Starting phenix.real_space_refine on Tue May 20 05:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v24_42897/05_2025/8v24_42897_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v24_42897/05_2025/8v24_42897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v24_42897/05_2025/8v24_42897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v24_42897/05_2025/8v24_42897.map" model { file = "/net/cci-nas-00/data/ceres_data/8v24_42897/05_2025/8v24_42897_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v24_42897/05_2025/8v24_42897_trim.cif" } resolution = 3.6 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= 0.002 sd= 0.064 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4 5.49 5 S 68 5.16 5 C 6310 2.51 5 N 1764 2.21 5 O 1901 1.98 5 H 9601 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19652 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5165 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 4, 'TRANS': 322} Chain: "B" Number of atoms: 4595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4595 Classifications: {'peptide': 301} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "C" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 5167 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 318} Chain: "D" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4609 Classifications: {'peptide': 302} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, '24G': 1, 'ACT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, '24G': 1, 'ACT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4669 SG CYS A 357 55.527 54.008 44.022 1.00 66.24 S ATOM 4719 SG CYS A 360 52.507 56.006 45.208 1.00 63.26 S ATOM 4897 SG CYS A 371 53.294 55.609 41.513 1.00 60.78 S ATOM 4933 SG CYS A 374 55.482 57.829 43.701 1.00 62.49 S ATOM 14412 SG CYS C 357 34.062 52.227 59.516 1.00 59.78 S ATOM 14462 SG CYS C 360 37.401 54.248 59.253 1.00 58.85 S ATOM 14640 SG CYS C 371 36.302 52.894 62.486 1.00 56.68 S ATOM 14676 SG CYS C 374 34.343 55.749 60.926 1.00 58.27 S Time building chain proxies: 8.91, per 1000 atoms: 0.45 Number of scatterers: 19652 At special positions: 0 Unit cell: (90.78, 108.936, 111.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 68 16.00 P 4 15.00 O 1901 8.00 N 1764 7.00 C 6310 6.00 H 9601 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.98 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 371 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 357 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 360 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 374 " pdb=" ZN B 403 " pdb="ZN ZN B 403 " - pdb=" NE2 HIS B 238 " pdb="ZN ZN B 403 " - pdb=" NE2 HIS B 79 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 371 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 374 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 360 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 357 " pdb=" ZN D 403 " pdb="ZN ZN D 403 " - pdb=" NE2 HIS D 238 " pdb="ZN ZN D 403 " - pdb=" NE2 HIS D 79 " Number of angles added : 12 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 53.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 102 through 121 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 139 through 154 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 176 through 192 Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.755A pdb=" N SER A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.818A pdb=" N ARG A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.863A pdb=" N LEU A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N MET A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.625A pdb=" N GLU A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.620A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 removed outlier: 4.268A pdb=" N LYS A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 341 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 197 through 204 removed outlier: 3.609A pdb=" N SER B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.884A pdb=" N ALA B 215 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.548A pdb=" N ARG B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.606A pdb=" N ASN B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 269 " --> pdb=" O HIS B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.667A pdb=" N HIS C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 68 through 72' Processing helix chain 'C' and resid 74 through 83 Processing helix chain 'C' and resid 84 through 98 removed outlier: 3.592A pdb=" N ARG C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 121 Processing helix chain 'C' and resid 122 through 131 removed outlier: 3.557A pdb=" N ASP C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 154 Processing helix chain 'C' and resid 156 through 170 removed outlier: 3.502A pdb=" N ALA C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP C 162 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 175 through 191 Processing helix chain 'C' and resid 195 through 210 