Starting phenix.real_space_refine on Thu Nov 14 11:25:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/11_2024/8geh_29970.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/11_2024/8geh_29970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/11_2024/8geh_29970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/11_2024/8geh_29970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/11_2024/8geh_29970.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/11_2024/8geh_29970.cif" } resolution = 4.0 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= 0.021 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: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 3853 2.51 5 N 1069 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5995 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 1812 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 8, 'TRANS': 292} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 714 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 578 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 19, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 438 Chain: "B" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2133 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 24, 'ASN:plan1': 12, 'HIS:plan': 1, 'ASN%COO:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 244 Chain: "G" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 312 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1723 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 664 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 236 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.77 Number of scatterers: 5995 At special positions: 0 Unit cell: (68.9, 98.58, 128.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 1062 8.00 N 1069 7.00 C 3853 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: 1.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 50.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.551A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 61 removed outlier: 4.009A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 114 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.850A pdb=" N CYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.907A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.429A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.757A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.591A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.634A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 86 removed outlier: 4.158A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.654A pdb=" N VAL R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 163 Processing helix chain 'R' and resid 165 through 172 removed outlier: 3.892A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 removed outlier: 3.963A pdb=" N TYR R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.597A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 236 removed outlier: 3.615A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 293 removed outlier: 3.523A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 294 through 299 removed outlier: 4.271A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 326 removed outlier: 3.631A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 212 removed outlier: 5.744A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.350A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.821A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.657A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.336A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 5.692A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1089 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: 2.10 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2024 1.34 - 1.46: 1381 1.46 - 1.57: 2692 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 6111 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.99e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.572 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.487 -0.036 2.00e-02 2.50e+03 3.30e+00 ... (remaining 6106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 8216 1.09 - 2.17: 175 2.17 - 3.26: 28 3.26 - 4.34: 10 4.34 - 5.43: 7 Bond angle restraints: 8436 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.44 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" N GLY B 202 " pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 111.46 114.89 -3.43 1.75e+00 3.27e-01 3.83e+00 angle pdb=" C VAL A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 121.54 125.12 -3.58 1.91e+00 2.74e-01 3.51e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 116.32 -5.43 3.00e+00 1.11e-01 3.27e+00 angle pdb=" CA ILE B 270 " pdb=" C ILE B 270 " pdb=" N CYS B 271 " ideal model delta sigma weight residual 118.71 116.64 2.07 1.15e+00 7.56e-01 3.24e+00 ... (remaining 8431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.91: 3159 10.91 - 21.82: 157 21.82 - 32.74: 77 32.74 - 43.65: 36 43.65 - 54.56: 9 Dihedral angle restraints: 3438 sinusoidal: 644 harmonic: 2794 Sorted by residual: dihedral pdb=" CA HIS B 183 " pdb=" C HIS B 183 " pdb=" N THR B 184 " pdb=" CA THR B 184 " ideal model delta harmonic sigma weight residual 180.00 -164.10 -15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ARG A 380 " pdb=" CB ARG A 380 " pdb=" CG ARG A 380 " pdb=" CD ARG A 380 " ideal model delta sinusoidal sigma weight residual -60.00 -109.66 49.66 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA ARG B 49 " pdb=" CB ARG B 49 " pdb=" CG ARG B 49 " pdb=" CD ARG B 49 " ideal model delta sinusoidal sigma weight residual 180.00 132.13 47.87 3 1.50e+01 4.44e-03 8.56e+00 ... (remaining 3435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 730 0.034 - 0.068: 233 0.068 - 0.102: 68 0.102 - 0.136: 18 0.136 - 0.171: 2 