Starting phenix.real_space_refine on Mon Jul 28 11:18:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rw9_24711/07_2025/7rw9_24711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rw9_24711/07_2025/7rw9_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_24711/07_2025/7rw9_24711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rw9_24711/07_2025/7rw9_24711.map" model { file = "/net/cci-nas-00/data/ceres_data/7rw9_24711/07_2025/7rw9_24711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rw9_24711/07_2025/7rw9_24711.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ASP:plan': 16, 'ASN:plan1': 5, 'HIS:plan': 2, 'GLU:plan': 23, 'ARG:plan': 10} 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: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 17, 'ASP:plan': 29, 'PHE:plan': 3, 'GLU:plan': 34, 'ARG:plan': 9} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} 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, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 6.89, per 1000 atoms: 0.66 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.35 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: 3.26 Time building geometry restraints manager: 3.64 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: 2.980 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.200 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (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 TRP 0.031 0.002 TRP B 217 HIS 0.005 0.001 HIS A 200 PHE 0.022 0.001 PHE M 118 TYR 0.031 0.002 TYR A 58 ARG 0.007 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.13017 ( 710) hydrogen bonds : angle 5.43883 ( 2094) covalent geometry : bond 0.00262 (10540) covalent geometry : angle 0.62833 (14434) *********************** 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 : 1.120 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: 0.2219 time to fit residues: 44.4492 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 : 1.116 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.0770 chunk 58 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 403 GLN B 305 ASN S 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.071753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056772 restraints weight = 52324.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058429 restraints weight = 28336.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.059283 restraints weight = 19164.535| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10540 Z= 0.138 Angle : 0.606 9.441 14434 Z= 0.315 Chirality : 0.039 0.167 1828 Planarity : 0.003 0.032 1823 Dihedral : 4.704 41.309 1552 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.11 % Favored : 94.61 % Rotamer: Outliers : 1.06 % Allowed : 8.28 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1448 helix: 1.62 (0.17), residues: 985 sheet: -1.38 (0.75), residues: 45 loop : -1.75 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.003 0.001 HIS B 149 PHE 0.016 0.001 PHE M 81 TYR 0.024 0.001 TYR A 58 ARG 0.006 0.001 ARG S 10 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 710) hydrogen bonds : angle 4.37249 ( 2094) covalent geometry : bond 0.00296 (10540) covalent geometry : angle 0.60618 (14434) *********************** 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 103 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 TYR cc_start: 0.8714 (m-10) cc_final: 0.7948 (m-80) REVERT: S 49 PHE cc_start: 0.9014 (m-80) cc_final: 0.8187 (m-10) REVERT: S 66 TYR cc_start: 0.7854 (m-10) cc_final: 0.7306 (m-10) REVERT: S 125 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8057 (tm-30) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.2004 time to fit residues: 30.8094 Evaluate side-chains 85 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 77 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.069987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.054869 restraints weight = 53489.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056383 restraints weight = 29199.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057642 restraints weight = 20076.500| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10540 Z= 0.154 Angle : 0.585 8.781 14434 Z= 0.304 Chirality : 0.039 0.165 1828 Planarity : 0.003 0.033 1823 Dihedral : 4.474 44.677 1550 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.04 % Favored : 94.68 % Rotamer: Outliers : 1.70 % Allowed : 10.72 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1448 helix: 1.83 (0.17), residues: 969 sheet: -1.00 (0.73), residues: 47 loop : -1.65 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.014 0.001 PHE M 81 TYR 0.016 0.001 TYR A 463 ARG 0.006 0.000 ARG S 10 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 710) hydrogen bonds : angle 4.26557 ( 2094) covalent geometry : bond 0.00340 (10540) covalent geometry : angle 0.58471 (14434) *********************** 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 100 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8491 (m) cc_final: 0.8220 (m) REVERT: B 56 ASN cc_start: 0.9342 (t0) cc_final: 0.9051 (m110) REVERT: M 1 MET cc_start: 0.7176 (mmt) cc_final: 0.6869 (mmt) REVERT: S 49 PHE cc_start: 0.9075 (m-80) cc_final: 0.8158 (m-10) REVERT: S 125 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7989 (tm-30) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 0.2090 time to fit residues: 30.5556 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 : 1.741 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain S residue 75 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 122 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 chunk 44 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.070567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055543 restraints weight = 52519.