Starting phenix.real_space_refine on Thu Jul 31 13:21:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z5c_14517/07_2025/7z5c_14517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z5c_14517/07_2025/7z5c_14517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z5c_14517/07_2025/7z5c_14517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z5c_14517/07_2025/7z5c_14517.map" model { file = "/net/cci-nas-00/data/ceres_data/7z5c_14517/07_2025/7z5c_14517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z5c_14517/07_2025/7z5c_14517.cif" } resolution = 4.16 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= 0.002 sd= 0.015 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 72 5.16 5 C 8767 2.51 5 N 2336 2.21 5 O 2532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13707 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4737 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 22, 'TRANS': 577} Chain: "B" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4578 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 552} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3192 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 378} Chain breaks: 3 Chain: "S" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1200 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'TRANS': 141} Time building chain proxies: 8.86, per 1000 atoms: 0.65 Number of scatterers: 13707 At special positions: 0 Unit cell: (104.32, 112.796, 128.444, 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 72 16.00 O 2532 8.00 N 2336 7.00 C 8767 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: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 7 sheets defined 61.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 51 through 68 removed outlier: 3.657A pdb=" N LYS A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.611A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.584A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 195 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 200 through 215 Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.085A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.777A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.508A pdb=" N LEU A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.796A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 401 through 415 removed outlier: 3.869A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.981A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.583A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.822A 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 552 through 563 removed outlier: 4.286A pdb=" N ALA A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 591 through 599 removed outlier: 3.935A pdb=" N LEU A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 26 through 43 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 56 Processing helix chain 'B' and resid 62 through 80 removed outlier: 3.833A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.685A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 117 through 131 removed outlier: 4.641A pdb=" N TYR B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.420A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.531A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.772A pdb=" N ASN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.813A 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 removed outlier: 3.680A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 350 through 361 removed outlier: 4.222A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 421 removed outlier: 4.196A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 removed outlier: 4.517A pdb=" N THR B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 461 through 472 removed outlier: 4.577A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.815A pdb=" N VAL B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.671A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 569 through 575 removed outlier: 3.878A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 4.035A 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 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 128 through 133 removed outlier: 4.041A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.760A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 95 removed outlier: 3.611A pdb=" N TYR S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 106 removed outlier: 3.630A pdb=" N ASN S 106 " --> pdb=" O ASP S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'M' and resid 245 through 248 removed outlier: 6.555A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG M 278 " --> pdb=" O VAL M 196 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL M 196 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS M 356 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU M 321 " --> pdb=" O LYS M 354 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS M 354 " --> pdb=" O GLU M 321 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG M 323 " --> pdb=" O VAL M 352 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL M 352 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA M 350 " --> pdb=" O PRO M 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 253 through 254 Processing sheet with id=AA5, first strand: chain 'M' and resid 287 through 294 removed outlier: 3.512A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 16 through 19 removed outlier: 3.700A pdb=" N PHE S 4 " --> pdb=" O CYS S 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 118 through 119 798 hydrogen bonds defined for protein. 