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.809A pdb=" N SER C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 238 Processing helix chain 'C' and resid 238 through 244 removed outlier: 4.453A pdb=" N SER C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.995A pdb=" N THR C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 281 through 312 removed outlier: 7.723A pdb=" N SER C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N GLU C 299 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 328 removed outlier: 3.602A pdb=" N GLU C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 352 removed outlier: 3.761A pdb=" N GLU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 211 through 215 removed outlier: 4.035A pdb=" N ALA D 215 " --> pdb=" O PHE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.603A pdb=" N ARG D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 264 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 16 removed outlier: 3.605A pdb=" N VAL B 48 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.380A pdb=" N VAL B 57 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 67 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 59 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 136 through 139 removed outlier: 6.355A pdb=" N SER B 154 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA B 260 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP B 156 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 173 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 136 through 139 removed outlier: 7.901A pdb=" N ALA B 257 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AA7, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.663A pdb=" N ARG D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.552A pdb=" N VAL D 57 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL D 67 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D 59 " --> pdb=" O CYS D 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 136 through 139 removed outlier: 6.704A pdb=" N SER D 154 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA D 260 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP D 156 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 136 through 139 removed outlier: 6.366A pdb=" N VAL D 130 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ALA D 257 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ILE D 132 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N THR D 259 " --> pdb=" O ILE D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 193 through 194 removed outlier: 6.574A pdb=" N GLY D 193 " --> pdb=" O VAL D 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 535 hydrogen bonds defined for protein. 1539 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: 6.59 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9577 1.03 - 1.23: 34 1.23 - 1.42: 4243 1.42 - 1.61: 5858 1.61 - 1.81: 112 Bond restraints: 19824 Sorted by residual: bond pdb=" N MET D 1 " pdb=" H3 MET D 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N MET B 1 " pdb=" H2 MET B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N MET B 1 " pdb=" H3 MET B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N MET D 1 " pdb=" H2 MET D 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ASN B 45 " pdb=" CA ASN B 45 " ideal model delta sigma weight residual 1.462 1.493 -0.032 9.50e-03 1.11e+04 1.13e+01 ... (remaining 19819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.99: 35544 6.99 - 13.98: 12 13.98 - 20.97: 0 20.97 - 27.96: 0 27.96 - 34.95: 3 Bond angle restraints: 35559 Sorted by residual: angle pdb=" C ASP A 343 " pdb=" CA ASP A 343 " pdb=" HA ASP A 343 " ideal model delta sigma weight residual 109.00 74.05 34.95 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N ASP A 343 " pdb=" CA ASP A 343 " pdb=" HA ASP A 343 " ideal model delta sigma weight residual 110.00 75.67 34.33 3.00e+00 1.11e-01 1.31e+02 angle pdb=" CB ASP A 343 " pdb=" CA ASP A 343 " pdb=" HA ASP A 343 " ideal model delta sigma weight residual 109.00 75.31 33.69 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C PRO D 46 " pdb=" CA PRO D 46 " pdb=" CB PRO D 46 " ideal model delta sigma weight residual 110.92 122.35 -11.43 1.22e+00 6.72e-01 8.77e+01 angle pdb=" N PRO D 46 " pdb=" CA PRO D 46 " pdb=" CB PRO D 46 " ideal model delta sigma weight residual 103.08 96.05 7.03 9.70e-01 1.06e+00 5.25e+01 ... (remaining 35554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 8888 33.80 - 67.61: 420 67.61 - 101.41: 54 101.41 - 135.21: 11 135.21 - 169.02: 5 Dihedral angle restraints: 9378 sinusoidal: 5164 harmonic: 4214 Sorted by residual: dihedral pdb=" CA ARG A 342 " pdb=" C ARG A 342 " pdb=" N ASP A 343 " pdb=" CA ASP A 343 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C1 24G B 401 " pdb=" C6 24G B 401 " pdb=" C7 24G B 401 " pdb=" O8 24G B 401 " ideal model delta sinusoidal sigma weight residual -175.79 -6.77 -169.02 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O5 24G B 401 " pdb=" C6 