Starting phenix.real_space_refine on Thu Feb 13 04:10:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tad_25771/02_2025/7tad_25771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tad_25771/02_2025/7tad_25771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tad_25771/02_2025/7tad_25771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tad_25771/02_2025/7tad_25771.map" model { file = "/net/cci-nas-00/data/ceres_data/7tad_25771/02_2025/7tad_25771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tad_25771/02_2025/7tad_25771.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= 0.001 sd= 1.095 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 49 5.16 5 C 5431 2.51 5 N 1471 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8550 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2620 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 337} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2595 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 337} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1666 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 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} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 759 SG CYS A 150 41.718 93.268 99.306 1.00 37.67 S ATOM 791 SG CYS A 155 38.621 94.313 101.290 1.00 47.37 S ATOM 825 SG CYS A 160 39.156 90.552 99.705 1.00 34.45 S ATOM 3396 SG CYS B 150 22.251 34.411 136.649 1.00 98.60 S ATOM 3428 SG CYS B 155 21.179 37.413 138.560 1.00101.80 S ATOM 3462 SG CYS B 160 24.512 37.614 136.784 1.00 76.62 S Time building chain proxies: 6.34, per 1000 atoms: 0.74 Number of scatterers: 8550 At special positions: 0 Unit cell: (68.224, 118.326, 178.022, 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 49 16.00 O 1597 8.00 N 1471 7.00 C 5431 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 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 155 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 160 " 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 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 80.4% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.611A pdb=" N LEU A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 4.002A pdb=" N TYR A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.627A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (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 124 through 138 removed outlier: 3.926A pdb=" N VAL A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 179 through 195 removed outlier: 4.486A pdb=" N ASP A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.836A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 331 through 340 Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.640A pdb=" N THR A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.907A pdb=" N ASN A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 404 removed outlier: 3.554A pdb=" N LYS A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.627A pdb=" N LEU B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.861A pdb=" N TYR B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.615A pdb=" N LEU B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.883A pdb=" N VAL B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 179 through 195 removed outlier: 4.669A pdb=" N ASP B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.955A 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 230 Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.793A pdb=" N LEU B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.563A pdb=" N ASN B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 403 Processing helix chain 'C' and resid 165 through 194 Processing helix chain 'C' and resid 197 through 226 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.500A pdb=" N LEU C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.568A pdb=" N GLN C 244 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 266 through 306 removed outlier: 3.760A pdb=" N ILE C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 350 Processing helix chain 'C' and resid 351 through 377 Processing helix chain 'D' and resid 165 through 194 Processing helix chain 'D' and resid 197 through 226 removed outlier: 3.600A pdb=" N ALA D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.700A pdb=" N GLY D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 250 through 263 Proline residue: D 260 - end of helix removed outlier: 4.025A pdb=" N GLU D 263 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 307 Processing helix chain 'D' and resid 317 through 350 removed outlier: 3.509A pdb=" N ASP