178 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 178 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 178 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 178 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 151 " -0.022 2.00e-02 2.50e+03 1.56e-02 4.25e+00 pdb=" CG PHE B 151 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 151 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 151 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 151 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 151 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 151 " -0.008 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 657 2.73 - 3.28: 8069 3.28 - 3.82: 12848 3.82 - 4.36: 15022 4.36 - 4.90: 27090 Nonbonded interactions: 63686 Sorted by model distance: nonbonded pdb=" O ILE R 962 " pdb=" OG1 THR R 966 " model vdw 2.192 2.440 nonbonded pdb=" O THR R1177 " pdb=" OG SER R1181 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR R1076 " pdb=" O VAL R1079 " model vdw 2.246 2.440 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.248 2.440 ... (remaining 63681 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: 0.790 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: 3.770 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.990 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 0.059 8856 Z= 0.356 Angle : 0.799 13.631 11976 Z= 0.461 Chirality : 0.051 0.374 1358 Planarity : 0.005 0.068 1507 Dihedral : 12.695 89.948 3175 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.26), residues: 1078 helix: 0.67 (0.29), residues: 345 sheet: -0.44 (0.31), residues: 266 loop : -2.13 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 178 HIS 0.011 0.002 HIS R1016 PHE 0.033 0.002 PHE B 151 TYR 0.020 0.002 TYR R1164 ARG 0.009 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.905 Fit side-chains REVERT: E 185 GLN cc_start: 0.8697 (mt0) cc_final: 0.8468 (mt0) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.1582 time to fit residues: 199.4655 Evaluate side-chains 139 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.0050 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN R1116 HIS R1191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8856 Z= 0.242 Angle : 0.612 9.246 11976 Z= 0.329 Chirality : 0.044 0.140 1358 Planarity : 0.004 0.047 1507 Dihedral : 5.151 31.219 1185 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.27 % Allowed : 10.45 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1078 helix: 1.29 (0.30), residues: 342 sheet: -0.32 (0.30), residues: 272 loop : -2.01 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 178 HIS 0.010 0.001 HIS R1016 PHE 0.024 0.002 PHE B 151 TYR 0.018 0.002 TYR R1112 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 0.982 Fit side-chains REVERT: A 215 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8022 (ptmm) REVERT: A 270 MET cc_start: 0.7489 (mtt) cc_final: 0.7199 (mtm) REVERT: B 137 ARG cc_start: 0.7107 (mmt90) cc_final: 0.6891 (mmt90) REVERT: B 323 ASP cc_start: 0.7617 (p0) cc_final: 0.7271 (p0) REVERT: E 38 ARG cc_start: 0.7365 (ttp-170) cc_final: 0.6892 (ttm170) REVERT: E 142 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.4732 (mtp) outliers start: 12 outliers final: 4 residues processed: 154 average time/residue: 1.2362 time to fit residues: 203.0408 Evaluate side-chains 147 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain R residue 955 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 268 ASN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 936 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8856 Z= 0.334 Angle : 0.651 9.298 11976 Z= 0.350 Chirality : 0.045 0.145 1358 Planarity : 0.005 0.049 1507 Dihedral : 5.238 31.564 1185 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.75 % Allowed : 14.04 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1078 helix: 1.41 (0.30), residues: 342 sheet: -0.26 (0.31), residues: 265 loop : -1.99 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.011 0.002 HIS R1016 PHE 0.032 0.002 PHE B 151 TYR 0.022 0.002 TYR R1112 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.196 Fit side-chains REVERT: A 220 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7737 (ttmm) REVERT: A 270 MET cc_start: 0.7456 (mtt) cc_final: 0.7158 (mtm) REVERT: B 323 ASP cc_start: 0.7654 (p0) cc_final: 0.7286 (p0) REVERT: E 38 ARG cc_start: 0.7414 (ttp-170) cc_final: 0.6955 (ttm170) REVERT: E 142 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.4832 (mtp) outliers start: 26 outliers final: 14 residues processed: 164 average time/residue: 1.3293 time to fit residues: 232.1474 Evaluate side-chains 163 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 968 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.0050 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 268 ASN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8856 Z= 0.176 Angle : 0.557 9.609 11976 Z= 0.299 Chirality : 0.042 0.145 1358 Planarity : 0.004 0.045 1507 Dihedral : 4.781 28.054 1185 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.43 % Allowed : 16.68 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1078 helix: 1.66 (0.30), residues: 344 sheet: -0.28 (0.30), residues: 281 loop : -1.80 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS R1016 PHE 0.022 0.001 PHE