Starting phenix.real_space_refine on Wed Mar 4 12:05:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z5c_14517/03_2026/7z5c_14517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z5c_14517/03_2026/7z5c_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_14517/03_2026/7z5c_14517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z5c_14517/03_2026/7z5c_14517.map" model { file = "/net/cci-nas-00/data/ceres_data/7z5c_14517/03_2026/7z5c_14517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z5c_14517/03_2026/7z5c_14517.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.00, per 1000 atoms: 0.22 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: 1.10 Conformation dependent library (CDL) restraints added in 593.7 milliseconds 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: 0.40 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: 2.18 Time building geometry restraints manager: 1.49 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: 2.640 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.960 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- 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 : 9.49 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (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 ARG 0.007 0.000 ARG A 464 TYR 0.027 0.001 TYR B 76 PHE 0.014 0.001 PHE B 581 TRP 0.016 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00255 (13951) covalent geometry : angle 0.54878 (18886) hydrogen bonds : bond 0.12962 ( 798) hydrogen bonds : angle 5.02742 ( 2334) *********************** 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 : 0.522 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: 0.8064 (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: 0.1300 time to fit residues: 37.1055 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 : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 A 531 HIS ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3728 r_free = 0.3728 target = 0.141797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136976 restraints weight = 20359.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126855 restraints weight = 31238.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124768 restraints weight = 35256.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124746 restraints weight = 42222.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124939 restraints weight = 32154.660| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1004 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= 0.132 Angle : 0.521 6.324 18886 Z= 0.277 Chirality : 0.041 0.152 2198 Planarity : 0.004 0.039 2403 Dihedral : 3.931 26.988 1868 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.21), residues: 1703 helix: 1.73 (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 ARG 0.005 0.000 ARG S 61 TYR 0.025 0.001 TYR B 136 PHE 0.019 0.001 PHE A 484 TRP 0.018 0.001 TRP M 421 HIS 0.010 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00301 (13951) covalent geometry : angle 0.52091 (18886) hydrogen bonds : bond 0.03919 ( 798) hydrogen bonds : angle 4.19485 ( 2334) *********************** 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 185 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8139 (tttm) cc_final: 0.7623 (tmtt) REVERT: A 546 ILE cc_start: 0.8874 (tt) cc_final: 0.8625 (tt) REVERT: A 568 GLN cc_start: 0.8445 (mp10) cc_final: 0.8214 (mp10) REVERT: B 564 ILE cc_start: 0.8512 (mm) cc_final: 0.8311 (mm) REVERT: M 327 PRO cc_start: 0.8762 (Cg_exo) cc_final: 0.8549 (Cg_endo) REVERT: S 1 MET cc_start: 0.7302 (ptm) cc_final: 0.6839 (ptm) REVERT: S 61 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7788 (ttm110) outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.1214 time to fit residues: 33.6378 Evaluate side-chains 142 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131673 restraints weight = 20518.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122447 restraints weight = 27756.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121771 restraints weight = 31488.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121910 restraints weight = 33775.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122127 restraints weight = 28926.792| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13951 Z= 0.117 Angle : 0.503 6.629 18886 Z= 0.265 Chirality : 0.040 0.160 2198 Planarity : 0.004 0.059 2403 Dihedral : 3.866 23.887 1868 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.07 % Allowed : 3.28 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1703 helix: 1.81 (0.17), residues: 977 sheet: 0.12 (0.40), residues: 185 loop : -0.72 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 15 TYR 0.015 0.001 TYR B 72 PHE 0.023 0.001 PHE A 530 TRP 0.013 0.001 TRP A 462 HIS 0.012 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00263 (13951) covalent geometry : angle 0.50306 (18886) hydrogen bonds : bond 0.03603 ( 798) hydrogen bonds : angle 4.07229 ( 2334) *********************** 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 184 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7565 (ptp) cc_final: 0.7024 (ptp) REVERT: A 546 ILE cc_start: 0.8820 (tt) cc_final: 0.8543 (tt) REVERT: B 110 MET cc_start: 0.8369 (mpp) cc_final: 0.7920 (mpp) REVERT: M 327 PRO cc_start: 0.8505 (Cg_exo) cc_final: 0.8303 (Cg_endo) REVERT: S 1 MET cc_start: 0.7267 (ptm) cc_final: 0.6911 (ptm) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1184 time to fit residues: 32.6507 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 : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** 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 = 0.3705 r_free = 0.3705 target = 0.139677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127022 restraints weight = 20701.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120963 restraints weight = 27761.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118699 restraints weight = 37692.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118926 restraints weight = 34380.