Starting phenix.real_space_refine on Thu Jul 2 12:15:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tad_25771/07_2026/7tad_25771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tad_25771/07_2026/7tad_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tad_25771/07_2026/7tad_25771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tad_25771/07_2026/7tad_25771.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tad_25771/07_2026/7tad_25771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tad_25771/07_2026/7tad_25771.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tad_25771/07_2026/7tad_25771.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tad_25771/07_2026/7tad_25771.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} 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: {'GLU:plan': 8, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} 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: {'ARG:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 1, 'GLN:plan1': 2, '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: 1.66, per 1000 atoms: 0.19 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: 0.58 Conformation dependent library (CDL) restraints added in 394.2 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 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: 0.14 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: 1.04 Time building geometry restraints manager: 0.80 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 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 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: 3.290 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.040 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 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 0.064 8682 Z= 0.139 Angle : 0.707 10.621 11742 Z= 0.356 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (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 ARG 0.010 0.001 ARG C 274 TYR 0.028 0.002 TYR D 365 PHE 0.014 0.002 PHE A 91 TRP 0.025 0.003 TRP C 235 HIS 0.017 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 8674) covalent geometry : angle 0.69678 / 0.35 (11736) hydrogen bonds : bond 0.12035 / 8.50 ( 636) hydrogen bonds : angle 4.69620 / 3.46 ( 1872) metal coordination : bond 0.02937 / 1.47 ( 8) metal coordination : angle 5.40160 / 3.37 ( 6) *********************** 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 : 0.324 Fit side-chains REVERT: B 245 LEU cc_start: 0.8744 (tp) cc_final: 0.8531 (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: 0.0669 time to fit residues: 12.0007 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.209102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169255 restraints weight = 10629.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172587 restraints weight = 7263.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174922 restraints weight = 5518.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.176432 restraints weight = 4539.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.177338 restraints weight = 3950.368| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8682 Z= 0.146 Angle : 0.583 7.745 11742 Z= 0.292 Chirality : 0.038 0.185 1398 Planarity : 0.005 0.074 1498 Dihedral : 5.006 54.413 1208 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.01 % Allowed : 7.49 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.25), residues: 1093 helix: 1.90 (0.18), residues: 828 sheet: 0.30 (0.95), residues: 32 loop : -0.54 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.025 0.002 TYR A 186 PHE 0.018 0.002 PHE C 366 TRP 0.015 0.002 TRP D 376 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 8674) covalent geometry : angle 0.58080 / 0.29 (11736) hydrogen bonds : bond 0.03965 / 2.58 ( 636) hydrogen bonds : angle 3.78416 / 2.77 ( 1872) metal coordination : bond 0.02045 / 0.98 ( 8) metal coordination : angle 2.22811 / 1.36 ( 6) *********************** 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 133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.327 Fit side-chains REVERT: A 330 TYR cc_start: 0.6840 (m-80) cc_final: 0.6283 (m-10) REVERT: C 234 MET cc_start: 0.5714 (ppp) cc_final: 0.5398 (ppp) REVERT: D 331 PHE cc_start: 0.7238 (m-80) cc_final: 0.7030 (m-80) outliers start: 9 outliers final: 8 residues processed: 127 average time/residue: 0.0778 time to fit residues: 14.1183 Evaluate side-chains 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 40 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.206601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168789 restraints weight = 10463.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171103 restraints weight = 7397.