Starting phenix.real_space_refine on Tue Aug 4 22:55:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ycf_72769/08_2026/9ycf_72769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ycf_72769/08_2026/9ycf_72769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ycf_72769/08_2026/9ycf_72769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ycf_72769/08_2026/9ycf_72769.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ycf_72769/08_2026/9ycf_72769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ycf_72769/08_2026/9ycf_72769.map" } resolution = 4.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 3 Type Number sf(0) Gaussians C 4199 2.51 5 N 1423 2.21 5 O 1423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7045 Number of models: 1 Model: "" Number of chains: 4 Chain: "G" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 274 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 5, 'HIS:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2257 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 414} Link IDs: {'PTRANS': 13, 'TRANS': 442} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1686 Unresolved non-hydrogen dihedrals: 1060 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 19, 'ASN:plan1': 36, 'GLU:plan': 23, 'PHE:plan': 12, 'TYR:plan': 18, 'ARG:plan': 10, 'TRP:plan': 3, 'ASP:plan': 19, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 618 Chain: "B" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2257 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 414} Link IDs: {'PTRANS': 13, 'TRANS': 442} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1686 Unresolved non-hydrogen dihedrals: 1060 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 19, 'ASN:plan1': 36, 'GLU:plan': 23, 'PHE:plan': 12, 'TYR:plan': 18, 'ARG:plan': 10, 'TRP:plan': 3, 'ASP:plan': 19, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 618 Chain: "C" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2257 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 414} Link IDs: {'PTRANS': 13, 'TRANS': 442} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1686 Unresolved non-hydrogen dihedrals: 1060 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 19, 'ASN:plan1': 36, 'GLU:plan': 23, 'PHE:plan': 12, 'TYR:plan': 18, 'ARG:plan': 10, 'TRP:plan': 3, 'ASP:plan': 19, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 618 Time building chain proxies: 1.90, per 1000 atoms: 0.27 Number of scatterers: 7045 At special positions: 0 Unit cell: (136.29, 96.465, 87.615, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1423 8.00 N 1423 7.00 C 4199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 517.3 milliseconds 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 15 sheets defined 39.3% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'G' and resid 21 through 38 removed outlier: 4.125A pdb=" N PHE G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 53 removed outlier: 3.549A pdb=" N VAL G 48 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS G 49 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 50 " --> pdb=" O ARG G 46 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 97 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 160 through 174 removed outlier: 3.786A pdb=" N LEU A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.347A pdb=" N ASN A 208 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS A 209 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN A 210 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 240 removed outlier: 3.883A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.705A pdb=" N ASN A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.696A pdb=" N PHE A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.847A pdb=" N VAL A 482 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 515 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 73 through 97 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 160 through 172 Processing helix chain 'B' and resid 195 through 201 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 216 through 240 removed outlier: 4.114A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 492 through 516 removed outlier: 3.863A pdb=" N ILE B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 97 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.958A pdb=" N VAL C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.733A pdb=" N VAL C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 241 removed outlier: 4.358A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 285 removed outlier: 3.540A pdb=" N GLN C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 removed outlier: 4.067A pdb=" N ASN C 331 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.674A pdb=" N ASN C 371 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.148A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'C' and resid 492 through 514 Processing helix chain 'C' and resid 515 through 518 Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.718A pdb=" N THR A 311 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 44 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LYS A 315 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS A 42 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS