Starting phenix.real_space_refine on Wed Mar 4 02:52:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rw9_24711/03_2026/7rw9_24711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rw9_24711/03_2026/7rw9_24711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rw9_24711/03_2026/7rw9_24711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rw9_24711/03_2026/7rw9_24711.map" model { file = "/net/cci-nas-00/data/ceres_data/7rw9_24711/03_2026/7rw9_24711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rw9_24711/03_2026/7rw9_24711.cif" } resolution = 3.9 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= 0.010 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 42 5.16 5 C 6691 2.51 5 N 1781 2.21 5 O 1851 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10365 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4516 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 22, 'TRANS': 590} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 16, 'ASN:plan1': 5, 'GLU:plan': 23, 'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 219 Chain: "B" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 3806 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 26, 'TRANS': 540} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 710 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 571 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 34, 'ASN:plan1': 17, 'ARG:plan': 9, 'ASP:plan': 29, 'GLN:plan1': 11, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 419 Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 953 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 2, 'TRANS': 132} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 98 Chain: "S" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1090 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 140} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 2.18, per 1000 atoms: 0.21 Number of scatterers: 10365 At special positions: 0 Unit cell: (93.45, 100.57, 119.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1851 8.00 N 1781 7.00 C 6691 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: 0.86 Conformation dependent library (CDL) restraints added in 509.4 milliseconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 5 sheets defined 74.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.840A pdb=" N ALA A 14 " --> pdb=" O MET A 10 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.749A pdb=" N GLU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.652A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.718A pdb=" N ALA A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.746A pdb=" N MET A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.674A pdb=" N ILE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 188 through 195 removed outlier: 4.115A pdb=" N VAL A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.945A pdb=" N LYS A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.575A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.681A pdb=" N CYS A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.505A pdb=" N GLU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.689A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 401 through 415 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.823A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.895A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.672A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 removed outlier: 6.284A pdb=" N ASN A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.632A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 590 Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.576A pdb=" N LEU A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 620 removed outlier: 3.762A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 82 through 85 Processing helix chain 'B' and resid 86 through 95 removed outlier: 4.288A pdb=" N SER B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.646A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 131 removed outlier: 4.986A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.230A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N CYS B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.522A pdb=" N ASP B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 168 removed outlier: 4.057A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.567A pdb=" N ALA B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.590A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.850A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.502A pdb=" N VAL B 384 " --> pdb=" O CYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 401 Processing helix chain 'B' and resid 403 through 421 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.645A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 499 through 513 removed outlier: 4.000A pdb=" N VAL B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.801A pdb=" N LEU B 529 " --> pdb=" O ILE B 525 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 531 " --> pdb=" O TRP B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 542 Processing helix chain 'B' and resid 556 through 565 removed outlier: 4.017A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 