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.171946 restraints weight = 5204.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.172355 restraints weight = 4572.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.172787 restraints weight = 4485.261| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8682 Z= 0.139 Angle : 0.551 10.837 11742 Z= 0.274 Chirality : 0.037 0.148 1398 Planarity : 0.004 0.058 1498 Dihedral : 4.813 49.604 1208 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.12 % Allowed : 9.50 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.26), residues: 1093 helix: 2.15 (0.18), residues: 830 sheet: 0.45 (0.97), residues: 30 loop : -0.09 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 236 TYR 0.025 0.002 TYR B 186 PHE 0.015 0.002 PHE B 90 TRP 0.020 0.002 TRP D 376 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8674) covalent geometry : angle 0.54909 / 0.27 (11736) hydrogen bonds : bond 0.03741 / 2.44 ( 636) hydrogen bonds : angle 3.66641 / 2.68 ( 1872) metal coordination : bond 0.01664 / 0.81 ( 8) metal coordination : angle 2.31001 / 1.46 ( 6) *********************** 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 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.248 Fit side-chains REVERT: A 330 TYR cc_start: 0.6835 (m-80) cc_final: 0.6339 (m-10) REVERT: A 339 ARG cc_start: 0.7513 (mmt180) cc_final: 0.7304 (mmt180) REVERT: A 390 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7320 (mmtp) REVERT: B 149 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6622 (mt-10) REVERT: B 156 CYS cc_start: 0.8364 (p) cc_final: 0.8132 (p) REVERT: B 225 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7088 (tm-30) REVERT: B 283 LYS cc_start: 0.8709 (pptt) cc_final: 0.8472 (pptt) REVERT: B 305 TYR cc_start: 0.8464 (m-80) cc_final: 0.8233 (m-10) REVERT: D 172 MET cc_start: 0.4378 (mpp) cc_final: 0.3657 (mtt) REVERT: D 331 PHE cc_start: 0.7095 (m-80) cc_final: 0.6801 (m-80) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.0859 time to fit residues: 15.8648 Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 0.0270 chunk 90 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4412 r_free = 0.4412 target = 0.201772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.161458 restraints weight = 10513.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164592 restraints weight = 7213.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.166740 restraints weight = 5476.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168261 restraints weight = 4521.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.169046 restraints weight = 3935.681| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 0.048 8682 Z= 0.151 Angle : 0.570 11.106 11742 Z= 0.282 Chirality : 0.037 0.146 1398 Planarity : 0.004 0.052 1498 Dihedral : 5.136 55.358 1208 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.46 % Allowed : 11.73 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.26), residues: 1093 helix: 2.19 (0.18), residues: 829 sheet: 0.12 (0.93), residues: 30 loop : -0.12 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.028 0.002 TYR A 186 PHE 0.017 0.002 PHE B 90 TRP 0.022 0.002 TRP D 376 HIS 0.004 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8674) covalent geometry : angle 0.56701 / 0.28 (11736) hydrogen bonds : bond 0.03852 / 2.49 ( 636) hydrogen bonds : angle 3.69453 / 2.68 ( 1872) metal coordination : bond 0.01803 / 0.88 ( 8) metal coordination : angle 2.44099 / 1.56 ( 6) *********************** 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 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.214 Fit side-chains REVERT: B 75 ARG cc_start: 0.6954 (ttm110) cc_final: 0.6643 (mtm180) REVERT: B 283 LYS cc_start: 0.8855 (pptt) cc_final: 0.8617 (pptt) REVERT: B 367 MET cc_start: 0.8174 (mpp) cc_final: 0.7900 (ptp) REVERT: D 172 MET cc_start: 0.4381 (mpp) cc_final: 0.3872 (mtt) outliers start: 22 outliers final: 15 residues processed: 134 average time/residue: 0.0920 time to fit residues: 17.0012 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 0.1980 chunk 89 optimal weight: 0.2980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4439 r_free = 0.4439 target = 0.205142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.164978 restraints weight = 10434.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.168151 restraints weight = 7133.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.170301 restraints weight = 5419.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171858 restraints weight = 4457.