Starting phenix.real_space_refine on Thu Jul 2 13:33:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tcg_25811/07_2026/7tcg_25811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tcg_25811/07_2026/7tcg_25811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tcg_25811/07_2026/7tcg_25811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tcg_25811/07_2026/7tcg_25811.map" model { file = "/net/cci-nas-00/data/ceres_data/7tcg_25811/07_2026/7tcg_25811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tcg_25811/07_2026/7tcg_25811.cif" } resolution = 3.8 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= 0.001 sd= 0.065 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 5763 2.51 5 N 1465 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8891 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5002 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'I0O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.20 Number of scatterers: 8891 At special positions: 0 Unit cell: (87.2, 88.072, 158.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 1 15.00 O 1623 8.00 N 1465 7.00 C 5763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 372.1 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 57.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.704A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 Processing helix chain 'A' and resid 43 through 47 removed outlier: 4.038A pdb=" N GLU A 46 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.797A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.844A pdb=" N ILE A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 120 removed outlier: 3.936A pdb=" N GLU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.738A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.771A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 221 removed outlier: 3.598A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 4.094A pdb=" N ILE A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.685A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 4.238A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N MET A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 325 removed outlier: 3.534A pdb=" N ILE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 4.152A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.792A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.636A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 3.863A pdb=" N ALA A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 550 removed outlier: 3.576A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 removed outlier: 4.162A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 555 " --> pdb=" O MET A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 5.369A pdb=" N ILE A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 602 removed outlier: 4.199A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 614 through 644 removed outlier: 3.811A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 622 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 641 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.665A pdb=" N GLU B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 158 removed outlier: 3.920A pdb=" N LYS B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.720A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 101 through 108 Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.554A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 145 through 157 Processing helix chain 'C' and resid 175 through 191 removed outlier: 3.544A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.958A pdb=" N LEU C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.608A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.808A pdb=" N LYS A 354 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 485 " --> pdb=" O LYS A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363 removed outlier: 3.766A pdb=" N VAL A 363 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 405 removed outlier: 7.613A pdb=" N ALA A 403 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 440 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 405 " --> pdb=" O LEU A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 29 removed outlier: 5.577A pdb=" N ALA B 6 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N HIS B 65 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS B 8 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR B 63 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 66 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 14 removed outlier: 3.510A pdb=" N TYR B 13 " --> pdb=" O GLN B 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 90 removed outlier: 3.501A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 213 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.193A pdb=" N ALA C 6 " --> pdb=" O HIS C 65 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N HIS C 65 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS C 