Starting phenix.real_space_refine on Wed Aug 7 10:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/08_2024/8v24_42897_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/08_2024/8v24_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/08_2024/8v24_42897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/08_2024/8v24_42897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/08_2024/8v24_42897_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/08_2024/8v24_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 Residue "A GLU 270": "OE1" <-> "OE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 331": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 9.99, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.59 Conformation dependent library (CDL) restraints added in 2.3 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: 1.86 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: 7.01 Time building geometry restraints manager: 16.41 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: 74.05 - 86.10: 3 86.10 - 98.16: 3 98.16 - 110.21: 18646 110.21 - 122.26: 14057 122.26 - 134.31: 2850 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: 0.940 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: 0.320 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 69.070 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.130 ------------------------------------------------------------------------------- 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 10223 Z= 0.272 Angle : 0.630 11.426 13797 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.563 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: 0.4780 time to fit residues: 93.6886 Evaluate side-chains 132 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 10223 Z= 0.302 Angle : 0.560 9.168 13797 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 *********************** 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 fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7477 (mp) REVERT: B 112 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8032 (t) REVERT: B 200 TYR cc_start: 0.8609 (t80) cc_final: 0.7920 (t80) REVERT: D 9 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7843 (mtm110) outliers start: 17 outliers final: 9 residues processed: 152 average time/residue: 0.4073 time to fit residues: 87.9658 Evaluate side-chains 142 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 62 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10223 Z= 0.221 Angle : 0.479 8.850 13797 Z= 0.258 Chirality : 0.038 0.354 1532 Planarity : 0.005 0.138 1786 Dihedral : 10.336 126.474 1525 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 2.19 % Allowed : 20.99 % Favored : 76.81 % 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: 0.08 (0.25), residues: 1245 helix: 1.35 (0.22), residues: 646 sheet: -1.25 (0.40), residues: 167 loop : -1.35 (0.30), residues: 432 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 0.007 0.001 PHE D 258 TYR 0.008 0.001 TYR C 230 ARG 0.002 0.000 ARG C 342 *********************** 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 164 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7491 (mp) REVERT: A 339 MET cc_start: 0.8192 (tpt) cc_final: 0.7709 (tpt) REVERT: B 112 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8021 (t) REVERT: B 292 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7275 (mt-10) outliers start: 23 outliers final: 14 residues processed: 159 average time/residue: 0.4626 time to fit residues: 104.6754 Evaluate side-chains 143 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 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 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 111 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10223 Z= 0.344 Angle : 0.514 9.045 13797 Z= 0.281 Chirality : 0.040 0.357 1532 Planarity : 0.005 0.138 1786 Dihedral : 10.061 134.156 1525 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.55 % Favored : 92.29 % Rotamer: Outliers : 2.77 % Allowed : 21.09 % Favored : 76.15 % 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: -0.16 (0.24), residues: 1245 helix: 1.19 (0.21), residues: 647 sheet: -1.33 (0.40), residues: 167 loop : -1.55 (0.29), residues: 431 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 0.011 0.001 PHE B 50 TYR 0.012 0.001 TYR A 368 ARG 0.002 0.000 ARG C 342 *********************** 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 159 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.8194 (tpt) cc_final: 0.7736 (tpt) REVERT: B 112 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8058 (t) REVERT: B 142 ASP cc_start: 0.8352 (t0) cc_final: 0.7854 (t0) REVERT: C 261 GLN cc_start: 0.8518 (tt0) cc_final: 0.8294 (tt0) REVERT: D 9 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7796 (mtm110) outliers start: 29 outliers final: 18 residues processed: 151 average time/residue: 0.4697 time to fit residues: 101.3973 Evaluate side-chains 147 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 183 MET 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 380 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 ARG 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 99 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 107 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10223 Z= 0.313 Angle : 0.503 8.998 13797 Z= 0.274 Chirality : 0.040 0.356 1532 Planarity : 0.005 0.138 1786 Dihedral : 9.290 124.929 1525 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.43 % Favored : 93.41 % Rotamer: Outliers : 2.77 % Allowed : 20.99 % 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: -0.06 (0.25), residues: 1245 helix: 1.24 (0.21), residues: 646 sheet: -1.27 (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 0.022 0.001 PHE A 318 TYR 0.010 0.001 TYR A 368 ARG 0.003 0.000 ARG C 342 *********************** 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 155 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.563 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: 0.7416 (ttp) cc_final: 0.7160 (mtp) REVERT: A 339 MET cc_start: 0.8250 (tpt) cc_final: 0.7774 (tpt) REVERT: A 348 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7798 (ptmm) REVERT: B 112 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8056 (t) REVERT: D 9 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7827 (mtm110) outliers start: 29 outliers final: 20 residues processed: 151 average time/residue: 0.4610 time to fit residues: 99.0085 Evaluate side-chains 148 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 348 LYS 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 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 380 ILE Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 138 VAL 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 40 optimal weight: 0.9990 chunk 107 optimal weight: 0.0070 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 10223 Z= 0.153 Angle : 0.445 8.587 13797 Z= 0.240 Chirality : 0.038 0.355 1532 Planarity : 0.004 0.135 1786 Dihedral : 8.318 110.865 1525 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 1.62 % Allowed : 21.66 % Favored : 76.72 % 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: 0.21 (0.25), residues: 1245 helix: 1.53 (0.22), residues: 646 sheet: -1.16 (0.40), residues: 167 loop : -1.44 (0.30), residues: 