Chirality restraints: 1051 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1048 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO R 168 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.05e+00 pdb=" N PRO B 236 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C THR B 87 " -0.017 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.006 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1650 2.80 - 3.33: 5824 3.33 - 3.85: 9406 3.85 - 4.38: 9766 4.38 - 4.90: 17270 Nonbonded interactions: 43916 Sorted by model distance: nonbonded pdb=" O LEU A 282 " pdb=" NE2 HIS A 357 " model vdw 2.276 3.120 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.289 3.040 nonbonded pdb=" ND1 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.331 3.120 nonbonded pdb=" NE1 TRP A 277 " pdb=" O SER A 349 " model vdw 2.352 3.120 nonbonded pdb=" NH2 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.357 3.120 ... (remaining 43911 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 0.053 6111 Z= 0.181 Angle : 0.433 5.428 8436 Z= 0.241 Chirality : 0.039 0.171 1051 Planarity : 0.002 0.032 1096 Dihedral : 10.847 54.562 1612 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.28), residues: 930 helix: 2.42 (0.24), residues: 415 sheet: 0.67 (0.44), residues: 163 loop : -0.52 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR R 141 ARG 0.004 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.688 Fit side-chains REVERT: A 380 ARG cc_start: 0.8813 (tmm-80) cc_final: 0.8369 (ttm170) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1370 time to fit residues: 11.5953 Evaluate side-chains 44 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6111 Z= 0.217 Angle : 0.451 4.905 8436 Z= 0.260 Chirality : 0.040 0.145 1051 Planarity : 0.003 0.030 1096 Dihedral : 3.792 15.151 1000 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.63 % Allowed : 10.06 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.28), residues: 930 helix: 2.81 (0.24), residues: 429 sheet: 0.50 (0.42), residues: 180 loop : -0.46 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 297 HIS 0.006 0.001 HIS B 225 PHE 0.010 0.001 PHE B 199 TYR 0.015 0.001 TYR R 199 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.728 Fit side-chains REVERT: A 380 ARG cc_start: 0.8779 (tmm-80) cc_final: 0.8323 (ttm170) REVERT: B 17 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8457 (tm-30) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.1185 time to fit residues: 9.0657 Evaluate side-chains 45 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6111 Z= 0.179 Angle : 0.412 5.084 8436 Z= 0.235 Chirality : 0.039 0.147 1051 Planarity : 0.003 0.029 1096 Dihedral : 3.703 19.635 1000 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.57 % Allowed : 14.47 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.28), residues: 930 helix: 3.07 (0.24), residues: 430 sheet: 0.42 (0.41), residues: 180 loop : -0.45 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 297 HIS 0.002 0.001 HIS B 54 PHE 0.009 0.001 PHE B 199 TYR 0.016 0.001 TYR R 199 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.679 Fit side-chains REVERT: A 380 ARG cc_start: 0.8753 (tmm-80) cc_final: 0.8221 (ttt90) REVERT: A 385 ARG cc_start: 0.8456 (mtt90) cc_final: 0.8216 (mtt90) REVERT: B 17 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8411 (tm-30) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.1369 time to fit residues: 10.4779 Evaluate side-chains 48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6111 Z= 0.126 Angle : 0.384 4.983 8436 Z= 0.218 Chirality : 0.038 0.140 1051 Planarity : 0.003 0.030 1096 Dihedral : 3.483 16.507 1000 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.57 % Allowed : 17.92 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.29), residues: 930 helix: 3.20 (0.24), residues: 431 sheet: 0.70 (0.42), residues: 169 loop : -0.47 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 297 HIS 0.002 0.001 HIS B 183 PHE 0.009 0.001 PHE B 241 TYR 0.016 0.001 TYR R 199 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.720 Fit side-chains REVERT: A 380 ARG cc_start: 0.8704 (tmm-80) cc_final: 0.8193 (ttt90) REVERT: A 385 ARG cc_start: 0.8464 (mtt90) cc_final: 0.7884 (mtt90) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.1327 time to fit residues: 10.8904 Evaluate side-chains 47 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6111 Z= 0.174 Angle : 0.410 5.119 8436 Z= 0.232 Chirality : 0.039 0.147 1051 Planarity : 0.003 0.028 1096 Dihedral : 3.520 16.409 1000 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.52 % Allowed : 19.81 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.29), residues: 930 helix: 3.26 (0.25), residues: 431 sheet: 0.38 (0.40), residues: 180 loop : -0.45 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 297 HIS 0.002 0.001 HIS B 225 PHE 0.009 0.001 PHE B 199 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.705 Fit side-chains REVERT: A 380 ARG cc_start: 0.8734 (tmm-80) cc_final: 0.8226 (ttt90) REVERT: A 385 ARG cc_start: 0.8499 (mtt90) cc_final: 0.8001 (mtt90) REVERT: B 273 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8568 (mp) REVERT: R 141 TYR cc_start: 0.7336 (t80) cc_final: 0.7124 (t80) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.1303 time to fit residues: 9.8719 Evaluate side-chains 47 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 0.0070 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.0030 chunk 7 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.018 6111 Z= 0.102 Angle : 0.377 4.951 8436 Z= 0.211 Chirality : 0.038 0.135 1051 Planarity : 0.002 0.029 1096 Dihedral : 3.271 14.049 1000 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.52 % Allowed : 20.75 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.29), residues: 930 helix: 3.33 (0.25), residues: 431 