8 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR C 63 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 38 removed outlier: 6.567A pdb=" N SER C 37 " --> pdb=" O ILE C 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 430 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2794 1.34 - 1.46: 1603 1.46 - 1.58: 4564 1.58 - 1.70: 2 1.70 - 1.82: 74 Bond restraints: 9037 Sorted by residual: bond pdb=" O5 I0O A 701 " pdb=" P2 I0O A 701 " ideal model delta sigma weight residual 1.658 1.607 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" C6 I0O A 701 " pdb=" C7 I0O A 701 " ideal model delta sigma weight residual 1.558 1.524 0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" CB PRO A 357 " pdb=" CG PRO A 357 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.55e+00 bond pdb=" C25 I0O A 701 " pdb=" C26 I0O A 701 " ideal model delta sigma weight residual 1.540 1.515 0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C20 I0O A 701 " pdb=" C21 I0O A 701 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.00e-02 2.50e+03 1.45e+00 ... (remaining 9032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11936 1.81 - 3.63: 171 3.63 - 5.44: 31 5.44 - 7.26: 4 7.26 - 9.07: 4 Bond angle restraints: 12146 Sorted by residual: angle pdb=" CB LYS A 335 " pdb=" CG LYS A 335 " pdb=" CD LYS A 335 " ideal model delta sigma weight residual 111.30 118.32 -7.02 2.30e+00 1.89e-01 9.30e+00 angle pdb=" CG1 ILE C 197 " pdb=" CB ILE C 197 " pdb=" CG2 ILE C 197 " ideal model delta sigma weight residual 110.70 101.63 9.07 3.00e+00 1.11e-01 9.15e+00 angle pdb=" N GLN C 188 " pdb=" CA GLN C 188 " pdb=" CB GLN C 188 " ideal model delta sigma weight residual 110.39 115.07 -4.68 1.66e+00 3.63e-01 7.94e+00 angle pdb=" CB MET A 132 " pdb=" CG MET A 132 " pdb=" SD MET A 132 " ideal model delta sigma weight residual 112.70 120.90 -8.20 3.00e+00 1.11e-01 7.48e+00 angle pdb=" C VAL A 612 " pdb=" N TRP A 613 " pdb=" CA TRP A 613 " ideal model delta sigma weight residual 121.54 126.70 -5.16 1.91e+00 2.74e-01 7.29e+00 ... (remaining 12141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4823 17.93 - 35.86: 538 35.86 - 53.79: 101 53.79 - 71.72: 17 71.72 - 89.65: 8 Dihedral angle restraints: 5487 sinusoidal: 2243 harmonic: 3244 Sorted by residual: dihedral pdb=" CA ASP C 218 " pdb=" C ASP C 218 " pdb=" N GLY C 219 " pdb=" CA GLY C 219 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLY A 609 " pdb=" C GLY A 609 " pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA SER A 610 " pdb=" C SER A 610 " pdb=" N GLU A 611 " pdb=" CA GLU A 611 " ideal model delta harmonic sigma weight residual 180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1158 0.053 - 0.106: 209 0.106 - 0.160: 29 0.160 - 0.213: 3 0.213 - 0.266: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB ILE C 197 " pdb=" CA ILE C 197 " pdb=" CG1 ILE C 197 " pdb=" CG2 ILE C 197 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE C 164 " pdb=" CA ILE C 164 " pdb=" CG1 ILE C 164 " pdb=" CG2 ILE C 164 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C9 I0O A 701 " pdb=" C10 I0O A 701 " pdb=" C8 I0O A 701 " pdb=" N16 I0O A 701 " both_signs ideal model delta sigma weight residual False -2.55 -2.37 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 1397 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C31 I0O A 701 " 0.062 2.00e-02 2.50e+03 5.24e-02 3.43e+01 pdb=" C32 I0O A 701 " -0.084 2.00e-02 2.50e+03 pdb=" C33 I0O A 701 " -0.020 2.00e-02 2.50e+03 pdb=" C34 I0O A 701 " -0.007 2.00e-02 2.50e+03 pdb=" C35 I0O A 701 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 I0O A 701 " 0.048 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" C27 I0O A 701 " -0.066 2.00e-02 2.50e+03 pdb=" C28 I0O A 701 " -0.006 2.00e-02 2.50e+03 pdb=" C29 I0O A 701 " 0.035 2.00e-02 2.50e+03 pdb=" C30 I0O A 701 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 I0O A 701 " -0.057 2.00e-02 2.50e+03 3.71e-02 1.72e+01 pdb=" C12 I0O A 701 " -0.018 2.00e-02 2.50e+03 pdb=" C14 I0O A 701 " -0.005 2.00e-02 2.50e+03 pdb=" C15 I0O A 701 " 0.036 2.00e-02 2.50e+03 pdb=" C5 I0O A 701 " 0.044 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 129 2.69 - 3.24: 8566 3.24 - 3.80: 12760 3.80 - 4.35: 15937 4.35 - 4.90: 27122 Nonbonded interactions: 64514 Sorted by model distance: nonbonded pdb=" OG1 THR B 101 " pdb=" OE1 GLU B 104 " model vdw 2.138 3.040 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.170 3.040 nonbonded pdb=" ND2 ASN A 362 " pdb=" OD1 ASN A 382 " model vdw 2.220 3.120 nonbonded pdb=" OG SER C 145 " pdb=" OE1 GLN C 148 " model vdw 2.266 3.040 nonbonded pdb=" ND2 ASN A 14 " pdb=" OE2 GLU A 107 " model vdw 2.322 3.120 ... (remaining 64509 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 1.890 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.140 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.080 9037 Z= 0.121 Angle : 0.557 9.073 12146 Z= 0.284 Chirality : 0.042 0.266 1400 Planarity : 0.004 0.063 1517 Dihedral : 15.197 