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.172695 restraints weight = 3867.736| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8682 Z= 0.112 Angle : 0.518 11.028 11742 Z= 0.255 Chirality : 0.035 0.130 1398 Planarity : 0.004 0.047 1498 Dihedral : 4.893 57.745 1208 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.01 % Allowed : 12.40 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.26), residues: 1093 helix: 2.48 (0.18), residues: 829 sheet: 0.26 (0.94), residues: 30 loop : -0.07 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 222 TYR 0.022 0.002 TYR A 186 PHE 0.024 0.001 PHE B 90 TRP 0.025 0.002 TRP C 245 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8674) covalent geometry : angle 0.51566 / 0.25 (11736) hydrogen bonds : bond 0.03320 / 2.16 ( 636) hydrogen bonds : angle 3.49786 / 2.55 ( 1872) metal coordination : bond 0.01442 / 0.69 ( 8) metal coordination : angle 2.16493 / 1.33 ( 6) *********************** 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 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.232 Fit side-chains REVERT: A 330 TYR cc_start: 0.6884 (m-80) cc_final: 0.6303 (m-10) REVERT: B 305 TYR cc_start: 0.8369 (m-80) cc_final: 0.8152 (m-10) REVERT: B 367 MET cc_start: 0.8187 (mpp) cc_final: 0.7904 (ptp) REVERT: D 172 MET cc_start: 0.4288 (mpp) cc_final: 0.3901 (mtt) outliers start: 18 outliers final: 12 residues processed: 135 average time/residue: 0.0865 time to fit residues: 15.9787 Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 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 316 LYS 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 71 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 0.0030 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.202148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.161959 restraints weight = 10385.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.164968 restraints weight = 7227.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.167125 restraints weight = 5542.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.168429 restraints weight = 4576.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.169600 restraints weight = 4006.843| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8682 Z= 0.136 Angle : 0.554 10.763 11742 Z= 0.274 Chirality : 0.036 0.134 1398 Planarity : 0.004 0.053 1498 Dihedral : 5.104 59.504 1208 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.46 % Allowed : 13.41 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.26), residues: 1093 helix: 2.43 (0.18), residues: 829 sheet: -0.39 (1.03), residues: 20 loop : -0.17 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 236 TYR 0.023 0.002 TYR B 186 PHE 0.029 0.002 PHE B 90 TRP 0.026 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8674) covalent geometry : angle 0.55113 / 0.27 (11736) hydrogen bonds : bond 0.03610 / 2.33 ( 636) hydrogen bonds : angle 3.57226 / 2.59 ( 1872) metal coordination : bond 0.01659 / 0.79 ( 8) metal coordination : angle 2.39341 / 1.46 ( 6) *********************** 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 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.6982 (m-80) cc_final: 0.6397 (m-10) REVERT: B 283 LYS cc_start: 0.8828 (pptt) cc_final: 0.8433 (pptt) REVERT: B 367 MET cc_start: 0.8043 (mpp) cc_final: 0.7801 (ptp) REVERT: D 172 MET cc_start: 0.4355 (mpp) cc_final: 0.4004 (mtt) outliers start: 22 outliers final: 18 residues processed: 130 average time/residue: 0.0812 time to fit residues: 14.9566 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 : 0.341 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 98 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 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 = 0.4403 r_free = 0.4403 target = 0.201033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165609 restraints weight = 10436.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165203 restraints weight = 6880.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165592 restraints weight = 5998.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165884 restraints weight = 5152.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166544 restraints weight = 4892.361| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8682 Z= 0.142 Angle : 0.561 10.939 11742 Z= 0.277 Chirality : 0.037 0.176 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.160 57.599 1208 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.57 % Allowed : 14.08 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.26), residues: 1093 helix: 2.30 (0.18), residues: 836 sheet: -0.67 (1.01), residues: 20 loop : -0.15 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 236 TYR 0.023 0.002 TYR B 186 PHE 0.033 0.002 PHE B 90 TRP 0.028 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 8674) covalent geometry : angle 