A 317 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL A 40 " --> pdb=" O HIS A 317 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 179 removed outlier: 4.916A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 51 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 361 Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA7, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.924A pdb=" N ILE A 432 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 33 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 187 through 194 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 187 through 194 current: chain 'B' and resid 296 through 318 removed outlier: 3.954A pdb=" N TRP B 341 " --> pdb=" O PHE B 352 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 348 through 352 current: chain 'B' and resid 365 through 368 Processing sheet with id=AA9, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB1, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.844A pdb=" N GLY B 411 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 430 through 434 removed outlier: 7.229A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 450 " --> pdb=" O TYR B 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 33 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 60 current: chain 'C' and resid 187 through 194 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 187 through 194 current: chain 'C' and resid 286 through 289 removed outlier: 3.681A pdb=" N TYR C 286 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 340 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.915A pdb=" N LEU C 321 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 405 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 430 through 435 removed outlier: 6.897A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1424 1.29 - 1.36: 1415 1.36 - 1.42: 0 1.42 - 1.48: 1423 1.48 - 1.55: 2776 Bond restraints: 7038 Sorted by residual: bond pdb=" C GLN C 302 " pdb=" N LEU C 303 " ideal model delta sigma weight residual 1.327 1.284 0.043 2.86e-02 1.22e+03 2.21e+00 bond pdb=" C THR A 318 " pdb=" N SER A 319 " ideal model delta sigma weight residual 1.323 1.301 0.021 1.64e-02 3.72e+03 1.66e+00 bond pdb=" C PRO B 246 " pdb=" O PRO B 246 " ideal model delta sigma weight residual 1.235 1.227 0.008 7.90e-03 1.60e+04 1.05e+00 bond pdb=" N VAL A 365 " pdb=" CA VAL A 365 " ideal model delta sigma weight residual 1.459 1.447 0.012 1.25e-02 6.40e+03 9.00e-01 bond pdb=" CA PRO C 265 " pdb=" C PRO C 265 " ideal model delta sigma weight residual 1.527 1.517 0.010 1.07e-02 8.73e+03 8.89e-01 ... (remaining 7033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 9463 1.23 - 2.46: 308 2.46 - 3.69: 24 3.69 - 4.91: 3 4.91 - 6.14: 2 Bond angle restraints: 9800 Sorted by residual: angle pdb=" C SER A 362 " pdb=" CA SER A 362 " pdb=" CB SER A 362 " ideal model delta sigma weight residual 116.54 110.40 6.14 1.15e+00 7.56e-01 2.85e+01 angle pdb=" CA SER A 362 " pdb=" C SER A 362 " pdb=" N ASN A 363 " ideal model delta sigma weight residual 119.52 117.15 2.37 7.90e-01 1.60e+00 8.96e+00 angle pdb=" N ILE A 148 " pdb=" CA ILE A 148 " pdb=" C ILE A 148 " ideal model delta sigma weight residual 113.10 110.34 2.76 9.70e-01 1.06e+00 8.12e+00 angle pdb=" N VAL B 482 " pdb=" CA VAL B 482 " pdb=" C VAL B 482 " ideal model delta sigma weight residual 113.20 110.49 2.71 9.60e-01 1.09e+00 7.99e+00 angle pdb=" C GLN B 462 " pdb=" N GLU B 463 " pdb=" CA GLU B 463 " ideal model delta sigma weight residual 121.56 125.83 -4.27 1.56e+00 4.11e-01 7.49e+00 ... (remaining 9795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.41: 3686 4.41 - 8.83: 348 8.83 - 13.24: 70 13.24 - 17.65: 15 17.65 - 22.07: 3 Dihedral angle restraints: 4122 sinusoidal: 0 harmonic: 4122 Sorted by residual: dihedral pdb=" CA GLN B 462 " pdb=" C GLN B 462 " pdb=" N GLU B 463 " pdb=" CA GLU B 463 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR A 100 " pdb=" C THR A 100 " pdb=" N THR A 101 " pdb=" CA THR A 101 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TYR A 250 " pdb=" C TYR A 250 " pdb=" N MET A 251 " pdb=" CA MET A 251 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 4119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 762 0.027 - 0.054: 303 0.054 - 0.081: 173 0.081 - 0.108: 89 0.108 - 0.135: 26 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA ILE B 57 " pdb=" N ILE B 57 " pdb=" C ILE B 57 " pdb=" CB ILE B 57 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE C 214 " pdb=" N ILE C 214 " pdb=" C ILE C 214 " pdb=" CB ILE C 214 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE A 59 " pdb=" N ILE A 59 " pdb=" C ILE A 59 " pdb=" CB ILE A 59 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1350 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 150 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.09e+00 pdb=" C SER C 150 " -0.018 2.00e-02 2.50e+03 pdb=" O SER C 150 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY C 151 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 149 " -0.005 2.00e-02 2.50e+03 9.50e-03 9.03e-01 pdb=" C ALA C 149 " 0.016 2.00e-02 2.50e+03 pdb=" O ALA C 149 " -0.006 2.00e-02 2.50e+03 pdb=" N SER C 150 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 