89.645 3401 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -0.53 (0.27), residues: 1115 helix: 1.10 (0.23), residues: 606 sheet: -0.34 (0.72), residues: 72 loop : -2.57 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.017 0.001 TYR B 222 PHE 0.012 0.001 PHE A 529 TRP 0.029 0.006 TRP A 605 HIS 0.002 0.000 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9037) covalent geometry : angle 0.55734 / 0.28 (12146) hydrogen bonds : bond 0.15625 / 9.93 ( 430) hydrogen bonds : angle 4.96083 / 3.58 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.221 Fit side-chains REVERT: A 226 LYS cc_start: 0.7594 (ptpt) cc_final: 0.7229 (mmtm) REVERT: C 134 TYR cc_start: 0.8376 (t80) cc_final: 0.8168 (t80) REVERT: C 234 THR cc_start: 0.8956 (m) cc_final: 0.8730 (t) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0744 time to fit residues: 14.8586 Evaluate side-chains 121 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.198680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159612 restraints weight = 11205.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154645 restraints weight = 14360.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149821 restraints weight = 14607.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149832 restraints weight = 14733.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148428 restraints weight = 12846.457| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9037 Z= 0.124 Angle : 0.514 6.476 12146 Z= 0.272 Chirality : 0.041 0.183 1400 Planarity : 0.003 0.037 1517 Dihedral : 5.687 74.554 1248 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.13 % Allowed : 8.76 % Favored : 90.10 % 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: -0.46 (0.26), residues: 1115 helix: 1.19 (0.22), residues: 611 sheet: -0.59 (0.65), residues: 85 loop : -2.62 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 122 TYR 0.021 0.001 TYR A 270 PHE 0.024 0.001 PHE C 82 TRP 0.016 0.003 TRP A 613 HIS 0.003 0.000 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9037) covalent geometry : angle 0.51439 / 0.27 (12146) hydrogen bonds : bond 0.04879 / 3.14 ( 430) hydrogen bonds : angle 4.11149 / 2.96 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.364 Fit side-chains REVERT: A 226 LYS cc_start: 0.7776 (ptpt) cc_final: 0.7374 (mmtm) REVERT: A 414 LYS cc_start: 0.8475 (tptm) cc_final: 0.7329 (tptp) REVERT: B 221 MET cc_start: 0.8067 (mmp) cc_final: 0.7546 (mmt) REVERT: C 134 TYR cc_start: 0.8297 (t80) cc_final: 0.8030 (t80) outliers start: 11 outliers final: 10 residues processed: 125 average time/residue: 0.0774 time to fit residues: 13.9030 Evaluate side-chains 124 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.185910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.140325 restraints weight = 11600.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138684 restraints weight = 18422.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.136183 restraints weight = 19658.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133912 restraints weight = 18891.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131977 restraints weight = 19481.075| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9037 Z= 0.107 Angle : 0.486 7.109 12146 Z= 0.256 Chirality : 0.040 0.175 1400 Planarity : 0.003 0.038 1517 Dihedral : 5.582 56.460 1248 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.44 % Allowed : 11.44 % Favored : 87.11 % 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: -0.28 (0.26), residues: 1115 helix: 1.37 (0.22), residues: 612 sheet: -0.61 (0.66), residues: 80 loop : -2.56 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 122 TYR 0.023 0.001 TYR A 270 PHE 0.018 0.001 PHE C 82 TRP 0.014 0.003 TRP A 613 HIS 0.002 0.000 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9037) covalent geometry : angle 0.48644 / 0.26 (12146) hydrogen bonds : bond 0.04359 / 2.79 ( 430) hydrogen bonds : angle 3.76059 / 2.67 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8383 (mmm) cc_final: 0.8100 (tpp) REVERT: A 226 LYS cc_start: 0.7718 (ptpt) cc_final: 0.7347 (mmtm) REVERT: A 414 LYS cc_start: 0.8491 (tptm) cc_final: 0.7384 (tptp) REVERT: C 134 TYR cc_start: 0.8211 (t80) cc_final: 0.7894 (t80) REVERT: C 221 MET cc_start: 0.7371 (tmm) cc_final: 0.7117 (tmm) outliers start: 14 outliers final: 12 residues processed: 131 average time/residue: 0.0880 time to fit residues: 16.5371 Evaluate side-chains 126 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 109 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.200349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.163318 restraints weight = 11250.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.160463 restraints weight = 26182.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.156979 restraints weight = 12472.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.154626 restraints weight = 15679.