R 989 TYR 0.009 0.001 TYR B 289 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.881 Fit side-chains REVERT: A 270 MET cc_start: 0.7423 (mtt) cc_final: 0.7184 (mtm) REVERT: B 214 ARG cc_start: 0.6664 (mtm180) cc_final: 0.6450 (mtt180) REVERT: R 936 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6420 (t-90) outliers start: 23 outliers final: 13 residues processed: 162 average time/residue: 1.2455 time to fit residues: 214.7644 Evaluate side-chains 164 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 1091 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 0.0060 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8856 Z= 0.165 Angle : 0.536 9.750 11976 Z= 0.288 Chirality : 0.041 0.157 1358 Planarity : 0.004 0.042 1507 Dihedral : 4.566 26.057 1185 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.64 % Allowed : 18.16 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.20 (0.27), residues: 1078 helix: 1.84 (0.30), residues: 344 sheet: -0.12 (0.30), residues: 281 loop : -1.74 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS R1016 PHE 0.024 0.001 PHE R 989 TYR 0.009 0.001 TYR E 192 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 0.916 Fit side-chains REVERT: A 221 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6310 (mtt) REVERT: A 270 MET cc_start: 0.7408 (mtt) cc_final: 0.7161 (mtm) REVERT: E 7 SER cc_start: 0.7770 (t) cc_final: 0.7490 (p) REVERT: R 936 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6379 (t-90) outliers start: 25 outliers final: 14 residues processed: 161 average time/residue: 1.2861 time to fit residues: 219.9561 Evaluate side-chains 166 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 1035 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.0010 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 chunk 86 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8856 Z= 0.142 Angle : 0.521 9.786 11976 Z= 0.277 Chirality : 0.041 0.165 1358 Planarity : 0.003 0.040 1507 Dihedral : 4.372 23.614 1185 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.06 % Allowed : 18.59 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.04 (0.27), residues: 1078 helix: 1.99 (0.30), residues: 344 sheet: 0.05 (0.31), residues: 274 loop : -1.70 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS R1016 PHE 0.025 0.001 PHE R 989 TYR 0.009 0.001 TYR R1074 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 0.881 Fit side-chains REVERT: A 60 MET cc_start: 0.8183 (tpp) cc_final: 0.7560 (mmm) REVERT: A 215 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7824 (mtpp) REVERT: A 220 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7928 (ttmm) REVERT: A 221 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6219 (mtt) REVERT: E 7 SER cc_start: 0.7730 (t) cc_final: 0.7510 (p) REVERT: R 936 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.6362 (t-90) REVERT: R 1062 ILE cc_start: 0.8094 (mt) cc_final: 0.7790 (tp) outliers start: 29 outliers final: 16 residues processed: 166 average time/residue: 1.2380 time to fit residues: 219.1371 Evaluate side-chains 173 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1066 SER Chi-restraints excluded: chain R residue 1091 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8856 Z= 0.256 Angle : 0.594 9.580 11976 Z= 0.317 Chirality : 0.043 0.177 1358 Planarity : 0.004 0.042 1507 Dihedral : 4.698 26.647 1185 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.27 % Allowed : 18.80 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.27), residues: 1078 helix: 1.78 (0.30), residues: 345 sheet: -0.13 (0.30), residues: 279 loop : -1.75 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS R1016 PHE 0.029 0.002 PHE R 989 TYR 0.024 0.002 TYR R1034 ARG 0.008 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.001 Fit side-chains REVERT: A 60 MET cc_start: 0.8179 (tpp) cc_final: 0.7751 (mmm) REVERT: A 221 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6419 (mtt) REVERT: A 270 MET cc_start: 0.7469 (mtt) cc_final: 0.7116 (mtm) REVERT: B 262 MET cc_start: 0.6833 (tpp) cc_final: 0.6310 (mpt) REVERT: E 7 SER cc_start: 0.7791 (t) cc_final: 0.7551 (p) REVERT: R 936 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.6293 (t-90) outliers start: 31 outliers final: 23 residues processed: 165 average time/residue: 1.2079 time to fit residues: 212.8547 Evaluate side-chains 171 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 1020 LEU Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1091 SER Chi-restraints excluded: chain R residue 1172 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 81 optimal weight: 0.0070 chunk 94 optimal weight: 0.0000 chunk 99 optimal weight: 0.6980 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8856 Z= 0.133 Angle : 0.533 10.563 11976 Z= 0.280 Chirality : 0.041 0.185 1358 Planarity : 0.003 0.039 1507 Dihedral : 4.280 22.506 1185 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.38 % Allowed : 19.54 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.02 (0.27), residues: 1078 helix: 1.99 (0.30), residues: 346 sheet: 0.18 (0.31), residues: 276 loop : -1.79 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.003 0.001 HIS R1116 PHE 0.027 0.001 PHE R 989 TYR 0.016 0.001 TYR R1034 ARG 0.009 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.009 Fit side-chains