3.827A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.518A pdb=" N PHE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.863A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 Processing helix chain 'M' and resid 97 through 103 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.566A pdb=" N LYS S 28 " --> pdb=" O ASP S 24 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 96 removed outlier: 3.669A pdb=" N TYR S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 138 removed outlier: 3.846A pdb=" N VAL S 131 " --> pdb=" O SER S 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 18 removed outlier: 7.024A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER M 17 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU M 5 " --> pdb=" O SER M 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.811A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.400A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS S 56 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL S 50 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 118 through 119 removed outlier: 3.673A pdb=" N LEU S 119 " --> pdb=" O GLU S 122 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2094 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: 1.63 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3397 1.34 - 1.46: 2037 1.46 - 1.58: 5045 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 10540 Sorted by residual: bond pdb=" CA ASP B 340 " pdb=" C ASP B 340 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.35e-02 5.49e+03 2.81e+00 bond pdb=" C ASN B 200 " pdb=" N PRO B 201 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.51e-02 4.39e+03 2.10e+00 bond pdb=" C ASP B 440 " pdb=" N GLU B 441 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.47e-02 4.63e+03 1.66e+00 bond pdb=" CA LYS A 24 " pdb=" C LYS A 24 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.12e-02 7.97e+03 1.59e+00 bond pdb=" CA LEU B 248 " pdb=" CB LEU B 248 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.62e-02 3.81e+03 1.25e+00 ... (remaining 10535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 14061 1.70 - 3.39: 302 3.39 - 5.09: 54 5.09 - 6.78: 12 6.78 - 8.48: 5 Bond angle restraints: 14434 Sorted by residual: angle pdb=" N ILE B 341 " pdb=" CA ILE B 341 " pdb=" C ILE B 341 " ideal model delta sigma weight residual 110.72 103.76 6.96 1.01e+00 9.80e-01 4.75e+01 angle pdb=" N LEU B 339 " pdb=" CA LEU B 339 " pdb=" C LEU B 339 " ideal model delta sigma weight residual 111.07 117.41 -6.34 1.07e+00 8.73e-01 3.51e+01 angle pdb=" N ILE B 341 " pdb=" CA ILE B 341 " pdb=" CB ILE B 341 " ideal model delta sigma weight residual 110.58 117.76 -7.18 1.50e+00 4.44e-01 2.29e+01 angle pdb=" C ARG A 399 " pdb=" N SER A 400 " pdb=" CA SER A 400 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N SER A 25 " pdb=" CA SER A 25 " pdb=" C SER A 25 " ideal model delta sigma weight residual 110.80 118.33 -7.53 2.13e+00 2.20e-01 1.25e+01 ... (remaining 14429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 5802 17.45 - 34.90: 415 34.90 - 52.36: 67 52.36 - 69.81: 10 69.81 - 87.26: 10 Dihedral angle restraints: 6304 sinusoidal: 1976 harmonic: 4328 Sorted by residual: dihedral pdb=" CA ARG A 399 " pdb=" C ARG A 399 " pdb=" N SER A 400 " pdb=" CA SER A 400 " ideal model delta harmonic sigma weight residual 180.00 145.56 34.44 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA CYS A 397 " pdb=" C CYS A 397 " pdb=" N ASP A 398 " pdb=" CA ASP A 398 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER A 458 " pdb=" C SER A 458 " pdb=" N GLU A 459 " pdb=" CA GLU A 459 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 6301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1481 0.051 - 0.101: 301 0.101 - 0.152: 42 0.152 - 0.203: 2 0.203 - 0.253: 2 Chirality restraints: 1828 Sorted by residual: chirality pdb=" CA LEU B 339 " pdb=" N LEU B 339 " pdb=" C LEU B 339 " pdb=" CB LEU B 339 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA SER A 25 " pdb=" N SER A 25 " pdb=" C SER A 25 " pdb=" CB SER A 25 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLU S 93 " pdb=" N GLU S 93 " pdb=" C GLU S 93 " pdb=" CB GLU S 93 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 1825 not shown) Planarity restraints: 1823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 58 " -0.010 2.00e-02 2.50e+03 1.27e-02 3.23e+00 pdb=" CG TYR A 58 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 58 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 58 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 58 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 58 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 58 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 603 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 604 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 217 " -0.013 2.00e-02 2.50e+03 1.12e-02 3.14e+00 pdb=" CG TRP B 217 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 217 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 217 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 217 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 217 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 217 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 217 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 