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118958 restraints weight = 30195.408| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1524 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= 0.127 Angle : 0.506 6.795 18886 Z= 0.265 Chirality : 0.040 0.173 2198 Planarity : 0.004 0.044 2403 Dihedral : 3.852 21.707 1868 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1703 helix: 1.81 (0.17), residues: 978 sheet: 0.17 (0.39), residues: 184 loop : -0.74 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 15 TYR 0.024 0.001 TYR B 136 PHE 0.018 0.001 PHE A 530 TRP 0.012 0.001 TRP A 462 HIS 0.014 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00295 (13951) covalent geometry : angle 0.50647 (18886) hydrogen bonds : bond 0.03507 ( 798) hydrogen bonds : angle 4.05019 ( 2334) *********************** 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 180 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8728 (tt) cc_final: 0.8488 (tt) REVERT: M 35 ASN cc_start: 0.6959 (t0) cc_final: 0.6655 (t0) REVERT: M 327 PRO cc_start: 0.8523 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: S 1 MET cc_start: 0.7103 (ptm) cc_final: 0.6776 (ptm) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1145 time to fit residues: 31.3140 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 : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** 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 = 0.3614 r_free = 0.3614 target = 0.132253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120615 restraints weight = 19798.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113881 restraints weight = 26611.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111832 restraints weight = 27143.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111685 restraints weight = 30246.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111918 restraints weight = 30249.972| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13951 Z= 0.109 Angle : 0.507 6.976 18886 Z= 0.263 Chirality : 0.040 0.163 2198 Planarity : 0.004 0.045 2403 Dihedral : 3.797 20.681 1868 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1703 helix: 1.85 (0.17), residues: 984 sheet: 0.42 (0.41), residues: 178 loop : -0.72 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 108 TYR 0.020 0.001 TYR B 136 PHE 0.024 0.001 PHE B 581 TRP 0.014 0.001 TRP A 462 HIS 0.018 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00244 (13951) covalent geometry : angle 0.50656 (18886) hydrogen bonds : bond 0.03275 ( 798) hydrogen bonds : angle 3.98113 ( 2334) *********************** 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 185 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8712 (tt) cc_final: 0.8497 (tt) REVERT: B 361 TYR cc_start: 0.8095 (m-10) cc_final: 0.7772 (m-10) REVERT: S 1 MET cc_start: 0.7018 (ptm) cc_final: 0.6731 (ptm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1198 time to fit residues: 33.0424 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 : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117463 restraints weight = 19916.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113139 restraints weight = 28302.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111673 restraints weight = 35770.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112025 restraints weight = 33339.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111996 restraints weight = 29419.973| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13951 Z= 0.165 Angle : 0.550 6.895 18886 Z= 0.283 Chirality : 0.042 0.200 2198 Planarity : 0.004 0.041 2403 Dihedral : 3.915 20.524 1868 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.21), residues: 1703 helix: 1.74 (0.17), residues: 985 sheet: 0.14 (0.39), residues: 186 loop : -0.75 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 15 TYR 0.021 0.002 TYR B 136 PHE 0.031 0.002 PHE A 530 TRP 0.010 0.001 TRP M 421 HIS 0.018 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00395 (13951) covalent geometry : angle 0.55023 (18886) hydrogen bonds : bond 0.03663 ( 798) hydrogen bonds : angle 4.13438 ( 2334) *********************** 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 169 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8818 (tt) cc_final: 0.8567 (tt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1062 time to fit residues: 27.2859 Evaluate side-chains 123 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 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 = 0.3608 r_free = 0.3608 target = 0.131647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119566 restraints weight = 19514.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113792 restraints weight = 28059.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113040 restraints weight = 30849.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113290 restraints weight = 31876.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113897 restraints weight = 27973.346| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1922 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= 0.114 Angle : 0.519 7.317 18886 Z= 0.270 Chirality : 0.040 0.153 2198 Planarity : 0.003 0.040 2403 Dihedral : 3.869 19.911 1868 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1703 helix: 1.78 (0.17), residues: 988 sheet: 0.29 (0.40), residues: 179 loop : -0.79 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 15 TYR 0.015 0.001 TYR A 88 PHE 0.018 0.001 PHE B 581 TRP 0.015 0.001 TRP A 462 HIS 0.015 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00258 (13951) covalent geometry : angle 0.51888 (18886) hydrogen bonds : bond 0.03348 ( 798) hydrogen bonds : angle 4.06111 ( 2334) *********************** 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 180 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8779 (tt) cc_final: 0.8503 (tt) REVERT: B 187 ILE cc_start: 0.7664 (mm) cc_final: 0.7252 (mm) REVERT: S 1 MET cc_start: 0.7374 (ptt) cc_final: 0.7036 (ptm) REVERT: S 21 MET cc_start: 0.7869 (ttp) cc_final: 0.7636 (ttp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1152 time to fit residues: 31.1077 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 : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 28 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 158 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** 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 = 0.3609 r_free = 0.3609 target = 0.132044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120757 restraints weight = 19553.