0.55810 / 0.28 (11736) hydrogen bonds : bond 0.03641 / 2.35 ( 636) hydrogen bonds : angle 3.61673 / 2.63 ( 1872) metal coordination : bond 0.01426 / 0.69 ( 8) metal coordination : angle 2.39428 / 1.53 ( 6) *********************** 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: 23 poor density : 117 time to evaluate : 0.251 Fit side-chains REVERT: A 330 TYR cc_start: 0.6974 (m-80) cc_final: 0.6445 (m-10) REVERT: B 283 LYS cc_start: 0.8515 (pptt) cc_final: 0.8208 (pptt) REVERT: D 172 MET cc_start: 0.4598 (mpp) cc_final: 0.4075 (mtt) outliers start: 23 outliers final: 20 residues processed: 131 average time/residue: 0.0703 time to fit residues: 13.3612 Evaluate side-chains 127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 319 LEU Chi-restraints excluded: chain A residue 322 VAL 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 28 optimal weight: 0.5980 chunk 82 optimal weight: 0.0670 chunk 32 optimal weight: 0.1980 chunk 58 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 106 optimal weight: 0.0970 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 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 = 0.4441 r_free = 0.4441 target = 0.205752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166792 restraints weight = 10356.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169901 restraints weight = 7310.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.171722 restraints weight = 5242.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.172574 restraints weight = 4149.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.173052 restraints weight = 4150.379| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8682 Z= 0.103 Angle : 0.534 10.988 11742 Z= 0.259 Chirality : 0.036 0.216 1398 Planarity : 0.004 0.046 1498 Dihedral : 4.675 49.622 1208 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.68 % Allowed : 16.42 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.26), residues: 1093 helix: 2.61 (0.18), residues: 831 sheet: -0.58 (1.00), residues: 20 loop : 0.05 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 236 TYR 0.020 0.001 TYR B 186 PHE 0.036 0.001 PHE B 90 TRP 0.031 0.002 TRP C 245 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 8674) covalent geometry : angle 0.53249 / 0.26 (11736) hydrogen bonds : bond 0.03106 / 2.02 ( 636) hydrogen bonds : angle 3.43390 / 2.49 ( 1872) metal coordination : bond 0.00917 / 0.43 ( 8) metal coordination : angle 1.95422 / 1.19 ( 6) *********************** 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 135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.6803 (m-80) cc_final: 0.6318 (m-10) REVERT: B 47 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6565 (tm-30) REVERT: B 283 LYS cc_start: 0.8705 (pptt) cc_final: 0.8396 (pptt) REVERT: B 367 MET cc_start: 0.8249 (mpp) cc_final: 0.7887 (ptp) REVERT: C 231 MET cc_start: 0.6969 (mpp) cc_final: 0.6240 (mpp) REVERT: D 172 MET cc_start: 0.4453 (mpp) cc_final: 0.3870 (mtt) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.0839 time to fit residues: 15.6487 Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 156 CYS 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 129 VAL Chi-restraints excluded: chain B residue 201 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.4980 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.0030 chunk 9 optimal weight: 1.9990 chunk 106 optimal weight: 0.0020 chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.1036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.208245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.170897 restraints weight = 10311.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172996 restraints weight = 6887.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.173856 restraints weight = 5243.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.173995 restraints weight = 4483.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.175403 restraints weight = 4445.704| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8682 Z= 0.101 Angle : 0.538 11.111 11742 Z= 0.261 Chirality : 0.036 0.181 1398 Planarity : 0.004 0.046 1498 Dihedral : 4.385 43.253 1208 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.45 % Allowed : 16.42 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.26), residues: 1093 helix: 2.73 (0.18), residues: 830 sheet: -0.54 (1.02), residues: 20 loop : 0.15 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.022 0.001 TYR B 186 PHE 0.018 0.001 PHE B 90 TRP 0.033 0.002 TRP C 245 HIS 0.003 0.000 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 8674) covalent geometry : angle 0.53653 / 0.26 (11736) hydrogen bonds : bond 0.02976 / 1.93 ( 636) hydrogen bonds : angle 