2334 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: 4.27 Time building geometry restraints manager: 4.14 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: 4485 1.34 - 1.46: 2863 1.46 - 1.58: 6492 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 13951 Sorted by residual: bond pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CA ILE M 430 " pdb=" CB ILE M 430 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.20e+00 bond pdb=" C ASN B 200 " pdb=" N PRO B 201 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.19e-01 bond pdb=" CA ASP A 474 " pdb=" CB ASP A 474 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.90e-01 bond pdb=" CB PRO B 231 " pdb=" CG PRO B 231 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.72e-01 ... (remaining 13946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 18568 1.72 - 3.44: 267 3.44 - 5.16: 38 5.16 - 6.88: 9 6.88 - 8.60: 4 Bond angle restraints: 18886 Sorted by residual: angle pdb=" C ALA A 590 " pdb=" CA ALA A 590 " pdb=" CB ALA A 590 " ideal model delta sigma weight residual 115.89 110.72 5.17 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA MET B 155 " pdb=" CB MET B 155 " pdb=" CG MET B 155 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N GLU B 498 " pdb=" CA GLU B 498 " pdb=" C GLU B 498 " ideal model delta sigma weight residual 114.04 109.98 4.06 1.24e+00 6.50e-01 1.07e+01 angle pdb=" C ASP A 473 " pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.29e+00 angle pdb=" CB MET B 58 " pdb=" CG MET B 58 " pdb=" SD MET B 58 " ideal model delta sigma weight residual 112.70 121.30 -8.60 3.00e+00 1.11e-01 8.21e+00 ... (remaining 18881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 7661 17.38 - 34.76: 735 34.76 - 52.14: 154 52.14 - 69.52: 15 69.52 - 86.90: 15 Dihedral angle restraints: 8580 sinusoidal: 3488 harmonic: 5092 Sorted by residual: dihedral pdb=" CA HIS A 493 " pdb=" C HIS A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP A 462 " pdb=" C TRP A 462 " pdb=" N TYR A 463 " pdb=" CA TYR A 463 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA MET B 155 " pdb=" C MET B 155 " pdb=" N VAL B 156 " pdb=" CA VAL B 156 " ideal model delta harmonic sigma weight residual -180.00 -163.57 -16.43 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1667 0.043 - 0.085: 410 0.085 - 0.128: 107 0.128 - 0.171: 13 0.171 - 0.214: 1 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CB VAL A 475 " pdb=" CA VAL A 475 " pdb=" CG1 VAL A 475 " pdb=" CG2 VAL A 475 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASP A 474 " pdb=" N ASP A 474 " pdb=" C ASP A 474 " pdb=" CB ASP A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 2195 not shown) Planarity restraints: 2403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 473 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.44e+00 pdb=" C ASP A 473 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 473 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 474 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 76 " 0.012 2.00e-02 2.50e+03 1.10e-02 2.41e+00 pdb=" CG TYR B 76 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 76 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 76 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 76 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 76 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 76 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 191 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO B 192 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " -0.019 5.00e-02 4.00e+02 ... (remaining 2400 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 361 2.71 - 3.26: 14103 3.26 - 3.81: 22028 3.81 - 4.35: 26783 4.35 - 4.90: 45063 Nonbonded interactions: 108338 Sorted by model distance: nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR M 83 " model vdw 2.167 3.040 nonbonded pdb=" NH2 ARG B 108 " pdb=" OH TYR B 136 " model vdw 2.170 3.120 nonbonded pdb=" OE2 GLU S 125 " pdb=" NZ LYS S 130 " model vdw 2.177 3.120 nonbonded pdb=" OE2 GLU M 179 " pdb=" OH TYR M 277 " model vdw 2.192 3.040 nonbonded pdb=" OG SER A 359 " pdb=" OG SER A 362 " model vdw 2.208 3.040 ... (remaining 108333 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: 2.620 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.580 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 0.047 13951 Z= 0.123 Angle : 0.549 8.596 18886 Z= 0.305 Chirality : 0.040 0.214 2198 Planarity : 0.003 0.034 2403 Dihedral : 14.207 86.898 5262 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.07 % Allowed : 0.26 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1703 