Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 19:38:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk2_23884/08_2023/7mk2_23884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk2_23884/08_2023/7mk2_23884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk2_23884/08_2023/7mk2_23884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk2_23884/08_2023/7mk2_23884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk2_23884/08_2023/7mk2_23884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk2_23884/08_2023/7mk2_23884.pdb" } resolution = 3.8 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= -0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 34 5.16 5 C 3390 2.51 5 N 914 2.21 5 O 993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 225": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 5333 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2675 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2656 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 57 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 832 SG CYS A 150 111.033 43.802 42.621 1.00 46.19 S ATOM 868 SG CYS A 155 110.325 45.039 46.143 1.00 47.27 S ATOM 902 SG CYS A 160 108.157 46.307 43.301 1.00 39.74 S ATOM 3503 SG CYS B 150 37.143 45.391 42.094 1.00 40.69 S ATOM 3535 SG CYS B 155 37.704 44.225 45.629 1.00 39.08 S ATOM 3569 SG CYS B 160 39.926 42.836 42.897 1.00 40.43 S Time building chain proxies: 3.25, per 1000 atoms: 0.61 Number of scatterers: 5333 At special positions: 0 Unit cell: (149.538, 92.2383, 62.8897, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 34 16.00 O 993 8.00 N 914 7.00 C 3390 6.00 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: 2.01 Conformation dependent library (CDL) restraints added in 786.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 157 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 150 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 160 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 155 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" ND1 HIS B 157 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 150 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 155 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 160 " Number of angles added : 6 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 67.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 40 through 59 removed outlier: 3.649A pdb=" N SER A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.613A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 160 through 178 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.374A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 230 removed outlier: 3.934A pdb=" N ARG A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.614A pdb=" N LEU A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 4.710A pdb=" N GLU A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.831A pdb=" N SER A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 270 " --> pdb=" O HIS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.126A pdb=" N ALA A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.827A pdb=" N LYS A 316 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 340 removed outlier: 3.903A pdb=" N LYS A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.510A pdb=" N ILE A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.567A pdb=" N CYS A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 59 removed outlier: 3.719A pdb=" N ALA B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 87 removed outlier: 3.711A pdb=" N LEU B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 101 removed outlier: 3.515A pdb=" N LYS B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 160 through 178 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.707A pdb=" N VAL B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 229 removed outlier: 3.767A pdb=" N LYS B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.705A pdb=" N SER B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.837A pdb=" N ARG B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.954A pdb=" N ASN B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.546A pdb=" N VAL B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.502A pdb=" N THR B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.500A pdb=" N LEU B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 398 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 removed outlier: 6.749A pdb=" N LYS B 68 " --> pdb=" O LEU B 112 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1759 1.34 - 1.46: 848 1.46 - 1.57: 2752 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 5405 Sorted by residual: bond pdb=" C VAL A 260 " pdb=" N PRO A 261 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.22e+00 bond pdb=" CG1 ILE A 183 " pdb=" CD1 ILE A 183 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CG1 ILE B 183 " pdb=" CD1 ILE B 183 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.82e+00 bond pdb=" CB MET A 367 " pdb=" CG MET A 367 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB CYS A 223 " pdb=" SG CYS A 223 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.13e+00 ... (remaining 5400 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.26: 112 106.26 - 112.55: 2972 112.55 - 118.84: 1477 118.84 - 125.12: 2717 125.12 - 131.41: 43 Bond angle restraints: 7321 Sorted by residual: angle pdb=" N VAL A 158 " pdb=" CA VAL A 158 " pdb=" C VAL A 158 " ideal model delta sigma weight residual 113.53 110.41 3.12 9.80e-01 1.04e+00 1.01e+01 angle pdb=" C SER B 276 " pdb=" N ASP B 277 " pdb=" CA ASP B 277 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.61e+00 angle pdb=" C GLU B 149 " pdb=" N CYS B 150 " pdb=" CA CYS B 150 " ideal model delta sigma weight residual 121.54 115.97 5.57 1.91e+00 2.74e-01 8.49e+00 angle pdb=" C VAL B 164 " pdb=" N ASP B 165 " pdb=" CA ASP B 165 " ideal model delta sigma weight residual 121.14 116.30 4.84 1.75e+00 3.27e-01 7.64e+00 angle pdb=" N VAL B 194 " pdb=" CA VAL B 194 " pdb=" C VAL B 194 " ideal model delta sigma