D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 378 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: 6.551A pdb=" N LYS B 68 " --> pdb=" O LEU B 112 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2859 1.35 - 1.47: 1825 1.47 - 1.59: 3918 1.59 - 1.71: 0 1.71 - 1.83: 72 Bond restraints: 8674 Sorted by residual: bond pdb=" CG LEU D 298 " pdb=" CD1 LEU D 298 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG PRO C 264 " pdb=" CD PRO C 264 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.15e+00 bond pdb=" CG PRO D 264 " pdb=" CD PRO D 264 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.59e-01 bond pdb=" CG LEU A 191 " pdb=" CD1 LEU A 191 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.39e-01 bond pdb=" C1 PLM C 501 " pdb=" C2 PLM C 501 " ideal model delta sigma weight residual 1.542 1.524 0.018 2.00e-02 2.50e+03 8.32e-01 ... (remaining 8669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 11485 2.12 - 4.25: 206 4.25 - 6.37: 37 6.37 - 8.50: 5 8.50 - 10.62: 3 Bond angle restraints: 11736 Sorted by residual: angle pdb=" CB MET D 172 " pdb=" CG MET D 172 " pdb=" SD MET D 172 " ideal model delta sigma weight residual 112.70 123.32 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA ARG D 236 " pdb=" CB ARG D 236 " pdb=" CG ARG D 236 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA GLU C 263 " pdb=" CB GLU C 263 " pdb=" CG GLU C 263 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.10e+00 angle pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " pdb=" CG LEU A 191 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.42e+00 angle pdb=" CB MET D 346 " pdb=" CG MET D 346 " pdb=" SD MET D 346 " ideal model delta sigma weight residual 112.70 120.72 -8.02 3.00e+00 1.11e-01 7.15e+00 ... (remaining 11731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4813 17.97 - 35.93: 398 35.93 - 53.90: 80 53.90 - 71.86: 14 71.86 - 89.83: 9 Dihedral angle restraints: 5314 sinusoidal: 2035 harmonic: 3279 Sorted by residual: dihedral pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " pdb=" CD GLU B 76 " pdb=" OE1 GLU B 76 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" N LYS B 370 " pdb=" CA LYS B 370 " pdb=" CB LYS B 370 " pdb=" CG LYS B 370 " ideal model delta sinusoidal sigma weight residual -180.00 -122.95 -57.05 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CB GLU D 240 " pdb=" CG GLU D 240 " pdb=" CD GLU D 240 " pdb=" OE1 GLU D 240 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1041 0.040 - 0.080: 268 0.080 - 0.120: 65 0.120 - 0.160: 20 0.160 - 0.200: 4 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA TYR A 186 " pdb=" N TYR A 186 " pdb=" C TYR A 186 " pdb=" CB TYR A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA TYR B 186 " pdb=" N TYR B 186 " pdb=" C TYR B 186 " pdb=" CB TYR B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA HIS A 157 " pdb=" N HIS A 157 " pdb=" C HIS A 157 " pdb=" CB HIS A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1395 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 259 " 0.079 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO C 260 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO C 260 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 260 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 250 " 0.065 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO D 251 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 341 " -0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 342 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " -0.052 5.00e-02 4.00e+02 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 98 2.68 - 3.24: 8585 3.24 - 3.79: 13616 3.79 - 4.35: 17170 4.35 - 4.90: 28482 Nonbonded interactions: 67951 Sorted by model distance: nonbonded pdb=" OD1 ASP A 277 " pdb=" OG1 THR A 310 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR D 237 " pdb=" OE2 GLU D 240 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASP A 120 " pdb=" OH TYR A 172 " model vdw 2.245 3.040 nonbonded pdb=" NH2 ARG A 325 " pdb=" OE1 GLU A 357 " model vdw 2.248 3.120 nonbonded pdb=" NZ LYS A 239 " pdb=" OD2 ASP A 275 " model vdw 2.259 3.120 ... (remaining 67946 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 41 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 166 or (resid 167 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 168 through 216 or \ (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 \ through 228 or (resid 229 and (name N or name CA or name C or name O or name CB \ )) or resid 230 through 257 or (resid 258 through 260 and (name N or name CA or \ name C or name O or name CB )) or