Starting phenix.real_space_refine on Tue Mar 3 21:59:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vih_32009/03_2026/7vih_32009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vih_32009/03_2026/7vih_32009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vih_32009/03_2026/7vih_32009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vih_32009/03_2026/7vih_32009.map" model { file = "/net/cci-nas-00/data/ceres_data/7vih_32009/03_2026/7vih_32009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vih_32009/03_2026/7vih_32009.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.002 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5702 2.51 5 N 1510 2.21 5 O 1660 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8938 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" 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: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "F" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2237 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain breaks: 2 Chain: "D" Number of atoms: 1826 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1820 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 226, 1820 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 bond proxies already assigned to first conformer: 1843 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'7I4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS D 305 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 305 " occ=0.50 Time building chain proxies: 1.93, per 1000 atoms: 0.22 Number of scatterers: 8938 At special positions: 0 Unit cell: (105.41, 117.03, 131.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 F 1 9.00 O 1660 8.00 N 1510 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 287 " distance=2.03 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: 0.67 Conformation dependent library (CDL) restraints added in 403.9 milliseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.5% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.604A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.687A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.792A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.011A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 49 through 73 Processing helix chain 'F' and resid 78 through 105 Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.973A pdb=" N TYR F 110 " --> pdb=" O ALA F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 148 Processing helix chain 'F' and resid 156 through 181 removed outlier: 4.068A pdb=" N LEU F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 3.502A pdb=" N GLY F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 234 removed outlier: 3.585A pdb=" N ARG F 234 " --> pdb=" O THR F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 282 Proline residue: F 271 - end of helix removed outlier: 4.012A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 314 removed outlier: 3.837A pdb=" N LEU F 297 " --> pdb=" O ALA F 293 " (cutoff:3.500A) Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 315 through 324 removed outlier: 3.545A pdb=" N ARG F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 32 removed outlier: 3.571A pdb=" N ARG D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.624A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 216 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 removed outlier: 4.105A pdb=" N ASP D 231 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.578A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.512A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.570A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 352 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 5.500A pdb=" N THR A 46 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN A 339 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 48 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 61 removed outlier: 6.957A pdb=" N ALA A 72 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET A 60 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 70 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 73 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU A 78 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 91 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 80 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 104 removed outlier: 4.297A pdb=" N GLY A 115 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 134 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.411A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.504A pdb=" N GLN A 219 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 211 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS A 217 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.521A pdb=" N CYS A 249 