24G B 401 " pdb=" C7 24G B 401 " pdb=" O8 24G B 401 " ideal model delta sinusoidal sigma weight residual 63.21 -129.86 -166.93 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1422 0.075 - 0.149: 104 0.149 - 0.224: 5 0.224 - 0.299: 0 0.299 - 0.373: 1 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA ASP A 343 " pdb=" N ASP A 343 " pdb=" C ASP A 343 " pdb=" CB ASP A 343 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA PHE D 50 " pdb=" N PHE D 50 " pdb=" C PHE D 50 " pdb=" CB PHE D 50 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE B 101 " pdb=" N ILE B 101 " pdb=" C ILE B 101 " pdb=" CB ILE B 101 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 1529 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 45 " 0.067 2.00e-02 2.50e+03 4.39e-01 2.90e+03 pdb=" CG ASN D 45 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN D 45 " -0.074 2.00e-02 2.50e+03 pdb=" ND2 ASN D 45 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 45 " -0.760 2.00e-02 2.50e+03 pdb="HD22 ASN D 45 " 0.756 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 45 " -0.101 2.00e-02 2.50e+03 4.36e-01 2.85e+03 pdb=" CG ASN B 45 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN B 45 " 0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN B 45 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 45 " 0.746 2.00e-02 2.50e+03 pdb="HD22 ASN B 45 " -0.750 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 46 " 0.027 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C PRO D 46 " -0.090 2.00e-02 2.50e+03 pdb=" O PRO D 46 " 0.032 2.00e-02 2.50e+03 pdb=" N PRO D 47 " 0.031 2.00e-02 2.50e+03 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1327 2.20 - 2.80: 40119 2.80 - 3.40: 54196 3.40 - 4.00: 70651 4.00 - 4.60: 110919 Nonbonded interactions: 277212 Sorted by model distance: nonbonded pdb=" H ASP A 343 " pdb=" HA ASP A 343 " model vdw 1.599 1.816 nonbonded pdb=" HH TYR D 39 " pdb=" OD1 ASN D 81 " model vdw 1.632 2.450 nonbonded pdb=" HE ARG C 80 " pdb=" OD1 ASP C 116 " model vdw 1.632 2.450 nonbonded pdb=" H ARG B 190 " pdb=" OE2 GLU B 234 " model vdw 1.633 2.450 nonbonded pdb=" OD1 ASP D 90 " pdb=" HZ2 LYS D 127 " model vdw 1.635 2.450 ... (remaining 277207 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 67 through 389 or resid 401)) selection = (chain 'C' and ((resid 67 and (name N or name CA or name C or name O )) or (resi \ d 68 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2)) or resid 69 through 346 or (resid 347 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 348 th \ rough 386 or (resid 387 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or (resid 388 and (name N or name CA or name \ C or name O )) or (resid 389 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or resid 401)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 286 or (resid 287 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 288 through 301 or resid 401 through 403)) } 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 group one per residue 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.330 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.650 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 : 0.004 0.104 10235 Z= 0.209 Angle : 0.633 11.426 13809 Z= 0.365 Chirality : 0.040 0.373 1532 Planarity : 0.004 0.099 1786 Dihedral : 20.509 169.017 3930 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % Rotamer: Outliers : 0.48 % Allowed : 22.33 % Favored : 77.19 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1245 helix: 1.43 (0.22), residues: 632 sheet: -1.62 (0.38), residues: 172 loop : -1.25 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 268 HIS 0.006 0.001 HIS B 238 PHE 0.042 0.001 PHE D 50 TYR 0.011 0.001 TYR C 230 ARG 0.002 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.13179 ( 515) hydrogen bonds : angle 5.27168 ( 1539) metal coordination : bond 0.00537 ( 12) metal coordination : angle 2.26449 ( 12) covalent geometry : bond 0.00414 (10223) covalent geometry : angle 0.63019 (13797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.7947 (mtp) cc_final: 0.7570 (mtt) outliers start: 5 outliers final: 2 residues processed: 139 average time/residue: 0.4843 time to fit residues: 94.9771 Evaluate side-chains 132 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 236 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.124280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.092505 restraints weight = 35145.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.097268 restraints weight = 17448.