101 " -0.004 2.00e-02 2.50e+03 7.99e-03 6.38e-01 pdb=" C THR C 101 " 0.014 2.00e-02 2.50e+03 pdb=" O THR C 101 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA C 102 " -0.005 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 5144 3.08 - 3.53: 7389 3.53 - 3.99: 8112 3.99 - 4.44: 9879 4.44 - 4.90: 14182 Nonbonded interactions: 44706 Sorted by model distance: nonbonded pdb=" N SER A 398 " pdb=" O SER A 398 " model vdw 2.621 2.496 nonbonded pdb=" N TYR C 250 " pdb=" N MET C 251 " model vdw 2.624 2.560 nonbonded pdb=" N SER A 348 " pdb=" O SER A 348 " model vdw 2.625 2.496 nonbonded pdb=" N ILE A 148 " pdb=" N ALA A 149 " model vdw 2.625 2.560 nonbonded pdb=" N SER B 404 " pdb=" O SER B 404 " model vdw 2.629 2.496 ... (remaining 44701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.00 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.002 0.043 7038 Z= 0.176 Angle : 0.525 6.143 9800 Z= 0.350 Chirality : 0.043 0.135 1353 Planarity : 0.002 0.010 1416 Dihedral : 4.657 22.067 1416 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.23), residues: 1409 helix: 1.68 (0.24), residues: 482 sheet: -1.23 (0.28), residues: 290 loop : -1.53 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.18 ( 7038) covalent geometry : angle 0.52548 / 0.35 ( 9800) hydrogen bonds : bond 0.15708 / 12.02 ( 497) hydrogen bonds : angle 7.65956 / 5.77 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0240 time to fit residues: 1.2443 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.0770 chunk 55 optimal weight: 9.9990 overall best weight: 3.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.030345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.023889 restraints weight = 112396.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.024101 restraints weight = 98403.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.024303 restraints weight = 88877.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.024440 restraints weight = 81670.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.024577 restraints weight = 75615.046| |-----------------------------------------------------------------------------| r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7038 Z= 0.213 Angle : 0.468 4.065 9800 Z= 0.303 Chirality : 0.043 0.141 1353 Planarity : 0.002 0.012 1416 Dihedral : 4.673 21.440 1416 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1409 helix: 2.36 (0.24), residues: 467 sheet: -1.59 (0.26), residues: 325 loop : -1.35 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.21 ( 7038) covalent geometry : angle 0.46829 / 0.30 ( 9800) hydrogen bonds : bond 0.03785 / 2.88 ( 497) hydrogen bonds : angle 5.76715 / 4.42 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0280 time to fit residues: 1.3344 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 30.0000 chunk 80 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 53 optimal weight: 50.0000 overall best weight: 10.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.028966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.022817 restraints weight = 118564.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.023064 restraints weight = 102003.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.023245 restraints weight = 90788.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.023413 restraints weight = 83178.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.023534 restraints weight = 77322.464| |-----------------------------------------------------------------------------| r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 7038 Z= 0.508 Angle : 0.777 8.482 9800 Z= 0.514 Chirality : 0.044 0.156 1353 Planarity : 0.005 0.019 1416 Dihedral : 6.752 29.899 1416 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.43 % Favored : 88.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.21), residues: 1409 helix: -0.30 (0.22), residues: 464 sheet: -2.42 (0.26), residues: 281 loop : -2.25 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.51 ( 7038) covalent geometry : angle 0.77714 / 0.51 ( 9800) hydrogen bonds : bond 0.07046 / 5.38 ( 497) hydrogen bonds : angle 8.12160 / 6.23 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0315 time to fit residues: 1.6189 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 92 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.0020 chunk 72 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.029157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.022867 restraints weight = 115249.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.023115 restraints weight = 99717.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.023282 restraints weight = 89012.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.023422 restraints weight = 81853.