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057212 restraints weight = 28600.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.058429 restraints weight = 19321.476| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10540 Z= 0.110 Angle : 0.550 10.295 14434 Z= 0.284 Chirality : 0.038 0.159 1828 Planarity : 0.003 0.035 1823 Dihedral : 4.316 45.270 1550 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.90 % Favored : 94.82 % Rotamer: Outliers : 1.80 % Allowed : 12.10 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1448 helix: 1.89 (0.17), residues: 976 sheet: -0.66 (0.75), residues: 47 loop : -1.64 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.017 0.001 PHE M 81 TYR 0.016 0.001 TYR A 463 ARG 0.004 0.000 ARG S 10 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 710) hydrogen bonds : angle 4.03030 ( 2094) covalent geometry : bond 0.00229 (10540) covalent geometry : angle 0.55043 (14434) *********************** 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 102 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8493 (m) cc_final: 0.8219 (m) REVERT: B 56 ASN cc_start: 0.9354 (t0) cc_final: 0.9095 (m-40) REVERT: B 70 TYR cc_start: 0.9075 (m-10) cc_final: 0.8603 (m-80) REVERT: S 49 PHE cc_start: 0.9011 (m-80) cc_final: 0.8156 (m-10) REVERT: S 125 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7990 (tm-30) outliers start: 17 outliers final: 11 residues processed: 99 average time/residue: 0.1916 time to fit residues: 29.5730 Evaluate side-chains 87 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 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 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 8 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.072816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.057067 restraints weight = 52324.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.058870 restraints weight = 27315.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060052 restraints weight = 18014.859| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10540 Z= 0.112 Angle : 0.548 11.410 14434 Z= 0.280 Chirality : 0.038 0.159 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.240 45.834 1550 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.90 % Favored : 94.82 % Rotamer: Outliers : 2.12 % Allowed : 13.16 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1448 helix: 2.00 (0.17), residues: 971 sheet: -0.44 (0.78), residues: 47 loop : -1.62 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.004 0.001 HIS A 133 PHE 0.010 0.001 PHE M 81 TYR 0.013 0.001 TYR A 463 ARG 0.008 0.000 ARG S 10 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 710) hydrogen bonds : angle 3.95851 ( 2094) covalent geometry : bond 0.00237 (10540) covalent geometry : angle 0.54795 (14434) *********************** 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: 20 poor density : 86 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8520 (m) cc_final: 0.8242 (m) REVERT: B 56 ASN cc_start: 0.9360 (t0) cc_final: 0.9106 (m-40) REVERT: B 70 TYR cc_start: 0.9069 (m-10) cc_final: 0.8556 (m-80) REVERT: M 65 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7998 (tt) REVERT: S 125 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7926 (tm-30) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.1930 time to fit residues: 30.6487 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 : 1.190 ------------------------------------------------------------------------------- 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 267 LEU 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 65 LEU Chi-restraints excluded: chain S residue 6 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.069224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054144 restraints weight = 53768.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.055808 restraints weight = 29374.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.057003 restraints weight = 19869.741| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10540 Z= 0.134 Angle : 0.556 11.438 14434 Z= 0.286 Chirality : 0.038 0.150 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.277 46.508 1550 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.97 % Favored : 94.75 % Rotamer: Outliers : 2.55 % Allowed : 14.01 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1448 helix: 2.04 (0.17), residues: 973 sheet: -0.28 (0.76), residues: 47 loop : -1.61 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.022 0.001 PHE M 81 TYR 0.012 0.001 TYR A 463 ARG 0.008 0.000 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 710) hydrogen bonds : angle 4.00050 ( 2094) covalent geometry : bond 0.00297 (10540) covalent geometry : angle 0.55562 (14434) *********************** 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 112 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8512 (m) cc_final: 0.8256 (m) REVERT: A 412 TYR cc_start: 0.8893 (t80) cc_final: 0.8684 (t80) REVERT: B 56 ASN cc_start: 0.9365 (t0) cc_final: 0.9164 (m-40) REVERT: B 70 TYR cc_start: 0.9054 (m-10) cc_final: 0.8614 (m-80) REVERT: B 175 MET cc_start: 0.8556 (pmm) cc_final: 0.7760 (ttm) REVERT: M 65 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8152 (tt) REVERT: S 42 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7780 (mtp85) REVERT: S 125 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7935 (tm-30) outliers start: 24 outliers final: 17 residues processed: 106 average time/residue: 0.1894 time to fit residues: 30.7147 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 : 1.224 ------------------------------------------------------------------------------- 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 A residue 548 PHE Chi-restraints excluded: chain B residue 150 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 2 ILE Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain S residue 6 LEU 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 50 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.069253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054266 restraints weight = 53877.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055917 restraints weight = 29311.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.057098 restraints weight = 19811.342| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.003 0.033 10540 Z= 0.123 Angle : 0.551 11.262 14434 Z= 0.282 Chirality : 0.038 0.198 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.235 46.228 1550 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.11 % Favored : 94.61 % Rotamer: Outliers : 2.65 % Allowed : 14.86 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1448 helix: 2.05 (0.17), residues: 981 sheet: -0.30 (0.76), residues: 47 loop : -1.53 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.013 0.001 PHE M 81 TYR 0.012 0.001 TYR A 463 ARG 0.006 0.000 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 710) hydrogen bonds : angle 3.93456 ( 2094) covalent geometry : bond 0.00269 (10540) covalent geometry : angle 0.55140 (14434) *********************** 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 112 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8477 (m) cc_final: 0.8214 (m) REVERT: B 56 ASN cc_start: 0.9384 (t0) cc_final: 0.9183 (m-40) REVERT: B 70 TYR cc_start: 0.9098 (m-10) cc_final: 0.8603 (m-80) REVERT: B 175 MET cc_start: 0.8569 (pmm) cc_final: 0.7793 (ttm) REVERT: S 42 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7627 (mtp85) REVERT: S 125 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7994 (tm-30) outliers start: 25 outliers final: 18 residues processed: 107 average time/residue: 0.2065 time to fit residues: 33.3349 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 : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 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 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 2 ILE Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain S residue 6 LEU 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 30 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 0.0060 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.069662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054705 restraints weight = 53482.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056373 restraints weight = 29011.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.057571 restraints weight = 19560.242| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2844 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= 0.109 Angle : 0.557 12.183 14434 Z= 0.283 Chirality : 0.038 0.194 1828 Planarity : 0.003 0.037 1823 Dihedral : 4.177 45.824 1550 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.63 % Favored : 95.10 % Rotamer: Outliers : 2.44 % Allowed : 15.07 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1448 helix: 2.06 (0.17), residues: 981 sheet: -0.95 (0.70), residues: 55 loop : -1.48 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.014 0.001 PHE S 67 TYR 0.012 0.001 TYR A 418 ARG 0.005 0.000 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 710) hydrogen bonds : angle 3.88907 ( 2094) covalent geometry : bond 0.00234 (10540) covalent geometry : angle 0.55689 (14434) *********************** 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 107 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8433 (m) cc_final: 0.8169 (m) REVERT: A 183 VAL cc_start: 0.7652 (OUTLIER) cc_final: 0.7289 (p) REVERT: B 70 TYR cc_start: 0.9143 (m-10) cc_final: 0.8588 (m-80) REVERT: B 91 PHE cc_start: 0.9078 (m-10) cc_final: 0.8629 (m-80) REVERT: B 175 MET cc_start: 0.8513 (pmm) cc_final: 0.7703 (ttm) REVERT: S 42 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7601 (mtp85) REVERT: S 125 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7970 (tm-30) outliers start: 23 outliers final: 19 residues processed: 101 average time/residue: 0.1786 time to fit residues: 28.6001 Evaluate side-chains 100 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 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 211 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 B residue 570 LEU Chi-restraints excluded: chain M residue 2 ILE 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 6 LEU 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 61 optimal weight: 0.0060 chunk 38 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.070174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055385 restraints weight = 53916.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057038 restraints weight = 29072.