Starting phenix.real_space_refine (version: dev) on Mon Dec 12 12:22:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw9_24711/12_2022/7rw9_24711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw9_24711/12_2022/7rw9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw9_24711/12_2022/7rw9_24711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw9_24711/12_2022/7rw9_24711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw9_24711/12_2022/7rw9_24711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw9_24711/12_2022/7rw9_24711.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 6.33, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 4.56 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: 0.60 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: 3.20 Time building geometry restraints manager: 4.87 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: 98.70 - 105.78: 165 105.78 - 112.87: 5925 112.87 - 119.96: 3489 119.96 - 127.04: 4777 127.04 - 134.13: 78 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 2.440 nonbonded pdb=" O ARG A 399 " pdb=" N ASN A 401 " model vdw 2.160 2.520 nonbonded pdb=" OH TYR A 247 " pdb=" OE2 GLU S 125 " model vdw 2.208 2.440 nonbonded pdb=" O HIS A 340 " pdb=" NH1 ARG A 346 " model vdw 2.214 2.520 nonbonded pdb=" O PRO A 219 " pdb=" OH TYR A 268 " model vdw 2.239 2.440 ... (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 ========== 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 11.030 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.070 Process input model: 30.330 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 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= 0.174 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 : 7.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.42 % Favored : 93.30 % Rotamer Outliers : 0.11 % 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.2245 time to fit residues: 45.3835 Evaluate side-chains 84 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0918 time to fit residues: 1.8644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 369 HIS A 448 ASN B 56 ASN B 305 ASN M 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10540 Z= 0.260 Angle : 0.608 9.136 14434 Z= 0.318 Chirality : 0.039 0.161 1828 Planarity : 0.003 0.032 1823 Dihedral : 4.619 36.486 1550 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.87 % Favored : 93.85 % Rotamer Outliers : 1.06 % 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: 0.87 (0.23), residues: 1448 helix: 1.63 (0.17), residues: 982 sheet: -1.33 (0.77), residues: 45 loop : -1.79 (0.31), residues: 421 *********************** 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 100 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.269 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.1878 time to fit residues: 27.7570 Evaluate side-chains 85 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1163 time to fit residues: 3.5198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 105 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 10540 Z= 0.148 Angle : 0.556 9.437 14434 Z= 0.286 Chirality : 0.038 0.199 1828 Planarity : 0.003 0.034 1823 Dihedral : 4.357 36.832 1550 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.11 % Favored : 94.61 % Rotamer Outliers : 1.17 % 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: 1.12 (0.23), residues: 1448 helix: 1.81 (0.17), residues: 984 sheet: -0.88 (0.75), residues: 45 loop : -1.75 (0.31), residues: 419 *********************** 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 102 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 98 average time/residue: 0.1959 time to fit residues: 29.5772 Evaluate side-chains 83 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1160 time to fit residues: 2.9438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 10540 Z= 0.176 Angle : 0.542 10.439 14434 Z= 0.280 Chirality : 0.037 0.158 1828 Planarity : 0.003 0.034 1823 Dihedral : 4.297 37.559 1550 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.25 % Favored : 94.48 % Rotamer Outliers : 0.96 % 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: 1.20 (0.23), residues: 1448 helix: 1.91 (0.17), residues: 973 sheet: -0.60 (0.77), residues: 45 loop : -1.75 (0.30), residues: 430 *********************** 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 95 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.1826 time to fit residues: 26.3344 Evaluate side-chains 81 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1014 time to fit residues: 2.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 10540 Z= 0.263 Angle : 0.574 9.182 14434 Z= 0.302 Chirality : 0.039 0.156 1828 Planarity : 0.003 0.034 1823 Dihedral : 4.421 39.194 1550 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.80 % Favored : 93.92 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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: 1.21 (0.23), residues: 1448 helix: 1.89 (0.17), residues: 980 sheet: -0.40 (0.78), residues: 45 loop : -1.75 (0.31), residues: 423 *********************** 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 94 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.2022 time to fit residues: 27.9206 Evaluate side-chains 84 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1072 time to fit residues: 3.5941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2582 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= 0.171 