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.023577 restraints weight = 76130.421| |-----------------------------------------------------------------------------| r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7038 Z= 0.208 Angle : 0.486 4.546 9800 Z= 0.312 Chirality : 0.043 0.140 1353 Planarity : 0.002 0.010 1416 Dihedral : 5.107 23.232 1416 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1409 helix: 1.25 (0.24), residues: 460 sheet: -2.55 (0.25), residues: 319 loop : -1.87 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.21 ( 7038) covalent geometry : angle 0.48577 / 0.31 ( 9800) hydrogen bonds : bond 0.03762 / 2.86 ( 497) hydrogen bonds : angle 6.29663 / 4.81 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0261 time to fit residues: 1.3250 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 97 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 110 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 62 optimal weight: 40.0000 chunk 7 optimal weight: 30.0000 overall best weight: 10.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.028639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.022517 restraints weight = 120282.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.022783 restraints weight = 102952.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.022982 restraints weight = 91037.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.023132 restraints weight = 82614.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.023282 restraints weight = 75786.452| |-----------------------------------------------------------------------------| r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 7038 Z= 0.494 Angle : 0.774 9.004 9800 Z= 0.510 Chirality : 0.045 0.163 1353 Planarity : 0.005 0.020 1416 Dihedral : 6.907 31.262 1416 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.20), residues: 1409 helix: -0.74 (0.22), residues: 467 sheet: -3.17 (0.28), residues: 224 loop : -2.69 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.49 ( 7038) covalent geometry : angle 0.77445 / 0.51 ( 9800) hydrogen bonds : bond 0.07016 / 5.35 ( 497) hydrogen bonds : angle 8.42537 / 6.48 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0300 time to fit residues: 1.5360 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 chunk 76 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 121 optimal weight: 8.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.028765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.022575 restraints weight = 118011.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.022839 restraints weight = 101589.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.023038 restraints weight = 89747.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.023176 restraints weight = 81503.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.023330 restraints weight = 75272.636| |-----------------------------------------------------------------------------| r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7038 Z= 0.313 Angle : 0.585 6.260 9800 Z= 0.381 Chirality : 0.043 0.142 1353 Planarity : 0.003 0.014 1416 Dihedral : 5.819 28.813 1416 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.21), residues: 1409 helix: 0.05 (0.23), residues: 466 sheet: -3.35 (0.27), residues: 249 loop : -2.46 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.31 ( 7038) covalent geometry : angle 0.58520 / 0.38 ( 9800) hydrogen bonds : bond 0.04874 / 3.71 ( 497) hydrogen bonds : angle 7.29467 / 5.61 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0242 time to fit residues: 1.3163 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 30.0000 chunk 105 optimal weight: 0.0980 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 76 optimal weight: 40.0000 chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 50.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.028806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.022613 restraints weight = 116556.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.022865 restraints weight = 99972.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.023065 restraints weight = 88699.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.023229 restraints weight = 80634.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.023330 restraints weight = 74800.582| |-----------------------------------------------------------------------------| r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7038 Z= 0.267 Angle : 0.538 5.840 9800 Z= 0.347 Chirality : 0.043 0.145 1353 Planarity : 0.003 0.011 1416 Dihedral : 5.339 26.836 1416 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.22), residues: 1409 helix: 0.76 (0.23), residues: 468 sheet: -3.54 (0.27), residues: 247 loop : -2.35 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.27 ( 7038) covalent geometry : angle 0.53821 / 0.35 ( 9800) hydrogen bonds : bond 0.04285 / 3.26 ( 497) hydrogen bonds : angle 6.85654 / 5.29 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0316 time to fit residues: 1.6082 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 95 optimal weight: 0.0470 chunk 109 optimal weight: 7.9990 chunk 123 optimal weight: 30.0000 chunk 79 optimal weight: 0.8980 overall best weight: 4.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.028985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.022715 restraints weight = 117192.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.022969 restraints weight = 100746.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.023173 restraints weight = 89371.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.023323 restraints weight = 81287.