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.058210 restraints weight = 19548.547| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2954 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= 0.104 Angle : 0.564 12.509 14434 Z= 0.284 Chirality : 0.038 0.194 1828 Planarity : 0.003 0.038 1823 Dihedral : 4.129 45.149 1550 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.42 % Favored : 95.30 % Rotamer: Outliers : 2.34 % Allowed : 15.82 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1448 helix: 2.05 (0.17), residues: 976 sheet: -0.88 (0.70), residues: 54 loop : -1.47 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.029 0.001 PHE S 107 TYR 0.016 0.001 TYR B 361 ARG 0.005 0.000 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 710) hydrogen bonds : angle 3.88275 ( 2094) covalent geometry : bond 0.00218 (10540) covalent geometry : angle 0.56427 (14434) *********************** 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 115 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8476 (m) cc_final: 0.8197 (m) REVERT: A 183 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7445 (p) REVERT: B 70 TYR cc_start: 0.9121 (m-10) cc_final: 0.8566 (m-80) REVERT: B 175 MET cc_start: 0.8494 (pmm) cc_final: 0.7702 (ttm) REVERT: S 42 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7558 (mtp85) REVERT: S 125 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7947 (tm-30) outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 0.1839 time to fit residues: 31.3724 Evaluate side-chains 100 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 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 211 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 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 6 LEU 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 6 optimal weight: 0.9980 chunk 111 optimal weight: 0.0270 chunk 134 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 0.0570 chunk 129 optimal weight: 4.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.070139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055331 restraints weight = 53460.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057014 restraints weight = 28866.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058193 restraints weight = 19480.800| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10540 Z= 0.106 Angle : 0.577 12.429 14434 Z= 0.287 Chirality : 0.038 0.202 1828 Planarity : 0.003 0.038 1823 Dihedral : 4.087 44.915 1550 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.42 % Favored : 95.30 % Rotamer: Outliers : 2.02 % Allowed : 16.88 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.23), residues: 1448 helix: 2.03 (0.17), residues: 974 sheet: -0.86 (0.69), residues: 55 loop : -1.47 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.007 0.001 HIS A 527 PHE 0.028 0.001 PHE M 81 TYR 0.014 0.001 TYR M 20 ARG 0.005 0.000 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 710) hydrogen bonds : angle 3.83945 ( 2094) covalent geometry : bond 0.00229 (10540) covalent geometry : angle 0.57741 (14434) ********************** 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 100 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8442 (m) cc_final: 0.8166 (m) REVERT: A 183 VAL cc_start: 0.7813 (OUTLIER) cc_final: 0.7590 (p) REVERT: B 70 TYR cc_start: 0.9112 (m-10) cc_final: 0.8558 (m-80) REVERT: B 91 PHE cc_start: 0.9127 (m-10) cc_final: 0.8674 (m-80) REVERT: B 175 MET cc_start: 0.8486 (pmm) cc_final: 0.7673 (ttm) REVERT: S 42 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7560 (mtp85) REVERT: S 125 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7975 (tm-30) outliers start: 19 outliers final: 17 residues processed: 94 average time/residue: 0.1787 time to fit residues: 26.4537 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 : 1.235 ------------------------------------------------------------------------------- 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 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 211 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 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 6 LEU 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 128 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.071382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.055734 restraints weight = 52563.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.057445 restraints weight = 28070.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.058722 restraints weight = 18776.686| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10540 Z= 0.118 Angle : 0.588 17.724 14434 Z= 0.293 Chirality : 0.038 0.193 1828 Planarity : 0.003 0.037 1823 Dihedral : 4.125 44.801 1550 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.63 % Favored : 95.10 % Rotamer: Outliers : 2.34 % Allowed : 16.45 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.23), residues: 1448 helix: 2.01 (0.17), residues: 974 sheet: -0.69 (0.69), residues: 54 loop : -1.46 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.007 0.001 HIS A 527 PHE 0.029 0.001 PHE M 81 TYR 0.021 0.001 TYR M 20 ARG 0.005 0.000 ARG S 10 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 710) hydrogen bonds : angle 3.90312 ( 2094) covalent geometry : bond 0.00265 (10540) covalent geometry : angle 0.58778 (14434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.73 seconds wall clock time: 55 minutes 58.67 seconds (3358.67 seconds total)