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117613 restraints weight = 26285.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114951 restraints weight = 34175.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115026 restraints weight = 33681.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114924 restraints weight = 28505.197| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13951 Z= 0.117 Angle : 0.517 7.629 18886 Z= 0.267 Chirality : 0.040 0.150 2198 Planarity : 0.003 0.040 2403 Dihedral : 3.843 20.231 1868 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1703 helix: 1.82 (0.17), residues: 987 sheet: 0.26 (0.40), residues: 179 loop : -0.77 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 15 TYR 0.016 0.001 TYR A 545 PHE 0.016 0.001 PHE B 581 TRP 0.014 0.001 TRP A 462 HIS 0.016 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00267 (13951) covalent geometry : angle 0.51731 (18886) hydrogen bonds : bond 0.03313 ( 798) hydrogen bonds : angle 4.07283 ( 2334) *********************** 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 175 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8706 (tt) cc_final: 0.8409 (tt) REVERT: S 1 MET cc_start: 0.7385 (ptt) cc_final: 0.7156 (ptm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1130 time to fit residues: 29.9173 Evaluate side-chains 131 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 0.0970 chunk 164 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.0970 chunk 143 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.132811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121092 restraints weight = 19700.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117233 restraints weight = 26715.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115030 restraints weight = 30829.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115156 restraints weight = 32024.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115364 restraints weight = 28813.738| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13951 Z= 0.107 Angle : 0.511 7.966 18886 Z= 0.264 Chirality : 0.040 0.161 2198 Planarity : 0.003 0.040 2403 Dihedral : 3.821 20.201 1868 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.21), residues: 1703 helix: 1.84 (0.17), residues: 988 sheet: 0.25 (0.40), residues: 181 loop : -0.78 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 15 TYR 0.021 0.001 TYR B 136 PHE 0.018 0.001 PHE A 523 TRP 0.015 0.001 TRP A 462 HIS 0.020 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00241 (13951) covalent geometry : angle 0.51123 (18886) hydrogen bonds : bond 0.03196 ( 798) hydrogen bonds : angle 4.02314 ( 2334) *********************** 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 177 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8680 (tt) cc_final: 0.8458 (tt) REVERT: S 1 MET cc_start: 0.7476 (ptt) cc_final: 0.7172 (ptm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1157 time to fit residues: 30.7881 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 : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 0.0980 chunk 72 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.130581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118850 restraints weight = 19607.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115675 restraints weight = 26361.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112958 restraints weight = 32945.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112839 restraints weight = 34531.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112839 restraints weight = 31291.130| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13951 Z= 0.143 Angle : 0.534 7.981 18886 Z= 0.277 Chirality : 0.041 0.167 2198 Planarity : 0.004 0.042 2403 Dihedral : 3.877 21.779 1868 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1703 helix: 1.81 (0.17), residues: 987 sheet: 0.12 (0.40), residues: 182 loop : -0.80 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 110 TYR 0.017 0.001 TYR A 545 PHE 0.016 0.002 PHE S 49 TRP 0.010 0.001 TRP M 421 HIS 0.015 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00341 (13951) covalent geometry : angle 0.53446 (18886) hydrogen bonds : bond 0.03449 ( 798) hydrogen bonds : angle 4.11333 ( 2334) ********************** 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 172 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8802 (tt) cc_final: 0.8542 (tt) REVERT: M 209 MET cc_start: 0.7743 (mmm) cc_final: 0.7518 (mmm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1105 time to fit residues: 28.8520 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 : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.131287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119480 restraints weight = 19662.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113763 restraints weight = 26595.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112170 restraints weight = 34634.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112771 restraints weight = 34315.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112661 restraints weight = 29125.743| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2171 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 : 0.547 21.280 18886 Z= 0.276 Chirality : 0.041 0.282 2198 Planarity : 0.004 0.066 2403 Dihedral : 3.873 21.722 1868 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1703 helix: 1.79 (0.17), residues: 988 sheet: 0.06 (0.40), residues: 184 loop : -0.78 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 10 TYR 0.015 0.001 TYR B 136 PHE 0.016 0.001 PHE S 49 TRP 0.013 0.001 TRP A 462 HIS 0.009 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00285 (13951) covalent geometry : angle 0.54684 (18886) hydrogen bonds : bond 0.03322 ( 798) hydrogen bonds : angle 4.06622 ( 2334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2176.04 seconds wall clock time: 38 minutes 38.42 seconds (2318.42 seconds total)