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR A 262 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 251 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277 removed outlier: 3.602A pdb=" N SER A 274 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 293 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A 306 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 295 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.859A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.281A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.696A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.869A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 185 through 191 removed outlier: 6.055A pdb=" N VAL D 34 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE D 199 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU D 36 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1309 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: 1.49 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1440 1.29 - 1.42: 2402 1.42 - 1.55: 5179 1.55 - 1.68: 5 1.68 - 1.81: 92 Bond restraints: 9118 Sorted by residual: bond pdb=" C16 7I4 F 401 " pdb=" N17 7I4 F 401 " ideal model delta sigma weight residual 1.441 1.154 0.287 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C19 7I4 F 401 " pdb=" C23 7I4 F 401 " ideal model delta sigma weight residual 1.537 1.415 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C18 7I4 F 401 " pdb=" C19 7I4 F 401 " ideal model delta sigma weight residual 1.533 1.412 0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N MET D 240 " pdb=" CA MET D 240 " ideal model delta sigma weight residual 1.457 1.528 -0.072 1.24e-02 6.50e+03 3.34e+01 bond pdb=" C19 7I4 F 401 " pdb=" C20 7I4 F 401 " ideal model delta sigma weight residual 1.538 1.637 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 9113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 12246 3.58 - 7.16: 70 7.16 - 10.74: 18 10.74 - 14.32: 4 14.32 - 17.90: 2 Bond angle restraints: 12340 Sorted by residual: angle pdb=" N VAL D 233 " pdb=" CA VAL D 233 " pdb=" C VAL D 233 " ideal model delta sigma weight residual 110.53 120.89 -10.36 9.40e-01 1.13e+00 1.21e+02 angle pdb=" N THR F 236 " pdb=" CA THR F 236 " pdb=" C THR F 236 " ideal model delta sigma weight residual 109.76 124.56 -14.80 1.59e+00 3.96e-01 8.67e+01 angle pdb=" C THR F 236 " pdb=" CA THR F 236 " pdb=" CB THR F 236 " ideal model delta sigma weight residual 109.84 98.27 11.57 1.63e+00 3.76e-01 5.04e+01 angle pdb=" N GLU D 236 " pdb=" CA GLU D 236 " pdb=" C GLU D 236 " ideal model delta sigma weight residual 111.14 103.92 7.22 1.08e+00 8.57e-01 4.47e+01 angle pdb=" C TYR F 98 " pdb=" CA TYR F 98 " pdb=" CB TYR F 98 " ideal model delta sigma weight residual 110.79 99.77 11.02 1.66e+00 3.63e-01 4.40e+01 ... (remaining 12335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 5333 35.68 - 71.37: 80 71.37 - 107.05: 9 107.05 - 142.74: 0 142.74 - 178.42: 3 Dihedral angle restraints: 5425 sinusoidal: 2128 harmonic: 3297 Sorted by residual: dihedral pdb=" C TYR F 98 " pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" CB TYR F 98 " ideal model delta harmonic sigma weight residual -122.60 -109.85 -12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" CB CYS F 184 " pdb=" SG CYS F 184 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -127.90 41.90 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.88 40.12 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 5422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.151: 1411 1.151 - 2.301: 0 2.301 - 3.452: 0 3.452 - 4.603: 0 4.603 - 5.753: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C19 7I4 F 401 " pdb=" C18 7I4 F 401 " pdb=" C20 7I4 F 401 " pdb=" C23 7I4 F 401 " both_signs ideal model delta sigma weight residual False -2.88 2.88 -5.75 2.00e-01 2.50e+01 8.28e+02 chirality pdb=" CA LEU F 174 " pdb=" N LEU F 174 " pdb=" C LEU F 174 " pdb=" CB LEU F 174 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL F 96 " pdb=" N VAL F 96 " pdb=" C VAL F 96 " pdb=" CB VAL F 96 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1409 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 307 " 0.092 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO F 308 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO F 308 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 308 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 241 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ASN D 241 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN D 241 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 242 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 117 " 0.018 2.00e-02 2.50e+03 1.87e-02 8.75e+00 pdb=" CG TRP F 117 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP F 117 