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.100293 restraints weight = 11368.542| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10235 Z= 0.199 Angle : 0.565 9.168 13809 Z= 0.293 Chirality : 0.041 0.354 1532 Planarity : 0.005 0.142 1786 Dihedral : 14.266 169.453 1526 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.99 % Favored : 92.85 % Rotamer: Outliers : 1.62 % Allowed : 21.37 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.10 (0.25), residues: 1245 helix: 1.19 (0.21), residues: 645 sheet: -1.43 (0.39), residues: 167 loop : -1.36 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.010 0.001 HIS B 238 PHE 0.012 0.001 PHE D 50 TYR 0.010 0.001 TYR A 368 ARG 0.003 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 515) hydrogen bonds : angle 4.27374 ( 1539) metal coordination : bond 0.00938 ( 12) metal coordination : angle 2.72531 ( 12) covalent geometry : bond 0.00464 (10223) covalent geometry : angle 0.55974 (13797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 112 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8161 (t) REVERT: B 200 TYR cc_start: 0.8687 (t80) cc_final: 0.8000 (t80) REVERT: D 9 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7830 (mtm110) outliers start: 17 outliers final: 9 residues processed: 152 average time/residue: 0.4761 time to fit residues: 102.1491 Evaluate side-chains 142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 175 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.126057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.094421 restraints weight = 34732.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.099348 restraints weight = 17031.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.102542 restraints weight = 10960.435| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10235 Z= 0.120 Angle : 0.467 8.704 13809 Z= 0.248 Chirality : 0.038 0.355 1532 Planarity : 0.005 0.138 1786 Dihedral : 10.010 120.680 1525 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.62 % Rotamer: Outliers : 2.00 % Allowed : 21.09 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1245 helix: 1.45 (0.22), residues: 646 sheet: -1.23 (0.40), residues: 167 loop : -1.31 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.006 0.001 HIS B 238 PHE 0.007 0.001 PHE C 271 TYR 0.008 0.001 TYR C 230 ARG 0.003 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 515) hydrogen bonds : angle 3.91660 ( 1539) metal coordination : bond 0.00552 ( 12) metal coordination : angle 2.19788 ( 12) covalent geometry : bond 0.00282 (10223) covalent geometry : angle 0.46245 (13797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.8156 (tpt) cc_final: 0.7717 (tpt) REVERT: B 112 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8106 (t) REVERT: B 292 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7292 (mt-10) outliers start: 21 outliers final: 14 residues processed: 154 average time/residue: 0.4613 time to fit residues: 101.5994 Evaluate side-chains 141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.123208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.092164 restraints weight = 35341.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.096646 restraints weight = 18363.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.099506 restraints weight = 12231.645| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10235 Z= 0.225 Angle : 0.524 8.943 13809 Z= 0.283 Chirality : 0.040 0.357 1532 Planarity : 0.005 0.138 1786 Dihedral : 9.835 128.861 1525 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.61 % Rotamer: Outliers : 2.67 % Allowed : 20.99 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 (0.25), residues: 1245 helix: 1.23 (0.21), residues: 647 sheet: -1.28 (0.40), residues: 167 loop : -1.52 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 268 HIS 0.011 0.001 HIS B 238 PHE 0.011 0.001 PHE B 50 TYR 0.012 0.001 TYR A 368 ARG 0.003 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 515) hydrogen bonds : angle 4.00474 ( 1539) metal coordination : bond 0.01085 ( 12) metal coordination : angle 3.01447 ( 12) covalent geometry : bond 0.00533 (10223) covalent geometry : angle 0.51631 (13797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.8220 (tpt) cc_final: 0.7778 (tpt) REVERT: B 112 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8201 (t) outliers start: 28 outliers final: 18 residues processed: 151 average time/residue: 0.4495 time to fit residues: 96.4036 Evaluate side-chains 144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.124434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.092508 restraints weight = 34985.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.097381 restraints weight = 17334.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.100484 restraints weight = 11257.770| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10235 Z= 0.181 Angle : 0.494 8.868 13809 Z= 0.266 Chirality : 0.039 0.355 1532 Planarity : 0.005 0.137 1786 Dihedral : 8.907 117.639 1525 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.73 % Rotamer: Outliers : 2.00 % Allowed : 21.76 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 (0.25), residues: 1245 helix: 1.30 (0.21), residues: 647 sheet: -1.22 (0.40), residues: 167 loop : -1.49 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.008 0.001 HIS B 238 PHE 0.020 0.001 PHE A 318 TYR 0.011 0.001 TYR C 230 ARG 0.003 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 515) hydrogen bonds : angle 3.89577 ( 1539) metal coordination : bond 0.00871 ( 12) metal coordination : angle 2.72278 ( 12) covalent geometry : bond 0.00427 (10223) covalent geometry : angle 0.48748 (13797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.8224 (tpt) cc_final: 0.7774 (tpt) REVERT: B 112 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8193 (t) outliers start: 21 outliers final: 16 residues processed: 143 average time/residue: 0.4457 time to fit residues: 91.6480 Evaluate side-chains 139 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 271 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.126311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.094475 restraints weight = 34812.