432 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 0.014 0.001 PHE A 318 TYR 0.011 0.001 TYR C 230 ARG 0.003 0.000 ARG C 342 *********************** 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 fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.8112 (tpt) cc_final: 0.7654 (tpt) REVERT: B 112 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7981 (t) REVERT: B 295 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7459 (tt) outliers start: 17 outliers final: 13 residues processed: 145 average time/residue: 0.4391 time to fit residues: 92.2871 Evaluate side-chains 139 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER 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 115 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10223 Z= 0.281 Angle : 0.486 8.747 13797 Z= 0.265 Chirality : 0.039 0.359 1532 Planarity : 0.005 0.136 1786 Dihedral : 8.055 88.997 1525 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.57 % Rotamer: Outliers : 2.00 % Allowed : 22.14 % 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: 0.12 (0.25), residues: 1245 helix: 1.46 (0.21), residues: 646 sheet: -1.19 (0.40), residues: 167 loop : -1.50 (0.30), residues: 432 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 0.013 0.001 PHE A 318 TYR 0.011 0.001 TYR A 368 ARG 0.003 0.000 ARG C 342 *********************** 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 151 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.517 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: 0.7423 (ttp) cc_final: 0.7164 (mtp) REVERT: A 339 MET cc_start: 0.8154 (tpt) cc_final: 0.7709 (tpt) REVERT: B 295 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7491 (tt) outliers start: 21 outliers final: 17 residues processed: 149 average time/residue: 0.5112 time to fit residues: 109.1309 Evaluate side-chains 143 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 255 LEU 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 146 GLU Chi-restraints excluded: chain B residue 295 LEU 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 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 73 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 108 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10223 Z= 0.175 Angle : 0.452 8.584 13797 Z= 0.245 Chirality : 0.038 0.357 1532 Planarity : 0.004 0.135 1786 Dihedral : 7.623 89.111 1525 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 1.53 % Allowed : 22.33 % Favored : 76.15 % 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: 0.26 (0.25), residues: 1245 helix: 1.57 (0.21), residues: 646 sheet: -1.06 (0.41), residues: 165 loop : -1.47 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 268 HIS 0.006 0.001 HIS B 238 PHE 0.029 0.001 PHE A 318 TYR 0.009 0.001 TYR C 230 ARG 0.004 0.000 ARG C 342 *********************** 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 144 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.7362 (ttp) cc_final: 0.7097 (mtp) REVERT: A 339 MET cc_start: 0.8118 (tpt) cc_final: 0.7701 (tpt) REVERT: A 347 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6754 (tp30) REVERT: A 350 ARG cc_start: 0.8410 (mtt180) cc_final: 0.7714 (mtm110) REVERT: B 295 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7460 (tt) outliers start: 16 outliers final: 13 residues processed: 142 average time/residue: 0.4440 time to fit residues: 90.8314 Evaluate side-chains 139 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 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 146 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10223 Z= 0.194 Angle : 0.454 8.574 13797 Z= 0.246 Chirality : 0.038 0.359 1532 Planarity : 0.004 0.134 1786 Dihedral : 7.462 89.096 1525 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.94 % Favored : 93.90 % Rotamer: Outliers : 1.62 % Allowed : 22.33 % Favored : 76.05 % 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: 0.30 (0.25), residues: 1245 helix: 1.63 (0.21), residues: 646 sheet: -1.07 (0.40), residues: 166 loop : -1.49 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 268 HIS 0.008 0.001 HIS B 238 PHE 0.023 0.001 PHE A 318 TYR 0.008 0.001 TYR A 304 ARG 0.004 0.000 ARG C 342 *********************** 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 150 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.912 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: 0.7377 (ttp) cc_final: 0.7114 (mtp) REVERT: A 347 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: A 350 ARG cc_start: 0.8380 (mtt180) cc_final: 0.7678 (mtm110) REVERT: B 184 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.7135 (mtm-85) REVERT: D 292 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5687 (pt0) outliers start: 17 outliers final: 14 residues processed: 148 average time/residue: 0.4407 time to fit residues: 94.7398 Evaluate side-chains 143 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 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 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 292 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10223 Z= 0.341 Angle : 0.521 8.995 13797 Z= 0.284 Chirality : 0.041 0.361 1532 Planarity : 0.005 0.136 1786 Dihedral : 7.641 81.769 1525 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.61 % Rotamer: Outliers : 1.81 % Allowed : 22.23 % Favored : 75.95 % 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: 0.05 (0.25), residues: 1245 helix: 1.40 (0.21), residues: 646 sheet: -1.12 (0.40), residues: 165 loop : -1.58 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 144 HIS 0.010 0.001 HIS B 238 PHE 0.038 0.002 PHE A 318 TYR 0.014 0.001 TYR A 368 ARG 0.003 0.000 ARG C 342 ********************** 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 152 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.443 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: 0.7438 (ttp) cc_final: 0.7180 (mtp) REVERT: D 292 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5804 (pt0) outliers start: 19 outliers final: 17 residues processed: 150 average time/residue: 0.4409 time to fit residues: 95.8943 Evaluate side-chains 150 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 255 LEU 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 183 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 Chi-restraints excluded: chain D residue 292 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.094122 restraints weight = 34798.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.098989 restraints weight = 17198.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.102158 restraints weight = 11145.682| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10223 Z= 0.201 Angle : 0.465 8.873 13797 Z= 0.251 Chirality : 0.038 0.358 1532 Planarity : 0.004 0.136 1786 Dihedral : 7.455 83.932 1525 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.62 % Rotamer: Outliers : 1.53 % Allowed : 22.81 % 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: 0.23 (0.25), residues: 1245 helix: 1.55 (0.21), residues: 646 sheet: -1.06 (0.40), residues: 165 loop : -1.50 (0.29), residues: 434 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 0.010 0.001 PHE A 318 TYR 0.008 0.001 TYR C 230 ARG 0.003 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4010.50 seconds wall clock time: 77 minutes 19.25 seconds (4639.25 seconds total)