helix: 1.64 (0.17), residues: 964 sheet: 0.09 (0.39), residues: 183 loop : -0.75 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 PHE 0.014 0.001 PHE B 581 TYR 0.027 0.001 TYR B 76 ARG 0.007 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.12962 ( 798) hydrogen bonds : angle 5.02742 ( 2334) covalent geometry : bond 0.00255 (13951) covalent geometry : angle 0.54878 (18886) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 PHE cc_start: 0.7122 (m-80) cc_final: 0.6915 (m-10) REVERT: B 83 MET cc_start: 0.8510 (tpp) cc_final: 0.8063 (tpp) REVERT: B 110 MET cc_start: 0.8472 (mpp) cc_final: 0.7845 (mpp) REVERT: M 35 ASN cc_start: 0.7048 (t0) cc_final: 0.6838 (t0) REVERT: S 1 MET cc_start: 0.6948 (ptm) cc_final: 0.6618 (ptm) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.2852 time to fit residues: 81.1027 Evaluate side-chains 135 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 154 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.130729 restraints weight = 20299.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124523 restraints weight = 26527.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122025 restraints weight = 36635.748| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13951 Z= 0.117 Angle : 0.508 6.428 18886 Z= 0.270 Chirality : 0.040 0.157 2198 Planarity : 0.004 0.039 2403 Dihedral : 3.891 27.058 1868 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.13 % Allowed : 2.16 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1703 helix: 1.76 (0.17), residues: 977 sheet: 0.24 (0.41), residues: 175 loop : -0.82 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 421 HIS 0.010 0.001 HIS B 149 PHE 0.017 0.001 PHE A 484 TYR 0.020 0.001 TYR B 136 ARG 0.005 0.000 ARG S 61 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 798) hydrogen bonds : angle 4.16977 ( 2334) covalent geometry : bond 0.00255 (13951) covalent geometry : angle 0.50824 (18886) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8821 (tt) cc_final: 0.8599 (tt) REVERT: A 568 GLN cc_start: 0.8396 (mp10) cc_final: 0.8127 (mp10) REVERT: M 327 PRO cc_start: 0.8735 (Cg_exo) cc_final: 0.8492 (Cg_endo) REVERT: S 1 MET cc_start: 0.7351 (ptm) cc_final: 0.6890 (ptm) REVERT: S 56 LYS cc_start: 0.7891 (pttt) cc_final: 0.7514 (ptpt) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.2447 time to fit residues: 68.4330 Evaluate side-chains 144 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 147 optimal weight: 0.0870 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 18 optimal weight: 0.0170 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127834 restraints weight = 20503.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119763 restraints weight = 27065.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118016 restraints weight = 31162.988| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13951 Z= 0.155 Angle : 0.533 6.532 18886 Z= 0.279 Chirality : 0.041 0.157 2198 Planarity : 0.004 0.057 2403 Dihedral : 3.929 23.510 1868 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1703 helix: 1.73 (0.17), residues: 977 sheet: 0.12 (0.39), residues: 185 loop : -0.72 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 421 HIS 0.012 0.001 HIS B 149 PHE 0.026 0.002 PHE A 530 TYR 0.014 0.001 TYR B 72 ARG 0.006 0.000 ARG S 15 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 798) hydrogen bonds : angle 4.17533 ( 2334) covalent geometry : bond 0.00369 (13951) covalent geometry : angle 0.53254 (18886) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7599 (ptp) cc_final: 0.7027 (ptp) REVERT: A 546 ILE cc_start: 0.8857 (tt) cc_final: 0.8568 (tt) REVERT: A 568 GLN cc_start: 0.8349 (mp10) cc_final: 0.8116 (mp10) REVERT: B 110 MET cc_start: 0.8397 (mpp) cc_final: 0.7919 (mpp) REVERT: M 327 PRO cc_start: 0.8762 (Cg_exo) cc_final: 0.8544 (Cg_endo) REVERT: S 1 MET cc_start: 0.7355 (ptm) cc_final: 0.6991 (ptm) REVERT: S 125 GLU cc_start: 0.8218 (tt0) cc_final: 0.8017 (tt0) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.3532 time to fit residues: 96.7772 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131248 restraints weight = 20335.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122647 restraints weight = 29757.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121101 restraints weight = 38738.734| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13951 Z= 0.118 Angle : 0.505 6.820 18886 Z= 0.266 Chirality : 0.040 0.176 2198 Planarity : 0.004 0.044 2403 Dihedral : 3.884 21.858 1868 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1703 helix: 1.79 (0.17), residues: 976 sheet: 0.18 (0.40), residues: 180 loop : -0.70 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.014 0.001 HIS B 149 PHE 0.011 0.001 PHE M 214 TYR 0.022 0.001 TYR B 136 ARG 0.006 0.000 ARG S 15 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 798) hydrogen bonds : angle 4.09256 ( 2334) covalent geometry : bond 0.00270 (13951) covalent geometry : angle 0.50456 (18886) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8868 (tt) cc_final: 0.8660 (tt) REVERT: A 568 GLN cc_start: 0.8342 (mp10) cc_final: 0.8140 (mp10) REVERT: M 327 PRO cc_start: 0.8519 (Cg_exo) cc_final: 0.8314 (Cg_endo) REVERT: S 1 MET cc_start: 0.7091 (ptm) cc_final: 0.6752 (ptm) REVERT: S 56 LYS cc_start: 0.7829 (pttt) cc_final: 0.7607 (ptmt) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.3179 time to fit residues: 91.4343 Evaluate side-chains 136 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 6 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 ASN ** 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 = 0.3581 r_free = 0.3581 target = 0.129677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117904 restraints weight = 19854.