weight residual 109.34 114.40 -5.06 2.08e+00 2.31e-01 5.92e+00 ... (remaining 7316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 2984 16.99 - 33.98: 294 33.98 - 50.98: 61 50.98 - 67.97: 9 67.97 - 84.96: 3 Dihedral angle restraints: 3351 sinusoidal: 1255 harmonic: 2096 Sorted by residual: dihedral pdb=" CA LYS B 119 " pdb=" C LYS B 119 " pdb=" N ASP B 120 " pdb=" CA ASP B 120 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CG ARG B 87 " pdb=" CD ARG B 87 " pdb=" NE ARG B 87 " pdb=" CZ ARG B 87 " ideal model delta sinusoidal sigma weight residual 180.00 136.94 43.06 2 1.50e+01 4.44e-03 9.95e+00 dihedral pdb=" CA GLU B 149 " pdb=" C GLU B 149 " pdb=" N CYS B 150 " pdb=" CA CYS B 150 " ideal model delta harmonic sigma weight residual -180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.87e+00 ... (remaining 3348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 561 0.036 - 0.071: 258 0.071 - 0.107: 62 0.107 - 0.143: 19 0.143 - 0.178: 2 Chirality restraints: 902 Sorted by residual: chirality pdb=" CA MET B 367 " pdb=" N MET B 367 " pdb=" C MET B 367 " pdb=" CB MET B 367 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ASP B 277 " pdb=" N ASP B 277 " pdb=" C ASP B 277 " pdb=" CB ASP B 277 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA ASP B 165 " pdb=" N ASP B 165 " pdb=" C ASP B 165 " pdb=" CB ASP B 165 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 899 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 141 " -0.027 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 142 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 261 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 59 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO B 60 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " -0.021 5.00e-02 4.00e+02 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 954 2.76 - 3.30: 5420 3.30 - 3.83: 8140 3.83 - 4.37: 9041 4.37 - 4.90: 15462 Nonbonded interactions: 39017 Sorted by model distance: nonbonded pdb=" O VAL B 303 " pdb=" NH1 ARG B 339 " model vdw 2.228 2.520 nonbonded pdb=" OD1 ASP B 152 " pdb=" N GLU B 153 " model vdw 2.271 2.520 nonbonded pdb=" O ASN B 307 " pdb=" OG1 THR B 310 " model vdw 2.273 2.440 nonbonded pdb=" O SER B 138 " pdb=" OG SER B 138 " model vdw 2.275 2.440 nonbonded pdb=" NH2 ARG B 325 " pdb=" OE2 GLU B 357 " model vdw 2.303 2.520 ... (remaining 39012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 144 or (resid 145 and (name N or name CA or nam \ e C or name O or name CB )) or resid 146 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 through 258 or (resid 2 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 261 or (resid 262 through 264 and (name N or name CA or name C or name O or nam \ e CB )) or resid 265 through 285 or (resid 286 and (name N or name CA or name C \ or name O or name CB )) or resid 287 through 350 or (resid 351 and (name N or na \ me CA or name C or name O or name CB )) or resid 352 through 389 or (resid 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 through 395 \ or (resid 396 and (name N or name CA or name C or name O or name CB )) or resid \ 397 or (resid 398 through 402 and (name N or name CA or name C or name O or nam \ e CB )) or resid 701)) selection = (chain 'B' and (resid 40 through 243 or (resid 244 and (name N or name CA or nam \ e C or name O or name CB )) or resid 245 through 286 or (resid 287 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 288 through 340 \ or (resid 341 and (name N or name CA or name C or name O or name CB )) or resid \ 342 through 399 or (resid 400 through 402 and (name N or name CA or name C or na \ me O or name CB )) or resid 701)) } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.820 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.290 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 0.054 5405 Z= 0.289 Angle : 0.692 7.876 7321 Z= 0.381 Chirality : 0.044 0.178 902 Planarity : 0.004 0.042 924 Dihedral : 14.228 84.962 1975 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 0.00 % 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: -1.60 (0.32), residues: 700 helix: -0.28 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -2.22 (0.36), residues: 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.626 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1433 time to fit residues: 24.1646 Evaluate side-chains 97 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 5405 Z= 0.246 Angle : 0.666 7.983 7321 Z= 0.343 Chirality : 0.042 0.171 902 Planarity : 0.004 0.044 924 Dihedral : 5.015 22.188 750 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 2.09 % 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: -1.53 (0.31), residues: 700 helix: -0.26 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -2.31 (0.36), residues: 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.627 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 110 average time/residue: 0.1328 time to fit residues: 20.2689 Evaluate side-chains 110 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0512 time to fit residues: 1.8108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.0370 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 43 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5405 Z= 0.160 Angle : 0.569 7.192 7321 Z= 0.295 Chirality : 0.040 0.163 902 Planarity : 0.003 0.040 924 Dihedral : 4.635 24.391 750 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.32), residues: 700 helix: -0.06 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -2.14 (0.36), residues: 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.622 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 111 average time/residue: 0.1276 time to fit residues: 20.0243 Evaluate side-chains 103 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0483 time to fit residues: 0.9717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 63 optimal weight: 0.0040 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.3370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5405 Z= 0.176 Angle : 0.571 7.325 7321 Z= 0.290 Chirality : 0.040 0.150 902 Planarity : 0.003 0.039 924 Dihedral : 4.442 23.400 750 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 2.44 % 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: -1.07 (0.32), residues: 700 helix: 0.07 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -2.08 (0.36), residues: 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.617 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 116 average time/residue: 0.1213 time to fit residues: 20.0533 Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0534 time to fit residues: 1.5708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.0060 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 5405 Z= 0.223 Angle : 0.618 8.501 7321 Z= 0.308 Chirality : 0.041 0.152 902 Planarity : 0.004 0.041 924 Dihedral : 4.474 22.668 750 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 1.05 % 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: -1.06 (0.32), residues: 700 helix: 0.09 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -2.09 (0.36), residues: 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.635 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 108 average time/residue: 0.1227 time to fit residues: 18.9622 Evaluate side-chains 105 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1335 time to fit residues: 1.5820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.0020 chunk 31 optimal weight: 0.0470 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.0000 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 overall best weight: 0.1488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 5405 Z= 0.143 Angle : 0.570 7.642 7321 Z= 0.282 Chirality : 0.039 0.143 902 Planarity : 0.003 0.037 924 Dihedral : 4.262 23.729 750 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 1.05 % 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: -0.88 (0.32), residues: 700 helix: 0.21 (0.26), residues: 446 sheet: None (None), residues: 0 loop : -1.98 (0.36), residues: 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.666 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 113 average time/residue: 0.1310 time to fit residues: 20.6516 Evaluate side-chains 104 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0585 time to fit residues: 1.1412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.0030 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 31 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 overall best weight: 0.1206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 5405 Z= 0.150 Angle : 0.604 9.171 7321 Z= 0.290 Chirality : 0.041 0.197 902 Planarity : 0.003 0.037 924 Dihedral : 4.240 23.513 750 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.32), residues: 700 helix: 0.24 (0.26), residues: 444 sheet: None (None), residues: 0 loop : -1.80 (0.37), residues: 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.605 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 100 average time/residue: 0.1314 time to fit residues: 18.5003 Evaluate side-chains 102 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0536 time to fit residues: 1.2209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5405 Z= 0.179 Angle : 0.600 8.350 7321 Z= 0.293 Chirality : 0.041 0.166 902 Planarity : 0.003 0.039 924 Dihedral : 4.193 22.243 750 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.70 % 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: -0.81 (0.32), residues: 700 helix: 0.25 (0.26), residues: 446 sheet: None (None), residues: 0 loop : -1.93 (0.37), residues: 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.570 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.1343 time to fit residues: 19.7639 Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2187 time to fit residues: 1.3930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN B 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 5405 Z= 0.290 Angle : 0.683 9.393 7321 Z= 0.340 Chirality : 0.043 0.178 902 Planarity : 0.004 0.042 924 Dihedral : 4.447 20.710 750 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 1.40 % 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: -0.85 (0.32), residues: 700 helix: 0.25 (0.26), residues: 438 sheet: None (None), residues: 0 loop : -1.95 (0.35), residues: 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.638 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.1365 time to fit residues: 21.4619 Evaluate side-chains 109 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0576 time to fit residues: 1.3695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 5405 Z= 0.184 Angle : 0.649 9.484 7321 Z= 0.318 Chirality : 0.041 0.138 902 Planarity : 0.003 0.044 924 Dihedral : 4.377 22.725 750 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.32), residues: 700 helix: 0.20 (0.26), residues: 444 sheet: None (None), residues: 0 loop : -1.84 (0.38), residues: 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.617 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1381 time to fit residues: 20.2074 Evaluate side-chains 102 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 0.0370 chunk 23 optimal weight: 0.0270 chunk 57 optimal weight: 0.0050 chunk 7 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 overall best weight: 0.0486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.170776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.149171 restraints weight = 6790.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.152468 restraints weight = 4173.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.154770 restraints weight = 2903.712| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 5405 Z= 0.148 Angle : 0.626 10.325 7321 Z= 0.303 Chirality : 0.040 0.141 902 Planarity : 0.003 0.040 924 Dihedral : 4.173 23.338 750 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.78 (0.32), residues: 700 helix: 0.22 (0.26), residues: 442 sheet: None (None), residues: 0 loop : -1.76 (0.37), residues: 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1323.84 seconds wall clock time: 24 minutes 35.48 seconds (1475.48 seconds total)