3.41170 / 2.47 ( 1872) metal coordination : bond 0.00819 / 0.36 ( 8) metal coordination : angle 1.71803 / 1.06 ( 6) *********************** 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 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 319 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7038 (tt) REVERT: A 330 TYR cc_start: 0.6672 (m-80) cc_final: 0.6246 (m-10) REVERT: B 47 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6599 (tm-30) REVERT: B 283 LYS cc_start: 0.8715 (pptt) cc_final: 0.8430 (pptt) REVERT: B 367 MET cc_start: 0.8335 (mpp) cc_final: 0.8057 (ptp) REVERT: D 172 MET cc_start: 0.4375 (mpp) cc_final: 0.3856 (mtt) outliers start: 13 outliers final: 10 residues processed: 130 average time/residue: 0.0795 time to fit residues: 14.9942 Evaluate side-chains 124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 193 VAL 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 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 82 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 77 optimal weight: 0.2980 chunk 55 optimal weight: 20.0000 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN D 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.206212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.166395 restraints weight = 10460.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.169613 restraints weight = 7253.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.171730 restraints weight = 5506.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.173086 restraints weight = 4535.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.174265 restraints weight = 3945.884| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8682 Z= 0.110 Angle : 0.563 11.164 11742 Z= 0.272 Chirality : 0.037 0.185 1398 Planarity : 0.004 0.046 1498 Dihedral : 4.431 39.162 1208 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.23 % Allowed : 17.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.26), residues: 1093 helix: 2.65 (0.18), residues: 838 sheet: -0.49 (1.04), residues: 20 loop : 0.16 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.017 0.001 TYR A 186 PHE 0.010 0.001 PHE C 331 TRP 0.038 0.002 TRP C 245 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8674) covalent geometry : angle 0.56133 / 0.27 (11736) hydrogen bonds : bond 0.03103 / 2.01 ( 636) hydrogen bonds : angle 3.45298 / 2.50 ( 1872) metal coordination : bond 0.00952 / 0.44 ( 8) metal coordination : angle 1.78052 / 1.15 ( 6) ********************** 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 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 319 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7087 (tt) REVERT: B 47 GLN cc_start: 0.7174 (mm-40) cc_final: 0.6667 (tm-30) REVERT: B 283 LYS cc_start: 0.8815 (pptt) cc_final: 0.8547 (pptt) REVERT: D 172 MET cc_start: 0.4285 (mpp) cc_final: 0.3987 (mtt) outliers start: 11 outliers final: 10 residues processed: 123 average time/residue: 0.0799 time to fit residues: 14.1753 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 193 VAL 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 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 108 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 76 optimal weight: 0.0870 chunk 33 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.203954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.168031 restraints weight = 10441.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.168480 restraints weight = 7405.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.168551 restraints weight = 5341.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169337 restraints weight = 4884.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170174 restraints weight = 4449.991| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8682 Z= 0.125 Angle : 0.594 11.214 11742 Z= 0.285 Chirality : 0.038 0.183 1398 Planarity : 0.004 0.046 1498 Dihedral : 4.592 45.152 1208 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.45 % Allowed : 17.21 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.26), residues: 1093 helix: 2.54 (0.18), residues: 836 sheet: -0.52 (1.05), residues: 20 loop : 0.23 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.017 0.001 TYR A 186 PHE 0.046 0.002 PHE B 90 TRP 0.036 0.002 TRP C 245 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 8674) covalent geometry : angle 0.59277 / 0.29 (11736) hydrogen bonds : bond 0.03345 / 2.16 ( 636) hydrogen bonds : angle 3.53625 / 2.57 ( 1872) metal coordination : bond 0.01139 / 0.55 ( 8) metal coordination : angle 1.92718 / 1.26 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.07 seconds wall clock time: 31 minutes 14.22 seconds (1874.22 seconds total)