Starting phenix.real_space_refine on Tue Sep 24 22:05:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw5_39623/09_2024/8yw5_39623.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw5_39623/09_2024/8yw5_39623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw5_39623/09_2024/8yw5_39623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw5_39623/09_2024/8yw5_39623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw5_39623/09_2024/8yw5_39623.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw5_39623/09_2024/8yw5_39623.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.078 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 54 5.16 5 C 5691 2.51 5 N 1553 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8937 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 237 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'2ML:plan-1': 1, 'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2954 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 367} Chain breaks: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 106 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1817 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2552 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.54, per 1000 atoms: 0.62 Number of scatterers: 8937 At special positions: 0 Unit cell: (77.112, 99.603, 168.147, 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 54 16.00 O 1639 8.00 N 1553 7.00 C 5691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 41.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'P' and resid 1 through 28 removed outlier: 3.548A pdb=" N PHE P 6 " --> pdb=" O AIB P 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 47 Processing helix chain 'R' and resid 124 through 164 Processing helix chain 'R' and resid 171 through 203 Processing helix chain 'R' and resid 208 through 217 removed outlier: 3.926A pdb=" N VAL R 212 " --> pdb=" O ASP R 208 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER R 213 " --> pdb=" O ASP R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 253 Processing helix chain 'R' and resid 265 through 273 Processing helix chain 'R' and resid 275 through 290 Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 308 through 334 removed outlier: 3.544A pdb=" N PHE R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 351 Processing helix chain 'R' and resid 353 through 359 removed outlier: 4.090A pdb=" N LEU R 357 " --> pdb=" O THR R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 366 removed outlier: 3.983A pdb=" N PHE R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 402 removed outlier: 4.600A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 419 Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.543A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.522A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.552A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.588A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.678A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.709A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.831A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.667A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.667A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.804A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 61 through 62 removed outlier: 3.953A pdb=" N THR R 61 " --> pdb=" O TRP R 68 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP R 68 " --> pdb=" O THR R 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.911A pdb=" N ILE R 79 " --> pdb=" O VAL R 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.640A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.220A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.573A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.144A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.943A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.705A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.651A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.645A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.826A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1314 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: 2.42 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2922 1.34 - 1.46: 2232 1.46 - 1.58: 3906 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9133 Sorted by residual: bond pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " ideal model delta sigma weight residual 1.525 1.576 -0.051 2.10e-02 2.27e+03 5.89e+00 bond pdb=" N AIB P 2 " pdb=" CA AIB P 2 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.55e+00 bond pdb=" N AIB P 20 " pdb=" CA AIB P 20 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.45e+00 bond pdb=" C GLN R 113 " pdb=" N PRO R 114 " ideal model delta sigma weight residual 1.326 1.346 -0.020 1.44e-02 4.82e+03 1.86e+00 bond pdb=" C 2ML P 13 " pdb=" O 2ML P 13 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 9128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 12069 1.22 - 2.45: 257 2.45 - 3.67: 54 3.67 - 4.90: 18 4.90 - 6.12: 5 Bond angle restraints: 12403 Sorted by residual: angle pdb=" N SER R 265 " pdb=" CA SER R 265 " pdb=" C SER R 265 " ideal model delta sigma weight residual 114.62 108.50 6.12 1.14e+00 7.69e-01 2.89e+01 angle pdb=" C GLN R 105 " pdb=" CA GLN R 105 " pdb=" CB GLN R 105 " ideal model delta sigma weight residual 116.54 110.68 5.86 1.15e+00 7.56e-01 2.60e+01 angle pdb=" C GLN R 293 " pdb=" CA GLN R 293 " pdb=" CB GLN R 293 " ideal model delta sigma weight residual 115.79 110.67 5.12 1.19e+00 7.06e-01 1.85e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 112.83 109.77 3.06 9.90e-01 1.02e+00 9.57e+00 angle pdb=" CA SER R 265 " pdb=" C SER R 265 " pdb=" N LEU R 266 " ideal model delta sigma weight residual 119.71 116.12 3.59 1.17e+00 7.31e-01 9.41e+00 ... (remaining 12398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4929 16.00 - 31.99: 326 31.99 - 47.99: 76 47.99 - 63.99: 21 63.99 - 79.98: 4 Dihedral angle restraints: 5356 sinusoidal: 2015 harmonic: 3341 Sorted by residual: dihedral pdb=" CA LEU R 352 " pdb=" C LEU R 352 " pdb=" N THR R 353 " pdb=" CA THR R 353 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" N LEU R 163 " pdb=" CA LEU R 163 " pdb=" CB LEU R 163 " pdb=" CG LEU R 163 " ideal model delta sinusoidal sigma weight residual -60.00 -119.97 59.97 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1078 0.044 - 0.088: 241 0.088 - 0.132: 68 0.132 - 0.175: 1 0.175 - 0.219: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " pdb=" CB1 2ML P 13 " pdb=" CB2 2ML P 13 " both_signs ideal model delta sigma weight residual False -2.84 -3.06 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA VAL N 93 " pdb=" N VAL N 93 " pdb=" C VAL N 93 " pdb=" CB VAL N 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1386 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO B 236 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 258 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 259 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 259 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 259 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 145 " 0.011 2.00e-02 2.50e+03 8.77e-03 1.54e+00 pdb=" CG TYR R 145 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR R 145 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR R 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 145 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR R 145 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 145 " 0.001 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 91 2.63 - 3.20: 7766 3.20 - 3.77: 13458 3.77 - 4.33: 19825 4.33 - 4.90: 32999 Nonbonded interactions: 74139 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.064 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.227 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.235 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.263 3.120 ... (remaining 74134 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 individual isotropic 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.950 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 0.051 9133 Z= 0.218 Angle : 0.495 6.124 12403 Z= 0.269 Chirality : 0.040 0.219 1389 Planarity : 0.003 0.042 1583 Dihedral : 11.963 79.981 3185 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.79 % Allowed : 6.39 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1127 helix: 0.11 (0.24), residues: 431 sheet: 0.05 (0.32), residues: 236 loop : -0.66 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS R 170 PHE 0.018 0.001 PHE N 108 TYR 0.021 0.001 TYR R 145 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 0.998 Fit side-chains REVERT: R 37 LYS cc_start: 0.6467 (mmtt) cc_final: 0.6226 (mmtt) REVERT: R 144 MET cc_start: 0.8492 (tmm) cc_final: 0.8177 (tmm) REVERT: R 231 MET cc_start: 0.8440 (ttp) cc_final: 0.8123 (ttt) REVERT: R 263 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7242 (m-10) REVERT: R 345 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: R 415 TRP cc_start: 0.6145 (t-100) cc_final: 0.5505 (t-100) REVERT: A 370 GLU cc_start: 0.7920 (pp20) cc_final: 0.7661 (tm-30) REVERT: A 390 GLN cc_start: 0.8817 (mt0) cc_final: 0.8317 (mt0) REVERT: B 101 MET cc_start: 0.9006 (mtp) cc_final: 0.8737 (mtp) REVERT: B 234 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.7783 (m-80) outliers start: 35 outliers final: 19 residues processed: 145 average time/residue: 1.1765 time to fit residues: 182.5694 Evaluate side-chains 120 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 263 PHE Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0770 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 293 GLN A 31 GLN A 357 HIS B 155 ASN B 259 GLN N 31 ASN N 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9133 Z= 0.169 Angle : 0.536 9.450 12403 Z= 0.286 Chirality : 0.041 0.160 1389 Planarity : 0.004 0.041 1583 Dihedral : 7.321 59.296 1289 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.79 % Allowed : 10.94 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1127 helix: 2.03 (0.24), residues: 427 sheet: 0.33 (0.34), residues: 235 loop : -0.55 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS A 220 PHE 0.018 0.001 PHE A 212 TYR 0.020 0.001 TYR R 145 ARG 0.006 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 0.958 Fit side-chains REVERT: R 277 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7609 (tt) REVERT: R 338 MET cc_start: 0.4303 (pmm) cc_final: 0.3770 (pmt) REVERT: R 345 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.5866 (m-80) REVERT: R 415 TRP cc_start: 0.5987 (t-100) cc_final: 0.5405 (t-100) REVERT: A 370 GLU cc_start: 0.7735 (pp20) cc_final: 0.7503 (pp20) REVERT: B 59 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8634 (t80) REVERT: B 101 MET cc_start: 0.8976 (mtp) cc_final: 0.8686 (mtp) REVERT: B 197 ARG cc_start: 0.7544 (mtp180) cc_final: 0.7279 (mtt-85) REVERT: B 234 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: B 325 MET cc_start: 0.8906 (tpp) cc_final: 0.8663 (tpp) REVERT: N 120 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7600 (tp40) outliers start: 35 outliers final: 18 residues processed: 123 average time/residue: 1.1326 time to fit residues: 149.9216 Evaluate side-chains 107 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 110 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 293 GLN A 31 GLN A 357 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9133 Z= 0.162 Angle : 0.503 8.790 12403 Z= 0.268 Chirality : 0.040 0.155 1389 Planarity : 0.003 0.040 1583 Dihedral : 6.768 59.490 1282 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.77 % Allowed : 11.59 % Favored : 83.64 % 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: 1.26 (0.26), residues: 1127 helix: 2.59 (0.24), residues: 426 sheet: 0.31 (0.34), residues: 231 loop : -0.54 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.022 0.001 TYR R 145 ARG 0.008 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 88 time to evaluate : 0.998 Fit side-chains REVERT: R 29 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.2901 (tpt) REVERT: R 145 TYR cc_start: 0.8086 (p90) cc_final: 0.6646 (p90) REVERT: R 231 MET cc_start: 0.8559 (ttt) cc_final: 0.8239 (ttt) REVERT: R 277 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7683 (tt) REVERT: R 345 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5832 (m-80) REVERT: R 415 TRP cc_start: 0.5859 (t-100) cc_final: 0.5278 (t-100) REVERT: A 370 GLU cc_start: 0.7727 (pp20) cc_final: 0.7465 (pp20) REVERT: B 101 MET cc_start: 0.8963 (mtp) cc_final: 0.8636 (mtp) REVERT: B 137 ARG cc_start: 0.7851 (tpp-160) cc_final: 0.7178 (tpt170) REVERT: B 197 ARG cc_start: 0.7512 (mtp180) cc_final: 0.7265 (mtt-85) REVERT: B 234 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 325 MET cc_start: 0.8902 (tpp) cc_final: 0.8572 (mpp) REVERT: N 80 TYR cc_start: 0.8112 (m-80) cc_final: 0.7711 (m-80) REVERT: N 120 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7639 (tp40) outliers start: 44 outliers final: 20 residues processed: 125 average time/residue: 0.9738 time to fit residues: 132.2654 Evaluate side-chains 109 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 