217 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 217 " 0.001 2.00e-02 2.50e+03 ... (remaining 1820 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 172 2.69 - 3.24: 10656 3.24 - 3.80: 15874 3.80 - 4.35: 19203 4.35 - 4.90: 32343 Nonbonded interactions: 78248 Sorted by model distance: nonbonded pdb=" O LEU B 398 " pdb=" OG1 THR B 401 " model vdw 2.140 3.040 nonbonded pdb=" O ARG A 399 " pdb=" N ASN A 401 " model vdw 2.160 3.120 nonbonded pdb=" OH TYR A 247 " pdb=" OE2 GLU S 125 " model vdw 2.208 3.040 nonbonded pdb=" O HIS A 340 " pdb=" NH1 ARG A 346 " model vdw 2.214 3.120 nonbonded pdb=" O PRO A 219 " pdb=" OH TYR A 268 " model vdw 2.239 3.040 ... (remaining 78243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.870 Find NCS groups from input model: 0.050 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 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 0.031 10540 Z= 0.136 Angle : 0.628 8.476 14434 Z= 0.354 Chirality : 0.041 0.253 1828 Planarity : 0.003 0.045 1823 Dihedral : 13.176 87.262 3478 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.42 % Favored : 93.30 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.44 (0.23), residues: 1448 helix: 1.28 (0.17), residues: 969 sheet: -1.98 (0.74), residues: 46 loop : -1.72 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 127 TYR 0.031 0.002 TYR A 58 PHE 0.022 0.001 PHE M 118 TRP 0.031 0.002 TRP B 217 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00262 (10540) covalent geometry : angle 0.62833 (14434) hydrogen bonds : bond 0.13017 ( 710) hydrogen bonds : angle 5.43883 ( 2094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.6764 (mmt) cc_final: 0.6481 (mmt) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.0981 time to fit residues: 19.6914 Evaluate side-chains 84 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 369 HIS B 56 ASN B 305 ASN M 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.072142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057049 restraints weight = 52448.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058804 restraints weight = 28584.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059930 restraints weight = 19310.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.060752 restraints weight = 14787.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.061270 restraints weight = 12302.825| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10540 Z= 0.133 Angle : 0.604 9.549 14434 Z= 0.313 Chirality : 0.039 0.165 1828 Planarity : 0.003 0.033 1823 Dihedral : 4.688 41.010 1552 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.32 % Favored : 94.41 % Rotamer: Outliers : 1.06 % Allowed : 8.17 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.88 (0.23), residues: 1448 helix: 1.62 (0.17), residues: 984 sheet: -1.39 (0.75), residues: 45 loop : -1.74 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 10 TYR 0.024 0.001 TYR A 58 PHE 0.017 0.001 PHE M 81 TRP 0.012 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00285 (10540) covalent geometry : angle 0.60366 (14434) hydrogen bonds : bond 0.04014 ( 710) hydrogen bonds : angle 4.37463 ( 2094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: B 70 TYR cc_start: 0.8677 (m-10) cc_final: 0.7909 (m-80) REVERT: S 49 PHE cc_start: 0.9016 (m-10) cc_final: 0.8199 (m-10) REVERT: S 66 TYR cc_start: 0.7826 (m-10) cc_final: 0.7312 (m-10) REVERT: S 125 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8021 (tm-30) outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 0.0850 time to fit residues: 13.1767 Evaluate side-chains 83 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 73 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 0.0040 chunk 75 optimal weight: 9.9990 chunk 139 optimal weight: 0.0040 chunk 14 optimal weight: 0.0470 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.070582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.055403 restraints weight = 53384.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057056 restraints weight = 29072.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.058251 restraints weight = 19667.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058765 restraints weight = 14989.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.059492 restraints weight = 12876.000| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10540 Z= 0.143 Angle : 0.580 8.900 14434 Z= 0.301 Chirality : 0.039 0.163 1828 Planarity : 0.003 0.033 1823 Dihedral : 4.456 44.041 1550 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.97 % Favored : 94.75 % Rotamer: Outliers : 1.59 % Allowed : 10.40 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.08 (0.23), residues: 1448 helix: 1.81 (0.17), residues: 971 sheet: -1.04 (0.72), residues: 47 loop : -1.69 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 10 TYR 0.016 0.001 TYR A 463 PHE 0.014 0.001 PHE M 56 TRP 0.012 0.001 TRP A 462 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00311 (10540) covalent geometry : angle 0.58030 (14434) hydrogen bonds : bond 0.03818 ( 710) hydrogen bonds : angle 4.24268 ( 2094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8457 (m) cc_final: 0.8186 (m) REVERT: B 56 ASN cc_start: 0.9322 (t0) cc_final: 0.9037 (m110) REVERT: M 1 MET cc_start: 0.7160 (mmt) cc_final: 0.6753 (mmt) REVERT: S 49 PHE cc_start: 0.9059 (m-80) cc_final: 0.8186 (m-10) REVERT: S 125 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8024 (tm-30) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.0840 time to fit residues: 12.6126 Evaluate side-chains 88 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain M residue 23 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 46 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.071322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.056238 restraints weight = 52797.