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.023447 restraints weight = 75750.253| |-----------------------------------------------------------------------------| r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7038 Z= 0.212 Angle : 0.482 5.052 9800 Z= 0.311 Chirality : 0.043 0.141 1353 Planarity : 0.002 0.012 1416 Dihedral : 4.955 24.322 1416 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.22), residues: 1409 helix: 1.45 (0.24), residues: 471 sheet: -3.42 (0.26), residues: 265 loop : -2.24 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.21 ( 7038) covalent geometry : angle 0.48232 / 0.31 ( 9800) hydrogen bonds : bond 0.03689 / 2.80 ( 497) hydrogen bonds : angle 6.35983 / 4.91 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.164 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0270 time to fit residues: 1.3015 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 101 optimal weight: 0.7980 chunk 128 optimal weight: 50.0000 chunk 45 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 127 optimal weight: 0.0970 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.028830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.022639 restraints weight = 117170.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.022860 restraints weight = 100856.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.023081 restraints weight = 90294.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.023238 restraints weight = 82214.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.023367 restraints weight = 76213.538| |-----------------------------------------------------------------------------| r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7038 Z= 0.292 Angle : 0.553 6.780 9800 Z= 0.359 Chirality : 0.043 0.147 1353 Planarity : 0.003 0.013 1416 Dihedral : 5.378 26.270 1416 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.22), residues: 1409 helix: 1.10 (0.24), residues: 468 sheet: -3.47 (0.29), residues: 225 loop : -2.48 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.29 ( 7038) covalent geometry : angle 0.55315 / 0.36 ( 9800) hydrogen bonds : bond 0.04574 / 3.48 ( 497) hydrogen bonds : angle 6.93062 / 5.36 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.244 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0260 time to fit residues: 1.3817 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 131 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 109 optimal weight: 8.9990 chunk 95 optimal weight: 0.0070 overall best weight: 1.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.029413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.022998 restraints weight = 113753.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.023221 restraints weight = 98172.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.023449 restraints weight = 88058.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.023614 restraints weight = 80330.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.023728 restraints weight = 74489.494| |-----------------------------------------------------------------------------| r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.016 7038 Z= 0.099 Angle : 0.395 4.138 9800 Z= 0.250 Chirality : 0.043 0.138 1353 Planarity : 0.002 0.009 1416 Dihedral : 4.191 20.249 1416 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.24), residues: 1409 helix: 2.69 (0.25), residues: 473 sheet: -3.21 (0.26), residues: 283 loop : -1.97 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00135 / 0.10 ( 7038) covalent geometry : angle 0.39477 / 0.25 ( 9800) hydrogen bonds : bond 0.02570 / 1.94 ( 497) hydrogen bonds : angle 5.29509 / 4.08 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0258 time to fit residues: 1.3429 Evaluate side-chains 21 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 42 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 33 optimal weight: 40.0000 chunk 76 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 25 optimal weight: 0.0670 chunk 94 optimal weight: 20.0000 chunk 19 optimal weight: 0.0370 chunk 95 optimal weight: 0.9990 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.029208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.022844 restraints weight = 113939.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.023092 restraints weight = 98543.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.023244 restraints weight = 87962.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.023442 restraints weight = 81008.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.023549 restraints weight = 75322.158| |-----------------------------------------------------------------------------| r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7038 Z= 0.151 Angle : 0.412 4.783 9800 Z= 0.263 Chirality : 0.043 0.138 1353 Planarity : 0.002 0.009 1416 Dihedral : 4.191 22.260 1416 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.24), residues: 1409 helix: 3.06 (0.24), residues: 461 sheet: -3.15 (0.27), residues: 273 loop : -1.98 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.15 ( 7038) covalent geometry : angle 0.41243 / 0.26 ( 9800) hydrogen bonds : bond 0.02970 / 2.25 ( 497) hydrogen bonds : angle 5.43538 / 4.20 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1001.68 seconds wall clock time: 17 minutes 48.19 seconds (1068.19 seconds total)