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 117 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 117 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 117 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 117 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP F 117 " 0.001 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 880 2.74 - 3.28: 8878 3.28 - 3.82: 14890 3.82 - 4.36: 18051 4.36 - 4.90: 32056 Nonbonded interactions: 74755 Sorted by model distance: nonbonded pdb=" O GLN A 74 " pdb=" OG SER A 97 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 244 " pdb=" OD1 ASP A 246 " model vdw 2.228 3.040 nonbonded pdb=" O LYS F 283 " pdb=" OG1 THR F 286 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR E 175 " pdb=" OE2 GLU D 8 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR D 290 " pdb=" O SER D 293 " model vdw 2.237 3.040 ... (remaining 74750 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=0.50 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: 1.480 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.040 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:8.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.006 0.287 9122 Z= 0.317 Angle : 0.800 17.898 12348 Z= 0.449 Chirality : 0.161 5.753 1412 Planarity : 0.006 0.135 1544 Dihedral : 13.996 178.421 3287 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 0.61 % Allowed : 0.41 % Favored : 98.98 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1121 helix: 2.00 (0.25), residues: 389 sheet: 0.08 (0.30), residues: 271 loop : -0.58 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 78 TYR 0.039 0.002 TYR F 98 PHE 0.021 0.001 PHE A 291 TRP 0.049 0.002 TRP F 117 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 9118) covalent geometry : angle 0.79989 (12340) SS BOND : bond 0.00235 ( 4) SS BOND : angle 1.27718 ( 8) hydrogen bonds : bond 0.14291 ( 464) hydrogen bonds : angle 5.61909 ( 1309) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.332 Fit side-chains REVERT: A 28 THR cc_start: 0.8719 (p) cc_final: 0.8423 (t) REVERT: E 34 MET cc_start: 0.8715 (mmm) cc_final: 0.8396 (mmm) REVERT: F 172 LEU cc_start: 0.6014 (mm) cc_final: 0.5745 (mm) REVERT: F 269 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.7239 (m100) outliers start: 6 outliers final: 2 residues processed: 164 average time/residue: 0.6396 time to fit residues: 110.8297 Evaluate side-chains 120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain D residue 233 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 174 GLN A 292 ASN E 171 ASN F 116 GLN F 156 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113316 restraints weight = 26880.343| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.42 r_work: 0.3087 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9122 Z= 0.208 Angle : 0.643 9.257 12348 Z= 0.329 Chirality : 0.044 0.249 1412 Planarity : 0.005 0.080 1544 Dihedral : 8.031 150.840 1252 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.27 % Allowed : 10.53 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1121 helix: 2.03 (0.25), residues: 389 sheet: 0.21 (0.30), residues: 276 loop : -0.59 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 78 TYR 0.038 0.002 TYR E 235 PHE 0.012 0.001 PHE D 334 TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS F 28 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9118) covalent geometry : angle 0.64208 (12340) SS BOND : bond 0.00477 ( 4) SS BOND : angle 1.36702 ( 8) hydrogen bonds : bond 0.04037 ( 464) hydrogen bonds : angle 4.53911 ( 1309) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.325 Fit side-chains REVERT: E 76 LYS cc_start: 0.8757 (ttmp) cc_final: 0.8168 (mptt) REVERT: E 179 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: F 90 SER cc_start: 0.7842 (p) cc_final: 0.7625 (p) REVERT: F 172 LEU cc_start: 0.5851 (mm) cc_final: 0.5469 (mm) REVERT: F 269 TRP cc_start: 0.7438 (OUTLIER) cc_final: 0.7186 (m100) REVERT: D 240 MET cc_start: 0.5454 (ppp) cc_final: 0.5099 (ppp) REVERT: D 247 MET cc_start: 0.8830 (mtp) cc_final: 0.8616 (mtm) outliers start: 32 outliers final: 8 residues processed: 132 average time/residue: 0.5465 time to fit residues: 76.7770 Evaluate side-chains 119 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 75 optimal weight: 0.0270 chunk 90 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 37 optimal weight: 0.0020 chunk 66 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.3046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN E 171 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119674 restraints weight = 22407.872| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.76 r_work: 0.3214 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9122 Z= 0.096 Angle : 0.502 6.010 12348 Z= 0.262 Chirality : 0.040 0.191 1412 Planarity : 