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109927 restraints weight = 27059.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108674 restraints weight = 30735.947| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13951 Z= 0.145 Angle : 0.532 6.863 18886 Z= 0.276 Chirality : 0.041 0.167 2198 Planarity : 0.004 0.063 2403 Dihedral : 3.889 20.403 1868 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1703 helix: 1.72 (0.17), residues: 987 sheet: 0.05 (0.39), residues: 186 loop : -0.74 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.019 0.001 HIS B 149 PHE 0.023 0.002 PHE B 581 TYR 0.021 0.001 TYR B 136 ARG 0.012 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 798) hydrogen bonds : angle 4.14587 ( 2334) covalent geometry : bond 0.00349 (13951) covalent geometry : angle 0.53198 (18886) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8817 (tt) cc_final: 0.8574 (tt) REVERT: A 568 GLN cc_start: 0.8401 (mp10) cc_final: 0.8051 (mp10) REVERT: S 1 MET cc_start: 0.7117 (ptm) cc_final: 0.6800 (ptm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3969 time to fit residues: 109.7546 Evaluate side-chains 130 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114724 restraints weight = 20447.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110431 restraints weight = 28865.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107824 restraints weight = 34965.966| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13951 Z= 0.239 Angle : 0.624 6.898 18886 Z= 0.324 Chirality : 0.044 0.195 2198 Planarity : 0.004 0.044 2403 Dihedral : 4.185 24.353 1868 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1703 helix: 1.46 (0.17), residues: 986 sheet: -0.20 (0.38), residues: 189 loop : -0.89 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 421 HIS 0.021 0.001 HIS B 149 PHE 0.032 0.002 PHE A 530 TYR 0.020 0.002 TYR A 545 ARG 0.006 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 798) hydrogen bonds : angle 4.46911 ( 2334) covalent geometry : bond 0.00583 (13951) covalent geometry : angle 0.62411 (18886) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8890 (tt) cc_final: 0.8647 (tt) REVERT: B 564 ILE cc_start: 0.8542 (mm) cc_final: 0.8329 (mm) REVERT: S 1 MET cc_start: 0.7601 (ptm) cc_final: 0.7309 (ptm) REVERT: S 82 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7785 (mm-30) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.4409 time to fit residues: 119.7958 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 147 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118354 restraints weight = 19860.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112502 restraints weight = 28622.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111552 restraints weight = 39824.893| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13951 Z= 0.124 Angle : 0.545 7.449 18886 Z= 0.285 Chirality : 0.042 0.214 2198 Planarity : 0.004 0.045 2403 Dihedral : 4.064 22.119 1868 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1703 helix: 1.58 (0.17), residues: 989 sheet: 0.06 (0.40), residues: 184 loop : -0.86 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 462 HIS 0.016 0.001 HIS B 149 PHE 0.021 0.002 PHE M 118 TYR 0.017 0.001 TYR B 136 ARG 0.005 0.000 ARG S 15 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 798) hydrogen bonds : angle 4.23552 ( 2334) covalent geometry : bond 0.00285 (13951) covalent geometry : angle 0.54484 (18886) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 5.093 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8822 (mt) cc_final: 0.8597 (mt) REVERT: A 546 ILE cc_start: 0.8788 (tt) cc_final: 0.8444 (tt) REVERT: B 187 ILE cc_start: 0.7716 (mm) cc_final: 0.7376 (mm) REVERT: S 1 MET cc_start: 0.7443 (ptm) cc_final: 0.7192 (ptm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.5047 time to fit residues: 133.6572 Evaluate side-chains 125 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 5.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 149 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124045 restraints weight = 19853.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121605 restraints weight = 27625.