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.057920 restraints weight = 28701.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.059096 restraints weight = 19392.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.059771 restraints weight = 14809.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.060430 restraints weight = 12479.071| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10540 Z= 0.110 Angle : 0.547 10.077 14434 Z= 0.282 Chirality : 0.037 0.152 1828 Planarity : 0.003 0.034 1823 Dihedral : 4.297 45.000 1550 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.04 % Favored : 94.68 % Rotamer: Outliers : 1.80 % Allowed : 11.89 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.20 (0.23), residues: 1448 helix: 1.88 (0.17), residues: 975 sheet: -0.70 (0.74), residues: 47 loop : -1.67 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 10 TYR 0.015 0.001 TYR A 463 PHE 0.022 0.001 PHE M 118 TRP 0.012 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00222 (10540) covalent geometry : angle 0.54660 (14434) hydrogen bonds : bond 0.03495 ( 710) hydrogen bonds : angle 4.03261 ( 2094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8489 (m) cc_final: 0.8208 (m) REVERT: B 56 ASN cc_start: 0.9325 (t0) cc_final: 0.9069 (m110) REVERT: B 70 TYR cc_start: 0.9056 (m-10) cc_final: 0.8588 (m-80) REVERT: M 1 MET cc_start: 0.6932 (mmt) cc_final: 0.6442 (mmt) REVERT: S 49 PHE cc_start: 0.9007 (m-80) cc_final: 0.8119 (m-10) REVERT: S 125 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7993 (tm-30) outliers start: 17 outliers final: 12 residues processed: 97 average time/residue: 0.0762 time to fit residues: 11.4540 Evaluate side-chains 87 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 23 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 40.0000 chunk 114 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 134 optimal weight: 0.0370 chunk 59 optimal weight: 4.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.069749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054853 restraints weight = 53239.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056499 restraints weight = 28948.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.057692 restraints weight = 19556.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058204 restraints weight = 15037.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.058914 restraints weight = 12853.213| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10540 Z= 0.127 Angle : 0.551 11.288 14434 Z= 0.284 Chirality : 0.038 0.148 1828 Planarity : 0.003 0.035 1823 Dihedral : 4.282 46.111 1550 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.97 % Favored : 94.75 % Rotamer: Outliers : 2.34 % Allowed : 12.31 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.33 (0.23), residues: 1448 helix: 1.98 (0.17), residues: 973 sheet: -0.84 (0.73), residues: 55 loop : -1.57 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 10 TYR 0.012 0.001 TYR A 463 PHE 0.020 0.002 PHE M 81 TRP 0.012 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00277 (10540) covalent geometry : angle 0.55091 (14434) hydrogen bonds : bond 0.03506 ( 710) hydrogen bonds : angle 3.99632 ( 2094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8475 (m) cc_final: 0.8214 (m) REVERT: B 56 ASN cc_start: 0.9324 (t0) cc_final: 0.9083 (m-40) REVERT: B 70 TYR cc_start: 0.9060 (m-10) cc_final: 0.8533 (m-80) REVERT: M 65 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7984 (tt) REVERT: S 125 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7999 (tm-30) outliers start: 22 outliers final: 14 residues processed: 102 average time/residue: 0.0786 time to fit residues: 12.3946 Evaluate side-chains 89 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 0.0010 chunk 119 optimal weight: 0.9990 chunk 88 optimal weight: 0.0370 chunk 125 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.5468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.070609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055718 restraints weight = 53477.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.057413 restraints weight = 28846.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.058609 restraints weight = 19410.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.059286 restraints weight = 14752.