resid 261 or (resid 262 through 265 and (name \ N or name CA or name C or name O or name CB )) or resid 266 through 287 or (res \ id 288 through 289 and (name N or name CA or name C or name O or name CB )) or r \ esid 290 through 337 or (resid 338 and (name N or name CA or name C or name O or \ name CB )) or resid 339 through 349 or (resid 350 through 351 and (name N or na \ me CA or name C or name O or name CB )) or resid 352 through 365 or (resid 366 a \ nd (name N or name CA or name C or name O or name CB )) or resid 367 through 370 \ or (resid 371 through 372 and (name N or name CA or name C or name O or name CB \ )) or resid 373 through 379 or (resid 388 and (name N or name CA or name C or n \ ame O or name CB )) or resid 389 through 391 or (resid 392 and (name N or name C \ A or name C or name O or name CB )) or resid 393 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 t \ hrough 399 and (name N or name CA or name C or name O or name CB )) or resid 400 \ or (resid 401 through 404 and (name N or name CA or name C or name O or name CB \ )) or resid 701)) selection = (chain 'B' and (resid 41 through 43 or (resid 44 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 58 or (resid 59 and (na \ me N or name CA or name C or name O or name CB )) or resid 60 through 114 or (re \ sid 115 and (name N or name CA or name C or name O or name CB or name CG )) or r \ esid 116 through 118 or (resid 119 and (name N or name CA or name C or name O or \ name CB )) or resid 120 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 123 through 137 or (resid 138 an \ d (name N or name CA or name C or name O or name CB )) or resid 139 through 144 \ or (resid 145 and (name N or name CA or name C or name O or name CB )) or resid \ 146 through 148 or (resid 149 and (name N or name CA or name C or name O or name \ CB )) or resid 150 through 195 or (resid 196 and (name N or name CA or name C o \ r name O or name CB )) or resid 197 through 242 or (resid 243 and (name N or nam \ e CA or name C or name O or name CB )) or resid 244 through 250 or (resid 251 an \ d (name N or name CA or name C or name O or name CB )) or resid 252 through 253 \ or (resid 254 through 256 and (name N or name CA or name C or name O or name CB \ )) or (resid 257 through 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 317 or (resid 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 through 378 or (resid 379 through 388 and (na \ me N or name CA or name C or name O or name CB )) or resid 389 through 401 or (r \ esid 402 through 404 and (name N or name CA or name C or name O or name CB )) or \ resid 701)) } ncs_group { reference = (chain 'C' and (resid 164 through 306 or (resid 307 and (name N or name CA or na \ me C or name O or name CB )) or resid 316 through 321 or (resid 322 and (name N \ or name CA or name C or name O or name CB )) or resid 323 through 325 or (resid \ 326 through 327 and (name N or name CA or name C or name O or name CB )) or resi \ d 328 through 332 or (resid 333 and (name N or name CA or name C or name O or na \ me CB )) or resid 334 through 343 or (resid 344 and (name N or name CA or name C \ or name O or name CB )) or resid 345 through 347 or (resid 348 and (name N or n \ ame CA or name C or name O or name CB )) or resid 349 through 378 or resid 501)) \ selection = (chain 'D' and (resid 164 through 258 or (resid 259 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 260 through 378 or resid 501)) } 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.790 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 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 : 0.003 0.036 8674 Z= 0.182 Angle : 0.697 10.621 11736 Z= 0.355 Chirality : 0.041 0.200 1398 Planarity : 0.007 0.119 1498 Dihedral : 14.284 89.830 3162 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.68 (0.24), residues: 1093 helix: 0.94 (0.17), residues: 825 sheet: 0.03 (0.95), residues: 32 loop : -1.00 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 235 HIS 0.017 0.001 HIS A 157 PHE 0.014 0.002 PHE A 91 TYR 0.028 0.002 TYR D 365 ARG 0.010 0.001 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.996 Fit side-chains REVERT: B 245 LEU cc_start: 0.8744 (tp) cc_final: 0.8532 (tp) REVERT: C 346 MET cc_start: 0.8742 (tpt) cc_final: 0.8480 (tpt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2041 time to fit residues: 35.8056 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.208125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.170651 restraints weight = 10442.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.171378 restraints weight = 7018.