404 ASN A 31 GLN A 357 HIS N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9133 Z= 0.327 Angle : 0.592 12.469 12403 Z= 0.307 Chirality : 0.043 0.161 1389 Planarity : 0.004 0.041 1583 Dihedral : 6.752 59.889 1277 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.98 % Allowed : 13.43 % Favored : 81.58 % 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: 1.12 (0.26), residues: 1127 helix: 2.39 (0.24), residues: 433 sheet: 0.22 (0.33), residues: 241 loop : -0.57 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 241 HIS 0.005 0.001 HIS R 170 PHE 0.025 0.002 PHE N 108 TYR 0.030 0.002 TYR R 145 ARG 0.009 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 88 time to evaluate : 1.013 Fit side-chains REVERT: R 29 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.3055 (tpt) REVERT: R 277 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7641 (tt) REVERT: R 338 MET cc_start: 0.4308 (pmm) cc_final: 0.3601 (pmt) REVERT: R 345 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5785 (m-80) REVERT: R 415 TRP cc_start: 0.5959 (t-100) cc_final: 0.5350 (t-100) REVERT: A 370 GLU cc_start: 0.7834 (pp20) cc_final: 0.7519 (pp20) REVERT: B 49 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7610 (mtp85) REVERT: B 153 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8163 (m-30) REVERT: B 234 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 258 ASP cc_start: 0.7555 (t0) cc_final: 0.7353 (t0) REVERT: B 325 MET cc_start: 0.9023 (tpp) cc_final: 0.8780 (tpp) REVERT: N 120 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7673 (tp40) outliers start: 46 outliers final: 24 residues processed: 125 average time/residue: 0.9904 time to fit residues: 134.2249 Evaluate side-chains 116 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 404 ASN A 31 GLN A 357 HIS N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9133 Z= 0.178 Angle : 0.505 9.522 12403 Z= 0.267 Chirality : 0.040 0.154 1389 Planarity : 0.003 0.044 1583 Dihedral : 6.522 59.468 1277 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.55 % Allowed : 14.84 % Favored : 80.61 % 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: 1.31 (0.26), residues: 1127 helix: 2.64 (0.24), residues: 433 sheet: 0.28 (0.34), residues: 237 loop : -0.55 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.015 0.001 PHE A 212 TYR 0.020 0.001 TYR R 145 ARG 0.010 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 87 time to evaluate : 0.904 Fit side-chains REVERT: R 29 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.3103 (tpt) REVERT: R 145 TYR cc_start: 0.8083 (p90) cc_final: 0.6736 (p90) REVERT: R 231 MET cc_start: 0.8575 (ttt) cc_final: 0.8187 (ttt) REVERT: R 277 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7742 (tt) REVERT: R 345 PHE cc_start: 0.6143 (OUTLIER) cc_final: 0.5758 (m-80) REVERT: R 415 TRP cc_start: 0.5828 (t-100) cc_final: 0.5223 (t-100) REVERT: A 370 GLU cc_start: 0.7801 (pp20) cc_final: 0.7407 (pp20) REVERT: B 49 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7642 (mtp85) REVERT: B 137 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7179 (tpt170) REVERT: B 197 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7290 (mtt-85) REVERT: B 234 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 325 MET cc_start: 0.8956 (tpp) cc_final: 0.8639 (mpp) REVERT: N 80 TYR cc_start: 0.8038 (m-80) cc_final: 0.7591 (m-80) REVERT: N 120 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7663 (tp40) outliers start: 42 outliers final: 20 residues processed: 122 average time/residue: 1.0078 time to fit residues: 133.2147 Evaluate side-chains 110 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN A 31 GLN A 357 HIS N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9133 Z= 0.185 Angle : 0.515 11.916 12403 Z= 0.268 Chirality : 0.040 0.149 1389 Planarity : 0.003 0.047 1583 Dihedral : 6.264 59.697 1275 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.12 % Allowed : 15.17 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1127 helix: 2.71 (0.24), residues: 433 sheet: 0.28 (0.34), residues: 238 loop : -0.55 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.016 0.001 PHE N 108 TYR 0.022 0.001 TYR R 145 ARG 0.011 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 89 time to evaluate : 1.103 Fit side-chains REVERT: R 29 MET cc_start: 0.5504 (OUTLIER) cc_final: 0.3157 (tpt) REVERT: R 145 TYR cc_start: 0.8071 (p90) cc_final: 