REVERT: A 60 MET cc_start: 0.8117 (tpp) cc_final: 0.7738 (mmm) REVERT: A 220 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7900 (ttmm) REVERT: A 221 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6221 (mtt) REVERT: A 270 MET cc_start: 0.7462 (mtt) cc_final: 0.7124 (mtm) REVERT: B 234 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7664 (t80) REVERT: B 262 MET cc_start: 0.6795 (tpp) cc_final: 0.6381 (mpt) REVERT: R 936 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.6257 (t-90) REVERT: R 1148 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7334 (mt) outliers start: 32 outliers final: 16 residues processed: 166 average time/residue: 1.2333 time to fit residues: 218.2620 Evaluate side-chains 166 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 1020 LEU Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1148 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 974 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8856 Z= 0.197 Angle : 0.563 9.917 11976 Z= 0.301 Chirality : 0.042 0.179 1358 Planarity : 0.004 0.040 1507 Dihedral : 4.437 22.934 1185 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.43 % Allowed : 20.70 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.03 (0.27), residues: 1078 helix: 1.94 (0.30), residues: 345 sheet: 0.10 (0.31), residues: 273 loop : -1.68 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.007 0.001 HIS R1016 PHE 0.029 0.002 PHE R 989 TYR 0.014 0.001 TYR B 289 ARG 0.009 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.944 Fit side-chains REVERT: A 60 MET cc_start: 0.8105 (tpp) cc_final: 0.7754 (mmm) REVERT: A 220 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7744 (ttmm) REVERT: A 221 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6385 (mtt) REVERT: A 270 MET cc_start: 0.7512 (mtt) cc_final: 0.7178 (mtm) REVERT: A 364 ASP cc_start: 0.7145 (m-30) cc_final: 0.6848 (m-30) REVERT: B 262 MET cc_start: 0.6827 (tpp) cc_final: 0.6348 (mpt) REVERT: B 336 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8216 (mt) REVERT: E 142 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.3906 (mtp) REVERT: R 936 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6315 (t-90) outliers start: 23 outliers final: 17 residues processed: 159 average time/residue: 1.1982 time to fit residues: 203.2017 Evaluate side-chains 171 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 999 ILE Chi-restraints excluded: chain R residue 1020 LEU Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1091 SER Chi-restraints excluded: chain R residue 1113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 0.0030 chunk 107 optimal weight: 0.0970 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8856 Z= 0.168 Angle : 0.563 13.190 11976 Z= 0.298 Chirality : 0.042 0.184 1358 Planarity : 0.004 0.038 1507 Dihedral : 4.364 22.596 1185 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.43 % Allowed : 20.91 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.01 (0.27), residues: 1078 helix: 1.91 (0.30), residues: 346 sheet: 0.15 (0.31), residues: 275 loop : -1.67 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS R1016 PHE 0.029 0.001 PHE R 989 TYR 0.012 0.001 TYR B 289 ARG 0.009 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.947 Fit side-chains REVERT: A 60 MET cc_start: 0.8104 (tpp) cc_final: 0.7757 (mmm) REVERT: A 220 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7731 (ttmm) REVERT: A 221 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6414 (mtt) REVERT: A 270 MET cc_start: 0.7477 (mtt) cc_final: 0.7153 (mtm) REVERT: B 262 MET cc_start: 0.6811 (tpp) cc_final: 0.6364 (mpt) REVERT: E 142 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.3823 (mtp) REVERT: R 936 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.6296 (t-90) REVERT: R 955 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7125 (mt) REVERT: R 1148 ILE cc_start: 0.7652 (mp) cc_final: 0.7434 (mt) REVERT: R 1172 MET cc_start: 0.4816 (ppp) cc_final: 0.4206 (ppp) outliers start: 23 outliers final: 16 residues processed: 158 average time/residue: 1.2143 time to fit residues: 204.6502 Evaluate side-chains 169 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 999 ILE Chi-restraints excluded: chain R residue 1020 LEU Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1091 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.0170 chunk 75 optimal weight: 0.5980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.154092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130798 restraints weight = 12583.157| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.31 r_work: 0.3620 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8856 Z= 0.235 Angle : 0.605 13.275 11976 Z= 0.321 Chirality : 0.043 0.185 1358 Planarity : 0.004 0.040 1507 Dihedral : 4.586 24.832 1185 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.85 % Allowed : 20.70 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.09 (0.27), residues: 1078 helix: 1.81 (0.30), residues: 346 sheet: 0.10 (0.31), residues: 278 loop : -1.69 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.009 0.001 HIS R1016 PHE 0.030 0.002 PHE R 989 TYR 0.017 0.001 TYR R1164 ARG 0.009 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.94 seconds wall clock time: 68 minutes 35.03 seconds (4115.03 seconds total)