Angle : 0.555 11.208 14434 Z= 0.282 Chirality : 0.037 0.150 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.286 38.730 1550 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.32 % Favored : 94.41 % Rotamer Outliers : 1.06 % 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: 1.98 (0.17), residues: 989 sheet: -0.19 (0.80), residues: 45 loop : -1.76 (0.31), residues: 414 *********************** 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 99 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.274 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 96 average time/residue: 0.2031 time to fit residues: 29.6931 Evaluate side-chains 79 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1066 time to fit residues: 2.5840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 64 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 10540 Z= 0.158 Angle : 0.553 12.362 14434 Z= 0.280 Chirality : 0.037 0.192 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.223 38.517 1550 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.52 % Favored : 94.20 % Rotamer Outliers : 0.85 % 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: 1.38 (0.23), residues: 1448 helix: 2.05 (0.17), residues: 977 sheet: -0.17 (0.78), residues: 45 loop : -1.74 (0.30), residues: 426 *********************** 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 88 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.250 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.1942 time to fit residues: 26.2015 Evaluate side-chains 78 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1122 time to fit residues: 2.5194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 109 optimal weight: 0.0670 chunk 126 optimal weight: 3.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 10540 Z= 0.150 Angle : 0.548 11.818 14434 Z= 0.277 Chirality : 0.038 0.192 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.172 38.074 1550 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.90 % Favored : 94.82 % Rotamer Outliers : 0.64 % 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: 1.39 (0.23), residues: 1448 helix: 2.03 (0.17), residues: 978 sheet: -0.06 (0.78), residues: 45 loop : -1.71 (0.30), residues: 425 *********************** 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 90 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.2005 time to fit residues: 27.0721 Evaluate side-chains 84 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1131 time to fit residues: 2.6672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 84 optimal weight: 0.0010 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2941 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= 0.161 Angle : 0.564 11.482 14434 Z= 0.285 Chirality : 0.037 0.194 1828 Planarity : 0.003 0.036 1823 Dihedral : 4.159 37.969 1550 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.04 % Favored : 94.68 % Rotamer Outliers : 0.32 % 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: 2.06 (0.17), residues: 975 sheet: 0.05 (0.78), residues: 45 loop : -1.73 (0.30), residues: 428 *********************** 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 84 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.242 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 84 average time/residue: 0.1933 time to fit residues: 25.4146 Evaluate side-chains 81 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1152 time to fit residues: 2.2004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 88 optimal weight: 0.0870 chunk 70 optimal weight: 0.0000 chunk 90 optimal weight: 0.9990 overall best weight: 0.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 10540 Z= 0.143 Angle : 0.591 18.645 14434 Z= 0.290 Chirality : 0.038 0.201 1828 Planarity : 0.003 0.037 1823 Dihedral : 4.102 37.506 1550 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.77 % Favored : 94.96 % Rotamer Outliers : 0.42 % 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: 1.38 (0.23), residues: 1448 helix: 1.99 (0.17), residues: 977 sheet: 0.15 (0.78), residues: 45 loop : -1.66 (0.30), residues: 426 ********************** 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 93 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.267 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 91 average time/residue: 0.2005 time to fit residues: 28.0534 Evaluate side-chains 82 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1070 time to fit residues: 1.9264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.072006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.056977 restraints weight = 52316.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.058663 restraints weight = 28311.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.059879 restraints weight = 19018.925| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10540 Z= 0.169 Angle : 0.578 15.431 14434 Z= 0.288 Chirality : 0.037 0.195 1828 Planarity : 0.003 0.037 1823 Dihedral : 4.092 37.510 1550 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.97 % Favored : 94.75 % Rotamer Outliers : 0.21 % 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: 1.48 (0.23), residues: 1448 helix: 2.07 (0.17), residues: 977 sheet: 0.15 (0.78), residues: 45 loop : -1.61 (0.31), residues: 426 =============================================================================== Job complete usr+sys time: 1781.55 seconds wall clock time: 33 minutes 27.33 seconds (2007.33 seconds total)