0.6849 (p90) REVERT: R 231 MET cc_start: 0.8564 (ttt) cc_final: 0.8170 (ttt) REVERT: R 277 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7820 (tt) REVERT: R 338 MET cc_start: 0.4164 (pmm) cc_final: 0.1945 (mmm) REVERT: R 345 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5755 (m-80) REVERT: R 415 TRP cc_start: 0.5814 (t-100) cc_final: 0.5233 (t-100) REVERT: A 370 GLU cc_start: 0.7854 (pp20) cc_final: 0.7428 (pp20) REVERT: B 49 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7662 (mtp85) REVERT: B 137 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7173 (tpt170) REVERT: B 234 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 325 MET cc_start: 0.8955 (tpp) cc_final: 0.8637 (mpp) REVERT: N 80 TYR cc_start: 0.7958 (m-80) cc_final: 0.7410 (m-80) outliers start: 38 outliers final: 20 residues processed: 121 average time/residue: 1.0811 time to fit residues: 142.2354 Evaluate side-chains 109 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN A 31 GLN A 357 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9133 Z= 0.214 Angle : 0.529 12.633 12403 Z= 0.276 Chirality : 0.041 0.152 1389 Planarity : 0.003 0.045 1583 Dihedral : 6.307 59.761 1275 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.33 % Allowed : 15.06 % Favored : 80.61 % 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: 1.31 (0.26), residues: 1127 helix: 2.66 (0.24), residues: 433 sheet: 0.27 (0.34), residues: 238 loop : -0.56 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.016 0.001 PHE N 108 TYR 0.023 0.001 TYR R 145 ARG 0.013 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 88 time to evaluate : 1.041 Fit side-chains REVERT: R 29 MET cc_start: 0.5614 (OUTLIER) cc_final: 0.3325 (tpt) REVERT: R 145 TYR cc_start: 0.8090 (p90) cc_final: 0.6861 (p90) REVERT: R 231 MET cc_start: 0.8557 (ttt) cc_final: 0.8158 (ttt) REVERT: R 277 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7808 (tt) REVERT: R 345 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5732 (m-80) REVERT: R 415 TRP cc_start: 0.5815 (t-100) cc_final: 0.5227 (t-100) REVERT: A 370 GLU cc_start: 0.7829 (pp20) cc_final: 0.7385 (pp20) REVERT: B 49 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7633 (mtp85) REVERT: B 137 ARG cc_start: 0.7873 (tpp-160) cc_final: 0.7204 (tpt170) REVERT: B 234 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: N 80 TYR cc_start: 0.7910 (m-80) cc_final: 0.7398 (m-80) REVERT: N 120 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7664 (tp40) outliers start: 40 outliers final: 21 residues processed: 121 average time/residue: 1.0475 time to fit residues: 137.1311 Evaluate side-chains 108 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN A 31 GLN A 357 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9133 Z= 0.171 Angle : 0.510 12.511 12403 Z= 0.265 Chirality : 0.040 0.147 1389 Planarity : 0.003 0.055 1583 Dihedral : 6.174 59.948 1275 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.47 % Allowed : 15.82 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1127 helix: 2.75 (0.24), residues: 433 sheet: 0.23 (0.34), residues: 240 loop : -0.51 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 170 PHE 0.014 0.001 PHE A 212 TYR 0.020 0.001 TYR R 145 ARG 0.012 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 1.065 Fit side-chains REVERT: R 29 MET cc_start: 0.5645 (OUTLIER) cc_final: 0.3437 (tpt) REVERT: R 231 MET cc_start: 0.8557 (ttt) cc_final: 0.8136 (ttt) REVERT: R 277 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7800 (tt) REVERT: R 338 MET cc_start: 0.4158 (pmm) cc_final: 0.2061 (mmt) REVERT: R 345 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5761 (m-80) REVERT: R 415 TRP cc_start: 0.5935 (t-100) cc_final: 0.5303 (t-100) REVERT: A 370 GLU cc_start: 0.7828 (pp20) cc_final: 0.7374 (pp20) REVERT: B 49 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7661 (mtp85) REVERT: B 137 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7157 (tpt170) REVERT: B 234 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 325 MET cc_start: 0.8901 (tpp) cc_final: 0.8662 (mpp) REVERT: N 80 TYR cc_start: 0.7848 (m-80) cc_final: 0.7417 (m-80) REVERT: N 120 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7689 (tp40) outliers start: 32 outliers final: 17 residues processed: 114 average time/residue: 1.0828 time to fit residues: 132.9534 Evaluate side-chains 109 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 