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.099450 restraints weight = 17050.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102604 restraints weight = 10993.232| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10235 Z= 0.111 Angle : 0.454 8.533 13809 Z= 0.243 Chirality : 0.038 0.355 1532 Planarity : 0.004 0.135 1786 Dihedral : 8.114 97.012 1525 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.18 % Favored : 93.65 % Rotamer: Outliers : 1.81 % Allowed : 21.95 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1245 helix: 1.51 (0.22), residues: 647 sheet: -1.17 (0.40), residues: 167 loop : -1.39 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 268 HIS 0.006 0.001 HIS B 238 PHE 0.024 0.001 PHE A 318 TYR 0.008 0.001 TYR C 230 ARG 0.004 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 515) hydrogen bonds : angle 3.72949 ( 1539) metal coordination : bond 0.00512 ( 12) metal coordination : angle 2.15367 ( 12) covalent geometry : bond 0.00263 (10223) covalent geometry : angle 0.44989 (13797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.8175 (tpt) cc_final: 0.7747 (tpt) REVERT: A 347 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6758 (tp30) REVERT: A 350 ARG cc_start: 0.8339 (mtt180) cc_final: 0.7710 (mtm110) REVERT: B 112 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8149 (t) outliers start: 19 outliers final: 14 residues processed: 144 average time/residue: 0.4454 time to fit residues: 92.2863 Evaluate side-chains 141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN C 308 GLN ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.125285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.093600 restraints weight = 34910.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.098438 restraints weight = 17249.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.101597 restraints weight = 11181.475| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10235 Z= 0.156 Angle : 0.474 8.622 13809 Z= 0.255 Chirality : 0.039 0.358 1532 Planarity : 0.004 0.135 1786 Dihedral : 7.657 87.994 1525 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.18 % Favored : 93.65 % Rotamer: Outliers : 1.72 % Allowed : 22.61 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1245 helix: 1.53 (0.21), residues: 646 sheet: -1.18 (0.40), residues: 167 loop : -1.46 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.008 0.001 HIS B 238 PHE 0.009 0.001 PHE A 318 TYR 0.009 0.001 TYR A 368 ARG 0.003 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 515) hydrogen bonds : angle 3.72476 ( 1539) metal coordination : bond 0.00746 ( 12) metal coordination : angle 2.44003 ( 12) covalent geometry : bond 0.00371 (10223) covalent geometry : angle 0.46822 (13797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.7396 (ttp) cc_final: 0.7145 (mtp) REVERT: A 339 MET cc_start: 0.8140 (tpt) cc_final: 0.7710 (tpt) outliers start: 18 outliers final: 16 residues processed: 146 average time/residue: 0.4691 time to fit residues: 99.3742 Evaluate side-chains 143 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 271 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN C 308 GLN ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.093894 restraints weight = 35029.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.098825 restraints weight = 17154.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.102053 restraints weight = 11066.032| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10235 Z= 0.142 Angle : 0.468 8.614 13809 Z= 0.251 Chirality : 0.038 0.355 1532 Planarity : 0.004 0.135 1786 Dihedral : 7.563 89.454 1525 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.02 % Favored : 93.82 % Rotamer: Outliers : 1.72 % Allowed : 22.61 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1245 helix: 1.56 (0.21), residues: 646 sheet: -1.10 (0.40), residues: 165 loop : -1.45 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.007 0.001 HIS B 238 PHE 0.029 0.001 PHE A 318 TYR 0.008 0.001 TYR A 304 ARG 0.004 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 515) hydrogen bonds : angle 3.67288 ( 1539) metal coordination : bond 0.00671 ( 12) metal coordination : angle 2.32040 ( 12) covalent geometry : bond 0.00338 (10223) covalent geometry : angle 0.46323 (13797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.7393 (ttp) cc_final: 0.7135 (mtp) REVERT: A 339 MET cc_start: 0.8143 (tpt) cc_final: 0.7731 (tpt) REVERT: A 350 ARG cc_start: 0.8362 (mtt180) cc_final: 0.7694 (mtm110) REVERT: B 184 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7217 (mtm-85) outliers start: 18 outliers final: 15 residues processed: 143 average time/residue: 0.4390 time to fit residues: 90.5492 Evaluate side-chains 141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 271 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN C 261 GLN ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.124919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.092890 restraints weight = 34877.