sheet: 0.68 (0.41), residues: 169 loop : -0.43 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 297 HIS 0.001 0.000 HIS B 142 PHE 0.006 0.001 PHE B 199 TYR 0.012 0.001 TYR R 199 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.793 Fit side-chains REVERT: A 380 ARG cc_start: 0.8696 (tmm-80) cc_final: 0.8196 (ttt90) REVERT: A 385 ARG cc_start: 0.8444 (mtt90) cc_final: 0.7959 (mtt90) REVERT: B 273 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8565 (mp) outliers start: 8 outliers final: 2 residues processed: 58 average time/residue: 0.1290 time to fit residues: 11.3108 Evaluate side-chains 49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6111 Z= 0.165 Angle : 0.448 10.066 8436 Z= 0.235 Chirality : 0.039 0.149 1051 Planarity : 0.002 0.028 1096 Dihedral : 3.390 14.244 1000 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.89 % Allowed : 21.70 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.29), residues: 930 helix: 3.39 (0.25), residues: 431 sheet: 0.59 (0.40), residues: 174 loop : -0.40 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 297 HIS 0.002 0.001 HIS B 225 PHE 0.009 0.001 PHE B 199 TYR 0.013 0.001 TYR R 199 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.636 Fit side-chains REVERT: A 380 ARG cc_start: 0.8734 (tmm-80) cc_final: 0.8225 (ttt90) REVERT: A 385 ARG cc_start: 0.8391 (mtt90) cc_final: 0.7844 (mtt90) REVERT: B 273 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8599 (mp) REVERT: R 141 TYR cc_start: 0.7573 (t80) cc_final: 0.7286 (t80) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 0.1324 time to fit residues: 10.6188 Evaluate side-chains 48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6111 Z= 0.244 Angle : 0.482 9.125 8436 Z= 0.260 Chirality : 0.040 0.150 1051 Planarity : 0.003 0.028 1096 Dihedral : 3.801 15.016 1000 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.52 % Allowed : 21.70 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.29), residues: 930 helix: 3.19 (0.25), residues: 433 sheet: 0.17 (0.39), residues: 180 loop : -0.53 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 199 TYR 0.018 0.001 TYR R 199 ARG 0.001 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.738 Fit side-chains REVERT: A 380 ARG cc_start: 0.8832 (tmm-80) cc_final: 0.8332 (ttt90) REVERT: A 385 ARG cc_start: 0.8436 (mtt90) cc_final: 0.7744 (mtt90) REVERT: B 273 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8589 (mp) REVERT: R 141 TYR cc_start: 0.7639 (t80) cc_final: 0.7308 (t80) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.1310 time to fit residues: 9.8197 Evaluate side-chains 48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0980 chunk 87 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6111 Z= 0.134 Angle : 0.436 9.452 8436 Z= 0.230 Chirality : 0.039 0.149 1051 Planarity : 0.002 0.028 1096 Dihedral : 3.467 13.462 1000 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.57 % Allowed : 23.90 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.29), residues: 930 helix: 3.28 (0.25), residues: 433 sheet: 0.39 (0.39), residues: 174 loop : -0.47 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 297 HIS 0.002 0.001 HIS R 93 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR R 199 ARG 0.001 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.676 Fit side-chains REVERT: A 380 ARG cc_start: 0.8785 (tmm-80) cc_final: 0.8280 (ttt90) REVERT: A 385 ARG cc_start: 0.8385 (mtt90) cc_final: 0.7719 (mtt90) REVERT: B 45 MET cc_start: 0.8490 (tpt) cc_final: 0.8180 (tpt) REVERT: B 273 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8617 (mp) REVERT: R 141 TYR cc_start: 0.7643 (t80) cc_final: 0.7364 (t80) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.1306 time to fit residues: 10.0220 Evaluate side-chains 49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6111 Z= 0.263 Angle : 0.492 8.801 8436 Z= 0.265 Chirality : 0.040 0.156 1051 Planarity : 0.003 0.028 1096 Dihedral : 3.829 13.054 1000 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.57 % Allowed : 23.27 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.29), residues: 930 helix: 3.13 (0.25), residues: 433 sheet: -0.05 (0.38), residues: 183 loop : -0.52 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 340 TYR 0.017 0.002 TYR R 199 ARG 0.001 0.000 ARG B 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.678 Fit side-chains REVERT: A 380 ARG cc_start: 0.8872 (tmm-80) cc_final: 0.8375 (ttt90) REVERT: A 385 ARG cc_start: 0.8438 (mtt90) cc_final: 0.7663 (mtt90) REVERT: B 45 MET cc_start: 0.8552 (tpt) cc_final: 0.8266 (tpt) REVERT: B 273 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8617 (mp) REVERT: R 141 TYR cc_start: 0.7731 (t80) cc_final: 0.7355 (t80) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.1355 time to fit residues: 9.9426 Evaluate side-chains 49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.084259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.072747 restraints weight = 22021.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.074165 restraints weight = 13491.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074929 restraints weight = 9503.762| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6111 Z= 0.168 Angle : 0.446 8.934 8436 Z= 0.238 Chirality : 0.039 0.152 1051 Planarity : 0.002 0.028 1096 Dihedral : 3.623 12.833 1000 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.89 % Allowed : 22.96 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.29), residues: 930 helix: 3.21 (0.25), residues: 433 sheet: 0.16 (0.39), residues: 176 loop : -0.47 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 297 HIS 0.002 0.001 HIS B 225 PHE 0.010 0.001 PHE B 199 TYR 0.015 0.001 TYR R 199 ARG 0.001 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.07 seconds wall clock time: 24 minutes 12.47 seconds (1452.47 seconds total)