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.173102 restraints weight = 6265.613| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8674 Z= 0.219 Angle : 0.585 7.819 11736 Z= 0.293 Chirality : 0.038 0.150 1398 Planarity : 0.005 0.074 1498 Dihedral : 5.074 53.337 1208 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.23 % Allowed : 7.15 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.99 (0.25), residues: 1093 helix: 1.88 (0.18), residues: 828 sheet: 0.30 (0.94), residues: 32 loop : -0.54 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 376 HIS 0.004 0.001 HIS B 80 PHE 0.019 0.002 PHE C 366 TYR 0.026 0.002 TYR A 186 ARG 0.004 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.898 Fit side-chains REVERT: A 330 TYR cc_start: 0.6866 (m-80) cc_final: 0.6326 (m-10) REVERT: B 367 MET cc_start: 0.8504 (mpp) cc_final: 0.8287 (ptp) REVERT: C 234 MET cc_start: 0.5782 (ppp) cc_final: 0.5546 (ppp) REVERT: D 331 PHE cc_start: 0.7241 (m-80) cc_final: 0.7020 (m-80) outliers start: 11 outliers final: 8 residues processed: 127 average time/residue: 0.1999 time to fit residues: 36.0270 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 96 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS C 176 HIS C 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.206673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166438 restraints weight = 10540.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.169584 restraints weight = 7199.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.171798 restraints weight = 5471.595| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8674 Z= 0.208 Angle : 0.545 10.502 11736 Z= 0.271 Chirality : 0.037 0.150 1398 Planarity : 0.004 0.059 1498 Dihedral : 4.829 51.103 1208 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.23 % Allowed : 9.50 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.44 (0.26), residues: 1093 helix: 2.15 (0.18), residues: 830 sheet: 0.40 (0.98), residues: 30 loop : -0.12 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 376 HIS 0.004 0.001 HIS B 80 PHE 0.015 0.002 PHE B 90 TYR 0.024 0.002 TYR B 186 ARG 0.003 0.000 ARG C 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.889 Fit side-chains REVERT: A 330 TYR cc_start: 0.6844 (m-80) cc_final: 0.6457 (m-80) REVERT: A 339 ARG cc_start: 0.7531 (mmt180) cc_final: 0.7300 (mmt180) REVERT: B 149 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6499 (mt-10) REVERT: B 156 CYS cc_start: 0.8258 (p) cc_final: 0.8057 (p) REVERT: B 225 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7116 (tm-30) REVERT: B 283 LYS cc_start: 0.8775 (pptt) cc_final: 0.8527 (pptt) REVERT: B 367 MET cc_start: 0.8345 (mpp) cc_final: 0.8130 (ptp) REVERT: C 187 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7209 (tt0) REVERT: D 172 MET cc_start: 0.4518 (mpp) cc_final: 0.3643 (mtt) REVERT: D 331 PHE cc_start: 0.7066 (m-80) cc_final: 0.6854 (m-80) outliers start: 20 outliers final: 13 residues processed: 130 average time/residue: 0.2093 time to fit residues: 37.5695 Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.0270 chunk 18 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 55 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN D 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.201588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.162291 restraints weight = 10236.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165221 restraints weight = 7074.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.167330 restraints weight = 5413.830| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8674 Z= 0.231 Angle : 0.566 11.378 11736 Z= 0.281 Chirality : 0.037 0.149 1398 Planarity : 0.004 0.053 1498 Dihedral : 5.135 55.187 1208 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.68 % Allowed : 11.28 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.47 (0.26), residues: 1093 helix: 2.19 (0.18), residues: 829 sheet: 0.09 (0.93), residues: 30 loop : -0.13 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 245 HIS 0.005 0.001 HIS B 80 PHE 0.018 0.002 PHE B 90 TYR 0.025 0.002 TYR A 186 ARG 0.004 0.000 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.949 Fit side-chains REVERT: A 330 TYR cc_start: 0.6949 (m-80) cc_final: 0.6327 (m-10) REVERT: B 75 ARG cc_start: 0.6991 (ttm110) cc_final: 0.6658 (mtm180) REVERT: B 283 LYS cc_start: 0.8788 (pptt) cc_final: 0.8567 (pptt) REVERT: D 172 MET cc_start: 0.4331 (mpp) cc_final: 0.3801 (mtt) outliers start: 24 outliers final: 18 residues processed: 136 average time/residue: 0.2178 time to fit residues: 40.7995 Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 278 GLN C 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.202120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.167587 restraints weight = 10108.