204 GLN R 293 GLN A 31 GLN A 357 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9133 Z= 0.179 Angle : 0.518 12.428 12403 Z= 0.269 Chirality : 0.040 0.147 1389 Planarity : 0.003 0.055 1583 Dihedral : 6.107 59.875 1273 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.58 % Allowed : 15.93 % 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: 1.40 (0.26), residues: 1127 helix: 2.76 (0.24), residues: 434 sheet: 0.27 (0.34), residues: 238 loop : -0.51 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 170 PHE 0.015 0.001 PHE N 108 TYR 0.019 0.001 TYR N 60 ARG 0.014 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 0.991 Fit side-chains REVERT: R 29 MET cc_start: 0.5665 (OUTLIER) cc_final: 0.3462 (tpt) REVERT: R 231 MET cc_start: 0.8563 (ttt) cc_final: 0.8149 (ttt) REVERT: R 277 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7816 (tt) REVERT: R 338 MET cc_start: 0.4175 (pmm) cc_final: 0.1693 (mmm) REVERT: R 345 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5758 (m-80) REVERT: R 415 TRP cc_start: 0.5934 (t-100) cc_final: 0.5325 (t-100) REVERT: A 370 GLU cc_start: 0.7809 (pp20) cc_final: 0.7370 (pp20) REVERT: B 49 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7657 (mtp85) REVERT: B 137 ARG cc_start: 0.7854 (tpp-160) cc_final: 0.7194 (tpt170) REVERT: B 234 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: B 325 MET cc_start: 0.8971 (tpp) cc_final: 0.8670 (mpp) REVERT: N 80 TYR cc_start: 0.7862 (m-80) cc_final: 0.7509 (m-80) outliers start: 33 outliers final: 19 residues processed: 114 average time/residue: 1.0844 time to fit residues: 133.0787 Evaluate side-chains 107 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 204 GLN R 293 GLN A 31 GLN A 357 HIS N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9133 Z= 0.212 Angle : 0.539 13.539 12403 Z= 0.279 Chirality : 0.041 0.150 1389 Planarity : 0.004 0.057 1583 Dihedral : 6.124 59.966 1270 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.25 % Allowed : 16.47 % Favored : 80.28 % 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: 1.35 (0.26), residues: 1127 helix: 2.70 (0.24), residues: 434 sheet: 0.24 (0.34), residues: 229 loop : -0.51 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.017 0.001 PHE N 108 TYR 0.022 0.001 TYR R 145 ARG 0.015 0.000 ARG R 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 0.903 Fit side-chains REVERT: R 29 MET cc_start: 0.5665 (OUTLIER) cc_final: 0.3456 (tpt) REVERT: R 231 MET cc_start: 0.8571 (ttt) cc_final: 0.8170 (ttt) REVERT: R 277 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7780 (tt) REVERT: R 338 MET cc_start: 0.4271 (pmm) cc_final: 0.1783 (mmm) REVERT: R 345 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5755 (m-80) REVERT: R 415 TRP cc_start: 0.5940 (t-100) cc_final: 0.5332 (t-100) REVERT: A 370 GLU cc_start: 0.7839 (pp20) cc_final: 0.7391 (pp20) REVERT: B 49 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7649 (mtp85) REVERT: B 137 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7202 (tpt170) REVERT: B 234 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: B 325 MET cc_start: 0.9007 (tpp) cc_final: 0.8705 (mpp) REVERT: N 80 TYR cc_start: 0.7870 (m-80) cc_final: 0.7625 (m-80) outliers start: 30 outliers final: 17 residues processed: 108 average time/residue: 1.0481 time to fit residues: 122.3699 Evaluate side-chains 102 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 204 GLN R 293 GLN R 404 ASN A 31 GLN A 357 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.192059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134056 restraints weight = 8932.428| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.08 r_work: 0.3330 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9133 Z= 0.216 Angle : 0.542 14.193 12403 Z= 0.280 Chirality : 0.041 0.151 1389 Planarity : 0.004 0.057 1583 Dihedral : 6.144 59.874 1270 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.93 % Allowed : 17.01 % Favored : 80.07 % 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: 1.36 (0.26), residues: 1127 helix: 2.69 (0.24), residues: 434 sheet: 0.26 (0.34), residues: 238 loop : -0.51 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.017 0.001 PHE N 108 TYR 0.022 0.001 TYR R 145 ARG 0.015 0.000 ARG R 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3323.16 seconds wall clock time: 59 minutes 5.27 seconds (3545.27 seconds total)