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059959 restraints weight = 12389.106| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10540 Z= 0.106 Angle : 0.551 11.848 14434 Z= 0.279 Chirality : 0.037 0.146 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.188 45.482 1550 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.70 % Favored : 95.03 % Rotamer: Outliers : 2.44 % Allowed : 13.59 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.40 (0.23), residues: 1448 helix: 2.03 (0.17), residues: 973 sheet: -0.78 (0.72), residues: 55 loop : -1.55 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 42 TYR 0.012 0.001 TYR A 463 PHE 0.017 0.001 PHE S 67 TRP 0.013 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00222 (10540) covalent geometry : angle 0.55080 (14434) hydrogen bonds : bond 0.03348 ( 710) hydrogen bonds : angle 3.88525 ( 2094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8484 (m) cc_final: 0.8208 (m) REVERT: A 183 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7143 (p) REVERT: B 56 ASN cc_start: 0.9333 (t0) cc_final: 0.9089 (m-40) REVERT: B 70 TYR cc_start: 0.9082 (m-10) cc_final: 0.8576 (m-80) REVERT: S 42 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7640 (mtp85) REVERT: S 125 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7919 (tm-30) outliers start: 23 outliers final: 17 residues processed: 102 average time/residue: 0.0757 time to fit residues: 12.1188 Evaluate side-chains 97 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.071791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056670 restraints weight = 52570.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058415 restraints weight = 27884.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059699 restraints weight = 18497.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.060543 restraints weight = 13873.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.060948 restraints weight = 11331.106| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10540 Z= 0.114 Angle : 0.550 11.730 14434 Z= 0.280 Chirality : 0.038 0.205 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.160 45.340 1550 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.77 % Favored : 94.96 % Rotamer: Outliers : 2.65 % Allowed : 14.12 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.44 (0.23), residues: 1448 helix: 2.05 (0.17), residues: 973 sheet: -0.83 (0.71), residues: 55 loop : -1.49 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 42 TYR 0.012 0.001 TYR A 418 PHE 0.018 0.001 PHE S 87 TRP 0.012 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00246 (10540) covalent geometry : angle 0.55009 (14434) hydrogen bonds : bond 0.03364 ( 710) hydrogen bonds : angle 3.89284 ( 2094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8463 (m) cc_final: 0.8199 (m) REVERT: A 183 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7249 (p) REVERT: B 70 TYR cc_start: 0.9071 (m-10) cc_final: 0.8591 (m-80) REVERT: S 42 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7541 (mtp85) REVERT: S 125 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7961 (tm-30) outliers start: 25 outliers final: 20 residues processed: 103 average time/residue: 0.0803 time to fit residues: 12.9565 Evaluate side-chains 97 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 66 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS B 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.070179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055215 restraints weight = 53075.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056881 restraints weight = 29073.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.058061 restraints weight = 19743.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058917 restraints weight = 15106.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.059265 restraints weight = 12428.722| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10540 Z= 0.112 Angle : 0.556 12.138 14434 Z= 0.283 Chirality : 0.037 0.197 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.140 45.146 1550 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.56 % Favored : 95.17 % Rotamer: Outliers : 2.34 % Allowed : 14.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.51 (0.23), residues: 1448 helix: 2.10 (0.17), residues: 971 sheet: -0.85 (0.70), residues: 55 loop : -1.43 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 10 TYR 0.011 0.001 TYR A 463 PHE 0.025 0.001 PHE M 81 TRP 0.013 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00243 (10540) covalent geometry : angle 0.55557 (14434) hydrogen bonds : bond 0.03347 ( 710) hydrogen bonds : angle 3.87758 ( 2094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8482 (m) cc_final: 0.8222 (m) REVERT: A 183 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7240 (p) REVERT: A 412 TYR cc_start: 0.8795 (t80) cc_final: 0.8570 (t80) REVERT: B 70 TYR cc_start: 0.9128 (m-10) cc_final: 0.8615 (m-80) REVERT: B 175 MET cc_start: 0.8520 (pmm) cc_final: 0.7725 (ttm) REVERT: S 42 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7587 (mtp85) REVERT: S 125 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8003 (tm-30) outliers start: 22 outliers final: 20 residues processed: 99 average time/residue: 0.0771 time to fit residues: 11.9458 Evaluate side-chains 101 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 118 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.070060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055097 restraints weight = 53401.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056772 restraints weight = 29106.