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.167472 restraints weight = 7274.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.168830 restraints weight = 6034.140| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8674 Z= 0.231 Angle : 0.566 10.795 11736 Z= 0.279 Chirality : 0.037 0.146 1398 Planarity : 0.004 0.049 1498 Dihedral : 5.198 58.930 1208 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.68 % Allowed : 12.29 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.49 (0.26), residues: 1093 helix: 2.24 (0.18), residues: 829 sheet: -0.39 (1.02), residues: 20 loop : -0.24 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.022 0.002 PHE B 90 TYR 0.024 0.002 TYR B 186 ARG 0.004 0.000 ARG C 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.912 Fit side-chains REVERT: A 330 TYR cc_start: 0.6957 (m-80) cc_final: 0.6377 (m-10) REVERT: D 172 MET cc_start: 0.4398 (mpp) cc_final: 0.3996 (mtt) outliers start: 24 outliers final: 18 residues processed: 136 average time/residue: 0.2080 time to fit residues: 39.0494 Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 68 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.200892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.165222 restraints weight = 10207.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165310 restraints weight = 7775.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165452 restraints weight = 6090.091| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8674 Z= 0.208 Angle : 0.551 11.102 11736 Z= 0.274 Chirality : 0.037 0.150 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.218 59.890 1208 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.46 % Allowed : 14.08 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.61 (0.26), residues: 1093 helix: 2.35 (0.18), residues: 829 sheet: -0.56 (1.03), residues: 20 loop : -0.25 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.029 0.002 PHE B 90 TYR 0.023 0.002 TYR B 186 ARG 0.002 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: A 330 TYR cc_start: 0.6966 (m-80) cc_final: 0.6473 (m-10) REVERT: C 231 MET cc_start: 0.7079 (mpp) cc_final: 0.6278 (mpp) REVERT: C 236 ARG cc_start: 0.6795 (mmm160) cc_final: 0.6387 (mmm160) REVERT: D 172 MET cc_start: 0.4405 (mpp) cc_final: 0.3865 (mtt) outliers start: 22 outliers final: 17 residues processed: 128 average time/residue: 0.1919 time to fit residues: 34.7650 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.197173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.161498 restraints weight = 10437.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.160219 restraints weight = 7441.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161304 restraints weight = 6597.123| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8674 Z= 0.298 Angle : 0.622 10.802 11736 Z= 0.309 Chirality : 0.039 0.196 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.415 57.716 1208 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.79 % Allowed : 14.19 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.21 (0.25), residues: 1093 helix: 2.05 (0.18), residues: 827 sheet: -0.95 (1.02), residues: 20 loop : -0.30 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 245 HIS 0.006 0.001 HIS A 300 PHE 0.033 0.002 PHE B 90 TYR 0.024 0.002 TYR B 186 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.918 Fit side-chains REVERT: A 330 TYR cc_start: 0.7172 (m-80) cc_final: 0.6773 (m-10) REVERT: B 283 LYS cc_start: 0.8597 (pptt) cc_final: 0.8218 (pptt) REVERT: B 367 MET cc_start: 0.8270 (mpp) cc_final: 0.7973 (ptp) REVERT: C 231 MET cc_start: 0.7299 (mpp) cc_final: 0.6921 (mpp) REVERT: D 172 MET cc_start: 0.4455 (mpp) cc_final: 0.4149 (mtt) outliers start: 25 outliers final: 21 residues processed: 131 average time/residue: 0.1871 time to fit residues: 35.0740 Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.199643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.163697 restraints weight = 10384.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.162979 restraints weight = 7778.