0.004 0.058 1544 Dihedral : 7.386 137.135 1250 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.45 % Allowed : 14.01 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1121 helix: 2.49 (0.25), residues: 389 sheet: 0.30 (0.30), residues: 270 loop : -0.49 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.027 0.001 TYR E 235 PHE 0.010 0.001 PHE D 189 TRP 0.016 0.001 TRP F 117 HIS 0.002 0.000 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9118) covalent geometry : angle 0.50164 (12340) SS BOND : bond 0.00351 ( 4) SS BOND : angle 0.81575 ( 8) hydrogen bonds : bond 0.03127 ( 464) hydrogen bonds : angle 4.08010 ( 1309) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8880 (t) cc_final: 0.8619 (p) REVERT: E 76 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8124 (mptt) REVERT: E 220 GLU cc_start: 0.7443 (tt0) cc_final: 0.6675 (tt0) REVERT: F 110 TYR cc_start: 0.4190 (m-10) cc_final: 0.3711 (m-80) REVERT: F 172 LEU cc_start: 0.5953 (mm) cc_final: 0.5540 (mm) REVERT: F 177 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6319 (tt) REVERT: F 269 TRP cc_start: 0.7308 (OUTLIER) cc_final: 0.7068 (m100) REVERT: D 240 MET cc_start: 0.5505 (ppp) cc_final: 0.5224 (ppp) REVERT: D 242 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5941 (mtm180) outliers start: 24 outliers final: 8 residues processed: 145 average time/residue: 0.5317 time to fit residues: 82.5554 Evaluate side-chains 129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 242 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN E 39 GLN E 77 ASN E 171 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.142321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111457 restraints weight = 21259.050| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.88 r_work: 0.3112 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9122 Z= 0.205 Angle : 0.582 7.347 12348 Z= 0.307 Chirality : 0.044 0.255 1412 Planarity : 0.005 0.060 1544 Dihedral : 7.093 121.254 1249 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.99 % Allowed : 13.91 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1121 helix: 2.12 (0.25), residues: 390 sheet: 0.25 (0.31), residues: 276 loop : -0.57 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.041 0.002 TYR E 235 PHE 0.013 0.001 PHE D 189 TRP 0.020 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9118) covalent geometry : angle 0.58151 (12340) SS BOND : bond 0.00477 ( 4) SS BOND : angle 1.36565 ( 8) hydrogen bonds : bond 0.03830 ( 464) hydrogen bonds : angle 4.36487 ( 1309) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.323 Fit side-chains REVERT: E 76 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8088 (mptt) REVERT: E 220 GLU cc_start: 0.7607 (tt0) cc_final: 0.6678 (tt0) REVERT: F 110 TYR cc_start: 0.4333 (m-10) cc_final: 0.3913 (m-80) REVERT: F 177 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6642 (tt) REVERT: F 269 TRP cc_start: 0.7432 (OUTLIER) cc_final: 0.7097 (m100) outliers start: 39 outliers final: 13 residues processed: 133 average time/residue: 0.5030 time to fit residues: 71.8518 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113038 restraints weight = 16890.960| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.50 r_work: 0.3173 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9122 Z= 0.145 Angle : 0.521 6.683 12348 Z= 0.278 Chirality : 0.042 0.234 1412 Planarity : 0.004 0.057 1544 Dihedral : 6.282 105.386 1249 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.56 % Allowed : 16.16 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.25), residues: 1121 helix: 2.15 (0.25), residues: 389 sheet: 0.23 (0.31), residues: 275 loop : -0.54 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.036 0.002 TYR E 235 PHE 0.011 0.001 PHE D 189 TRP 0.023 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9118) covalent geometry : angle 0.52103 (12340) SS BOND : bond 0.00408 ( 4) SS BOND : angle 0.83966 ( 8) hydrogen bonds : bond 0.03476 ( 464) hydrogen bonds : angle 4.20962 ( 1309) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.297 Fit side-chains REVERT: E 43 LYS cc_start: 0.8042 (ptpt) cc_final: 0.6883 (ptmm) REVERT: E 76 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8065 (mptt) REVERT: F 110 TYR cc_start: 0.4510 (m-10) cc_final: 0.4136 (m-80) REVERT: F 177 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6560 (tt) REVERT: F 269 TRP cc_start: 0.7452 (OUTLIER) cc_final: 0.7114 (m100) outliers start: 25 outliers final: 14 residues processed: 136 average time/residue: 0.4993 time to fit residues: 72.6835 Evaluate side-chains 134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116973 restraints weight = 20098.441| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.78 r_work: 0.3192 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9122 Z= 0.106 