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.097703 restraints weight = 17283.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.100784 restraints weight = 11246.251| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10235 Z= 0.181 Angle : 0.494 8.881 13809 Z= 0.266 Chirality : 0.039 0.359 1532 Planarity : 0.005 0.136 1786 Dihedral : 7.557 85.328 1525 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.59 % Favored : 93.25 % Rotamer: Outliers : 1.81 % Allowed : 22.33 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1245 helix: 1.49 (0.21), residues: 646 sheet: -1.11 (0.40), residues: 165 loop : -1.51 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 268 HIS 0.009 0.001 HIS B 238 PHE 0.027 0.001 PHE A 318 TYR 0.014 0.001 TYR C 230 ARG 0.004 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 515) hydrogen bonds : angle 3.74258 ( 1539) metal coordination : bond 0.00868 ( 12) metal coordination : angle 2.62993 ( 12) covalent geometry : bond 0.00431 (10223) covalent geometry : angle 0.48809 (13797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.7395 (ttp) cc_final: 0.7141 (mtp) REVERT: A 339 MET cc_start: 0.8139 (tpt) cc_final: 0.7747 (tpt) REVERT: A 350 ARG cc_start: 0.8395 (mtt180) cc_final: 0.7714 (mtm110) REVERT: B 112 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8188 (t) outliers start: 19 outliers final: 16 residues processed: 148 average time/residue: 0.4669 time to fit residues: 99.9985 Evaluate side-chains 148 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.127963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.095998 restraints weight = 34778.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.100955 restraints weight = 17060.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.104220 restraints weight = 11021.994| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 10235 Z= 0.101 Angle : 0.448 8.673 13809 Z= 0.240 Chirality : 0.038 0.357 1532 Planarity : 0.004 0.135 1786 Dihedral : 7.352 88.323 1525 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.62 % Rotamer: Outliers : 1.05 % Allowed : 23.09 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1245 helix: 1.66 (0.22), residues: 649 sheet: -1.01 (0.40), residues: 165 loop : -1.40 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 268 HIS 0.005 0.001 HIS B 238 PHE 0.016 0.001 PHE A 318 TYR 0.013 0.001 TYR C 230 ARG 0.004 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.02812 ( 515) hydrogen bonds : angle 3.56521 ( 1539) metal coordination : bond 0.00448 ( 12) metal coordination : angle 2.02457 ( 12) covalent geometry : bond 0.00242 (10223) covalent geometry : angle 0.44429 (13797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.7382 (ttp) cc_final: 0.7118 (mtp) REVERT: A 339 MET cc_start: 0.8080 (tpt) cc_final: 0.7730 (tpt) REVERT: A 350 ARG cc_start: 0.8357 (mtt180) cc_final: 0.7670 (mtm110) REVERT: B 184 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7299 (mtm-85) outliers start: 11 outliers final: 10 residues processed: 143 average time/residue: 0.4520 time to fit residues: 92.9871 Evaluate side-chains 139 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.093138 restraints weight = 35200.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.098010 restraints weight = 17397.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.101075 restraints weight = 11266.763| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.004 0.076 10235 Z= 0.183 Angle : 0.498 8.932 13809 Z= 0.268 Chirality : 0.040 0.362 1532 Planarity : 0.005 0.136 1786 Dihedral : 7.467 83.368 1524 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.51 % Favored : 93.33 % Rotamer: Outliers : 1.24 % Allowed : 23.09 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1245 helix: 1.53 (0.21), residues: 649 sheet: -1.07 (0.40), residues: 165 loop : -1.45 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 144 HIS 0.009 0.001 HIS B 238 PHE 0.016 0.001 PHE A 318 TYR 0.013 0.001 TYR C 230 ARG 0.003 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 515) hydrogen bonds : angle 3.70196 ( 1539) metal coordination : bond 0.00855 ( 12) metal coordination : angle 2.61589 ( 12) covalent geometry : bond 0.00436 (10223) covalent geometry : angle 0.49205 (13797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5353.26 seconds wall clock time: 93 minutes 10.51 seconds (5590.51 seconds total)