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120646 restraints weight = 34956.611| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13951 Z= 0.123 Angle : 0.530 7.656 18886 Z= 0.278 Chirality : 0.041 0.195 2198 Planarity : 0.004 0.042 2403 Dihedral : 4.015 21.579 1868 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1703 helix: 1.64 (0.17), residues: 989 sheet: 0.12 (0.40), residues: 184 loop : -0.84 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.016 0.001 HIS B 149 PHE 0.018 0.001 PHE B 581 TYR 0.019 0.001 TYR B 136 ARG 0.006 0.000 ARG S 15 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 798) hydrogen bonds : angle 4.21404 ( 2334) covalent geometry : bond 0.00284 (13951) covalent geometry : angle 0.53021 (18886) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8785 (tt) cc_final: 0.8435 (tt) REVERT: S 1 MET cc_start: 0.7548 (ptm) cc_final: 0.7264 (ptm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.3111 time to fit residues: 81.0693 Evaluate side-chains 128 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** 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 = 0.3598 r_free = 0.3598 target = 0.131448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123354 restraints weight = 19688.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119046 restraints weight = 30066.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118150 restraints weight = 43911.498| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13951 Z= 0.125 Angle : 0.531 8.243 18886 Z= 0.277 Chirality : 0.041 0.157 2198 Planarity : 0.004 0.041 2403 Dihedral : 3.964 21.670 1868 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1703 helix: 1.65 (0.17), residues: 988 sheet: 0.10 (0.40), residues: 184 loop : -0.86 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.019 0.001 HIS B 149 PHE 0.018 0.001 PHE M 118 TYR 0.015 0.001 TYR A 88 ARG 0.006 0.000 ARG S 15 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 798) hydrogen bonds : angle 4.18623 ( 2334) covalent geometry : bond 0.00290 (13951) covalent geometry : angle 0.53107 (18886) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.852 Fit side-chains REVERT: A 110 ARG cc_start: 0.6827 (mtm-85) cc_final: 0.6593 (mtm-85) REVERT: A 132 LEU cc_start: 0.8700 (mt) cc_final: 0.8492 (mt) REVERT: A 546 ILE cc_start: 0.8820 (tt) cc_final: 0.8526 (tt) REVERT: M 209 MET cc_start: 0.7557 (mmm) cc_final: 0.7266 (mmm) REVERT: S 1 MET cc_start: 0.7656 (ptm) cc_final: 0.7330 (ptm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3899 time to fit residues: 100.3984 Evaluate side-chains 129 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.131433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119969 restraints weight = 19719.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114709 restraints weight = 29437.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113586 restraints weight = 34882.844| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13951 Z= 0.130 Angle : 0.565 20.162 18886 Z= 0.287 Chirality : 0.042 0.394 2198 Planarity : 0.004 0.042 2403 Dihedral : 3.958 22.079 1868 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1703 helix: 1.63 (0.17), residues: 988 sheet: 0.09 (0.40), residues: 184 loop : -0.87 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.020 0.001 HIS B 149 PHE 0.023 0.001 PHE A 523 TYR 0.027 0.001 TYR B 76 ARG 0.005 0.000 ARG S 15 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 798) hydrogen bonds : angle 4.17928 ( 2334) covalent geometry : bond 0.00306 (13951) covalent geometry : angle 0.56464 (18886) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.682 Fit side-chains REVERT: A 132 LEU cc_start: 0.8775 (mt) cc_final: 0.8573 (mt) REVERT: A 546 ILE cc_start: 0.8767 (tt) cc_final: 0.8493 (tt) REVERT: M 209 MET cc_start: 0.7650 (mmm) cc_final: 0.7363 (mmm) REVERT: S 1 MET cc_start: 0.7595 (ptm) cc_final: 0.7313 (ptm) REVERT: S 132 LEU cc_start: 0.8848 (mt) cc_final: 0.8479 (mt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2416 time to fit residues: 60.7169 Evaluate side-chains 128 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 0.8980 chunk 158 optimal weight: 0.0370 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 147 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 157 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** 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 = 0.3612 r_free = 0.3612 target = 0.132431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120413 restraints weight = 19828.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114853 restraints weight = 27011.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112707 restraints weight = 33867.202| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13951 Z= 0.112 Angle : 0.544 16.197 18886 Z= 0.279 Chirality : 0.041 0.252 2198 Planarity : 0.004 0.039 2403 Dihedral : 3.902 21.943 1868 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1703 helix: 1.71 (0.17), residues: 989 sheet: 0.09 (0.40), residues: 182 loop : -0.87 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 462 HIS 0.018 0.001 HIS B 149 PHE 0.047 0.001 PHE M 118 TYR 0.022 0.001 TYR B 76 ARG 0.006 0.000 ARG S 15 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 798) hydrogen bonds : angle 4.11335 ( 2334) covalent geometry : bond 0.00252 (13951) covalent geometry : angle 0.54398 (18886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6335.64 seconds wall clock time: 118 minutes 40.32 seconds (7120.32 seconds total)