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.057982 restraints weight = 19634.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.058607 restraints weight = 15006.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059279 restraints weight = 12670.717| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10540 Z= 0.108 Angle : 0.558 12.342 14434 Z= 0.282 Chirality : 0.038 0.201 1828 Planarity : 0.003 0.037 1823 Dihedral : 4.120 44.885 1550 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.63 % Favored : 95.10 % Rotamer: Outliers : 2.34 % Allowed : 14.44 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.51 (0.23), residues: 1448 helix: 2.09 (0.17), residues: 972 sheet: -0.73 (0.71), residues: 54 loop : -1.43 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 10 TYR 0.013 0.001 TYR A 418 PHE 0.029 0.001 PHE S 107 TRP 0.013 0.001 TRP A 462 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00233 (10540) covalent geometry : angle 0.55828 (14434) hydrogen bonds : bond 0.03324 ( 710) hydrogen bonds : angle 3.86180 ( 2094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8446 (m) cc_final: 0.8185 (m) REVERT: A 183 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7257 (p) REVERT: A 412 TYR cc_start: 0.8784 (t80) cc_final: 0.8557 (t80) REVERT: B 70 TYR cc_start: 0.9111 (m-10) cc_final: 0.8573 (m-80) REVERT: B 175 MET cc_start: 0.8493 (pmm) cc_final: 0.7691 (ttm) REVERT: M 116 LEU cc_start: 0.7792 (tp) cc_final: 0.7591 (tt) REVERT: S 9 ASN cc_start: 0.8402 (p0) cc_final: 0.8028 (p0) REVERT: S 42 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7698 (mtp85) REVERT: S 125 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7973 (tm-30) outliers start: 22 outliers final: 16 residues processed: 100 average time/residue: 0.0693 time to fit residues: 10.9139 Evaluate side-chains 95 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 0.2980 chunk 121 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.071806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055139 restraints weight = 52003.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056874 restraints weight = 28638.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058155 restraints weight = 19571.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058993 restraints weight = 15050.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.059492 restraints weight = 12598.328| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10540 Z= 0.117 Angle : 0.568 12.197 14434 Z= 0.288 Chirality : 0.038 0.200 1828 Planarity : 0.003 0.037 1823 Dihedral : 4.193 45.015 1550 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.49 % Favored : 95.23 % Rotamer: Outliers : 2.02 % Allowed : 15.39 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.46 (0.23), residues: 1448 helix: 2.05 (0.17), residues: 975 sheet: -0.84 (0.71), residues: 55 loop : -1.45 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 42 TYR 0.009 0.001 TYR A 463 PHE 0.019 0.001 PHE M 81 TRP 0.012 0.001 TRP A 462 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00257 (10540) covalent geometry : angle 0.56776 (14434) hydrogen bonds : bond 0.03343 ( 710) hydrogen bonds : angle 3.90119 ( 2094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8463 (m) cc_final: 0.8189 (m) REVERT: A 183 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7314 (p) REVERT: A 412 TYR cc_start: 0.8823 (t80) cc_final: 0.8603 (t80) REVERT: B 70 TYR cc_start: 0.9112 (m-10) cc_final: 0.8622 (m-80) REVERT: B 175 MET cc_start: 0.8516 (pmm) cc_final: 0.7723 (ttm) REVERT: S 9 ASN cc_start: 0.8308 (p0) cc_final: 0.8108 (p0) REVERT: S 42 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7686 (mtp85) REVERT: S 125 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7961 (tm-30) outliers start: 19 outliers final: 17 residues processed: 97 average time/residue: 0.0722 time to fit residues: 11.0909 Evaluate side-chains 98 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.069537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054608 restraints weight = 53523.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056274 restraints weight = 29176.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.057461 restraints weight = 19784.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.058047 restraints weight = 15158.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058720 restraints weight = 12877.690| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10540 Z= 0.120 Angle : 0.584 17.133 14434 Z= 0.293 Chirality : 0.038 0.199 1828 Planarity : 0.003 0.037 1823 Dihedral : 4.198 44.814 1550 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.03 % Rotamer: Outliers : 1.91 % Allowed : 15.39 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.46 (0.23), residues: 1448 helix: 2.02 (0.17), residues: 974 sheet: -0.88 (0.69), residues: 55 loop : -1.36 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 42 TYR 0.025 0.001 TYR M 20 PHE 0.019 0.001 PHE M 81 TRP 0.012 0.001 TRP A 462 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00265 (10540) covalent geometry : angle 0.58416 (14434) hydrogen bonds : bond 0.03389 ( 710) hydrogen bonds : angle 3.90536 ( 2094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.31 seconds wall clock time: 27 minutes 53.55 seconds (1673.55 seconds total)