Angle : 0.489 6.804 12348 Z= 0.260 Chirality : 0.041 0.206 1412 Planarity : 0.004 0.059 1544 Dihedral : 5.575 87.506 1249 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.76 % Allowed : 17.28 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1121 helix: 2.35 (0.25), residues: 390 sheet: 0.25 (0.31), residues: 276 loop : -0.49 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.032 0.001 TYR E 235 PHE 0.010 0.001 PHE D 189 TRP 0.028 0.001 TRP F 117 HIS 0.002 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9118) covalent geometry : angle 0.48934 (12340) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.53920 ( 8) hydrogen bonds : bond 0.03160 ( 464) hydrogen bonds : angle 4.02652 ( 1309) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.280 Fit side-chains REVERT: A 157 VAL cc_start: 0.8897 (t) cc_final: 0.8654 (p) REVERT: E 43 LYS cc_start: 0.8072 (ptpt) cc_final: 0.6969 (ptmm) REVERT: E 76 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8123 (mptt) REVERT: F 110 TYR cc_start: 0.4201 (m-10) cc_final: 0.3809 (m-80) REVERT: F 269 TRP cc_start: 0.7361 (OUTLIER) cc_final: 0.7053 (m100) REVERT: D 296 TYR cc_start: 0.7051 (t80) cc_final: 0.6698 (t80) outliers start: 27 outliers final: 12 residues processed: 140 average time/residue: 0.4986 time to fit residues: 74.8162 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 0.0370 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113174 restraints weight = 29603.875| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.60 r_work: 0.3112 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9122 Z= 0.152 Angle : 0.524 6.669 12348 Z= 0.277 Chirality : 0.042 0.225 1412 Planarity : 0.004 0.060 1544 Dihedral : 5.701 83.712 1249 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.86 % Allowed : 18.10 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1121 helix: 2.25 (0.25), residues: 390 sheet: 0.25 (0.30), residues: 277 loop : -0.52 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.037 0.002 TYR E 235 PHE 0.011 0.001 PHE D 189 TRP 0.029 0.001 TRP F 117 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9118) covalent geometry : angle 0.52414 (12340) SS BOND : bond 0.00388 ( 4) SS BOND : angle 0.78121 ( 8) hydrogen bonds : bond 0.03458 ( 464) hydrogen bonds : angle 4.13647 ( 1309) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.283 Fit side-chains REVERT: A 211 ASP cc_start: 0.7742 (t70) cc_final: 0.7290 (t70) REVERT: E 43 LYS cc_start: 0.8094 (ptpt) cc_final: 0.6964 (ptmm) REVERT: E 76 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8056 (mptt) REVERT: F 110 TYR cc_start: 0.4214 (m-10) cc_final: 0.3814 (m-80) REVERT: F 172 LEU cc_start: 0.6007 (mm) cc_final: 0.5538 (mm) REVERT: F 235 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5115 (mt) REVERT: F 269 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.7094 (m100) outliers start: 28 outliers final: 14 residues processed: 135 average time/residue: 0.5112 time to fit residues: 73.7851 Evaluate side-chains 135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.0010 chunk 96 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN E 39 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117188 restraints weight = 27809.065| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.46 r_work: 0.3172 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9122 Z= 0.110 Angle : 0.504 7.160 12348 Z= 0.265 Chirality : 0.041 0.200 1412 Planarity : 0.004 0.059 1544 Dihedral : 5.376 75.167 1249 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.15 % Allowed : 18.51 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1121 helix: 2.40 (0.25), residues: 391 sheet: 0.37 (0.31), residues: 272 loop : -0.49 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.033 0.001 TYR E 235 PHE 0.010 0.001 PHE D 189 TRP 0.027 0.001 TRP F 117 HIS 0.002 0.000 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9118) covalent geometry : angle 0.50440 (12340) SS BOND : bond 0.00335 ( 4) SS BOND : angle 0.57491 ( 8) hydrogen bonds : bond 0.03178 ( 464) hydrogen bonds : angle 4.00752 ( 1309) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.311 Fit side-chains REVERT: A 157 VAL cc_start: 0.8876 (t) cc_final: 0.8630 (p) REVERT: A 211 ASP cc_start: 0.7615 (t70) cc_final: 0.7342 (t70) REVERT: A 261 MET cc_start: 0.8433 (tpp) cc_final: 0.8216 (ttm) REVERT: E 43 LYS cc_start: 0.7983 (ptpt) cc_final: 0.6851 (ptmm) REVERT: E 76 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8082 (mptt) REVERT: E 183 GLN cc_start: 0.8248 (mt0) cc_final: 0.7955 (pt0) REVERT: E 186 GLN cc_start: 0.8534 (tt0) cc_final: 0.8117 (pt0) REVERT: F 110 TYR cc_start: 0.4219 (m-10) cc_final: 0.3879 (m-80) REVERT: F 172 LEU cc_start: 0.6036 (mm) cc_final: 0.5555 (mm) REVERT: F 235 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5091 (mt) outliers start: 21 outliers final: 14 residues processed: 135 average time/residue: 0.5073 time to fit residues: 73.3387 Evaluate side-chains 135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN E 39 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115883 restraints weight = 18851.192| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.78 r_work: 0.3198 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9122 Z= 0.117 Angle : 0.521 9.528 12348 Z= 0.270 Chirality : 0.041 0.200 1412 Planarity : 0.004 0.060 1544 Dihedral : 5.361 73.879 1249 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.35 % Allowed : 19.02 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1121 helix: 2.39 (0.25), residues: 391 sheet: 0.43 (0.31), residues: 271 loop : -0.48 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 160 TYR 0.034 0.001 TYR E 235 PHE 0.011 0.001 PHE D 189 TRP 0.026 0.001 TRP F 117 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9118) covalent geometry : angle 0.52042 (12340) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.99473 ( 8) hydrogen bonds : bond 0.03218 ( 464) hydrogen bonds : angle 4.02397 ( 1309) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8848 (t) cc_final: 0.8605 (p) REVERT: A 211 ASP cc_start: 0.7575 (t70) cc_final: 0.7157 (t70) REVERT: E 43 LYS cc_start: 0.8027 (ptpt) cc_final: 0.6922 (ptmm) REVERT: E 76 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8172 (mptt) REVERT: E 160 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.7103 (mtp85) REVERT: E 183 GLN cc_start: 0.8193 (mt0) cc_final: 0.7886 (pt0) REVERT: E 186 GLN cc_start: 0.8497 (tt0) cc_final: 0.8151 (pt0) REVERT: F 110 TYR cc_start: 0.4104 (m-10) cc_final: 0.3758 (m-80) REVERT: F 172 LEU cc_start: 0.5989 (mm) cc_final: 0.5512 (mm) REVERT: F 235 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5087 (mt) outliers start: 23 outliers final: 15 residues processed: 138 average time/residue: 0.5072 time to fit residues: 75.1315 Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN E 39 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115988 restraints weight = 16545.794| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.49 r_work: 0.3213 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9122 Z= 0.118 Angle : 0.527 8.931 12348 Z= 0.273 Chirality : 0.041 0.201 1412 Planarity : 0.004 0.060 1544 Dihedral : 5.341 72.931 1249 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.76 % Allowed : 18.61 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1121 helix: 2.35 (0.25), residues: 391 sheet: 0.45 (0.31), residues: 275 loop : -0.45 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.034 0.001 TYR E 235 PHE 0.010 0.001 PHE D 189 TRP 0.025 0.001 TRP F 117 HIS 0.004 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9118) covalent geometry : angle 0.52697 (12340) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.80217 ( 8) hydrogen bonds : bond 0.03189 ( 464) hydrogen bonds : angle 4.00604 ( 1309) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8948 (t) cc_final: 0.8729 (p) REVERT: E 43 LYS cc_start: 0.8060 (ptpt) cc_final: 0.6980 (ptmm) REVERT: E 76 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8172 (mptt) REVERT: E 160 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7233 (mtp85) REVERT: E 183 GLN cc_start: 0.8285 (mt0) cc_final: 0.8023 (pt0) REVERT: E 186 GLN cc_start: 0.8632 (tt0) cc_final: 0.8249 (pt0) REVERT: F 110 TYR cc_start: 0.4366 (m-10) cc_final: 0.3978 (m-80) REVERT: F 172 LEU cc_start: 0.6138 (mm) cc_final: 0.5671 (mm) REVERT: F 235 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.5213 (mt) outliers start: 27 outliers final: 17 residues processed: 136 average time/residue: 0.4941 time to fit residues: 72.1193 Evaluate side-chains 135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115978 restraints weight = 21468.920| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.93 r_work: 0.3189 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9122 Z= 0.117 Angle : 0.530 10.167 12348 Z= 0.274 Chirality : 0.041 0.200 1412 Planarity : 0.004 0.060 1544 Dihedral : 5.321 71.379 1249 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 19.53 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1121 helix: 2.31 (0.25), residues: 391 sheet: 0.38 (0.31), residues: 276 loop : -0.45 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.034 0.001 TYR E 235 PHE 0.010 0.001 PHE D 189 TRP 0.039 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9118) covalent geometry : angle 0.52989 (12340) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.81702 ( 8) hydrogen bonds : bond 0.03190 ( 464) hydrogen bonds : angle 4.02871 ( 1309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3274.66 seconds wall clock time: 56 minutes 33.52 seconds (3393.52 seconds total)