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164359 restraints weight = 6522.283| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8674 Z= 0.223 Angle : 0.574 10.966 11736 Z= 0.283 Chirality : 0.038 0.222 1398 Planarity : 0.004 0.045 1498 Dihedral : 5.176 54.261 1208 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.79 % Allowed : 14.86 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.44 (0.26), residues: 1093 helix: 2.21 (0.18), residues: 829 sheet: -1.08 (0.97), residues: 20 loop : -0.19 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.035 0.002 PHE B 90 TYR 0.023 0.002 TYR B 186 ARG 0.002 0.000 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: A 330 TYR cc_start: 0.7169 (m-80) cc_final: 0.6663 (m-10) REVERT: B 283 LYS cc_start: 0.8582 (pptt) cc_final: 0.8248 (pptt) REVERT: C 231 MET cc_start: 0.7173 (mpp) cc_final: 0.6762 (mpp) REVERT: D 172 MET cc_start: 0.4555 (mpp) cc_final: 0.4209 (mtt) outliers start: 25 outliers final: 23 residues processed: 130 average time/residue: 0.1792 time to fit residues: 33.7412 Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 chunk 13 optimal weight: 0.0030 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.2568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.203667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.165067 restraints weight = 10480.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.168103 restraints weight = 7463.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.171749 restraints weight = 5291.499| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8674 Z= 0.159 Angle : 0.541 10.664 11736 Z= 0.266 Chirality : 0.036 0.182 1398 Planarity : 0.004 0.045 1498 Dihedral : 5.062 56.414 1208 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.90 % Allowed : 16.09 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.84 (0.26), residues: 1093 helix: 2.48 (0.18), residues: 832 sheet: -0.85 (0.98), residues: 20 loop : -0.02 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.037 0.001 PHE B 90 TYR 0.021 0.001 TYR B 186 ARG 0.003 0.000 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6276 (m-10) REVERT: A 330 TYR cc_start: 0.6918 (m-80) cc_final: 0.6473 (m-10) REVERT: B 47 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6640 (tm-30) REVERT: B 283 LYS cc_start: 0.8754 (pptt) cc_final: 0.8481 (pptt) REVERT: C 231 MET cc_start: 0.6998 (mpp) cc_final: 0.6415 (mpp) REVERT: D 172 MET cc_start: 0.4479 (mpp) cc_final: 0.4161 (mtt) outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 0.2053 time to fit residues: 38.2630 Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.0670 chunk 43 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS C 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.201160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.166959 restraints weight = 10192.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.165835 restraints weight = 8808.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.167902 restraints weight = 7867.178| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8674 Z= 0.212 Angle : 0.588 11.171 11736 Z= 0.286 Chirality : 0.038 0.192 1398 Planarity : 0.004 0.045 1498 Dihedral : 5.184 58.880 1208 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.68 % Allowed : 16.31 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.72 (0.26), residues: 1093 helix: 2.38 (0.18), residues: 830 sheet: -0.92 (1.00), residues: 20 loop : 0.04 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.019 0.002 PHE B 90 TYR 0.021 0.002 TYR B 186 ARG 0.004 0.000 ARG B 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.6456 (m-10) REVERT: A 330 TYR cc_start: 0.7010 (m-80) cc_final: 0.6561 (m-10) REVERT: C 231 MET cc_start: 0.7135 (mpp) cc_final: 0.6669 (mpp) REVERT: D 172 MET cc_start: 0.4431 (mpp) cc_final: 0.4070 (mtt) outliers start: 15 outliers final: 14 residues processed: 129 average time/residue: 0.1955 time to fit residues: 35.8717 Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 98 optimal weight: 0.0870 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.206208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.171615 restraints weight = 10010.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.169671 restraints weight = 7253.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.171270 restraints weight = 6461.663| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8674 Z= 0.167 Angle : 0.571 11.115 11736 Z= 0.278 Chirality : 0.036 0.178 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.040 57.958 1208 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.68 % Allowed : 16.76 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.94 (0.26), residues: 1093 helix: 2.51 (0.18), residues: 832 sheet: -0.71 (1.02), residues: 20 loop : 0.19 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.016 0.001 PHE B 90 TYR 0.020 0.001 TYR B 186 ARG 0.004 0.000 ARG B 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.63 seconds wall clock time: 62 minutes 5.89 seconds (3725.89 seconds total)