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.154841 restraints weight = 12909.087| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9037 Z= 0.106 Angle : 0.484 8.229 12146 Z= 0.254 Chirality : 0.040 0.175 1400 Planarity : 0.003 0.046 1517 Dihedral : 5.044 55.150 1248 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.65 % Allowed : 13.20 % Favored : 85.15 % 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: -0.20 (0.26), residues: 1115 helix: 1.44 (0.23), residues: 612 sheet: -0.67 (0.66), residues: 80 loop : -2.53 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 122 TYR 0.023 0.001 TYR A 270 PHE 0.012 0.001 PHE A 606 TRP 0.013 0.002 TRP A 605 HIS 0.002 0.000 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9037) covalent geometry : angle 0.48418 / 0.25 (12146) hydrogen bonds : bond 0.04250 / 2.73 ( 430) hydrogen bonds : angle 3.64238 / 2.58 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8396 (mmm) cc_final: 0.8173 (tpp) REVERT: A 226 LYS cc_start: 0.7878 (ptpt) cc_final: 0.7390 (mmtm) REVERT: A 414 LYS cc_start: 0.8475 (tptm) cc_final: 0.7344 (tptp) REVERT: B 221 MET cc_start: 0.8171 (mmp) cc_final: 0.7568 (mmt) REVERT: C 134 TYR cc_start: 0.8226 (t80) cc_final: 0.7800 (t80) REVERT: C 217 LYS cc_start: 0.7866 (tptp) cc_final: 0.7120 (tptm) REVERT: C 221 MET cc_start: 0.7409 (tmm) cc_final: 0.7087 (tmm) outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 0.0794 time to fit residues: 14.6262 Evaluate side-chains 126 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 510 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.184906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.141766 restraints weight = 11723.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.138826 restraints weight = 19793.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136448 restraints weight = 19472.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134887 restraints weight = 18695.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.134026 restraints weight = 18891.931| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9037 Z= 0.106 Angle : 0.488 8.972 12146 Z= 0.256 Chirality : 0.040 0.144 1400 Planarity : 0.003 0.047 1517 Dihedral : 4.888 58.643 1248 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.55 % Allowed : 14.33 % Favored : 84.12 % 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: -0.16 (0.27), residues: 1115 helix: 1.49 (0.23), residues: 612 sheet: -0.65 (0.66), residues: 80 loop : -2.53 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.024 0.001 TYR A 270 PHE 0.027 0.001 PHE C 82 TRP 0.015 0.002 TRP A 605 HIS 0.002 0.000 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9037) covalent geometry : angle 0.48847 / 0.26 (12146) hydrogen bonds : bond 0.04147 / 2.65 ( 430) hydrogen bonds : angle 3.56401 / 2.53 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8391 (mmm) cc_final: 0.8186 (tpp) REVERT: A 226 LYS cc_start: 0.7801 (ptpt) cc_final: 0.7421 (mmtm) REVERT: A 414 LYS cc_start: 0.8534 (tptm) cc_final: 0.7477 (tptp) REVERT: C 134 TYR cc_start: 0.8186 (t80) cc_final: 0.7780 (t80) REVERT: C 221 MET cc_start: 0.7360 (tmm) cc_final: 0.7109 (tmm) outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 0.0891 time to fit residues: 15.9895 Evaluate side-chains 131 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 97 optimal weight: 0.0060 chunk 49 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.200260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.158677 restraints weight = 11245.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.159915 restraints weight = 23092.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.161031 restraints weight = 16039.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.161317 restraints weight = 9389.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.162525 restraints weight = 7691.182| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9037 Z= 0.098 Angle : 0.474 6.341 12146 Z= 0.249 Chirality : 0.040 0.138 1400 Planarity : 0.003 0.045 1517 Dihedral : 4.788 59.711 1248 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.34 % Allowed : 14.95 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.27), residues: 1115 helix: 1.55 (0.23), residues: 613 sheet: -0.97 (0.64), residues: 84 loop : -2.49 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.025 0.001 TYR A 270 PHE 0.011 0.001 PHE A 606 TRP 0.017 0.003 TRP A 605 HIS 0.002 0.000 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 9037) covalent geometry : angle 0.47352 / 0.25 (12146) hydrogen bonds : bond 0.03818 / 2.44 ( 430) hydrogen bonds : angle 3.46596 / 2.46 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 202 MET cc_start: 0.7951 (mmp) cc_final: 0.7412 (mmt) REVERT: A 226 LYS cc_start: 0.7827 (ptpt) cc_final: 0.7430 (mmtm) REVERT: A 414 LYS cc_start: 0.8488 (tptm) cc_final: 0.7547 (tptp) REVERT: A 483 PHE cc_start: 0.7693 (t80) cc_final: 0.7476 (t80) REVERT: B 221 MET cc_start: 0.7984 (mmp) cc_final: 0.7521 (mmt) REVERT: C 134 TYR cc_start: 0.8160 (t80) cc_final: 0.7766 (t80) REVERT: C 217 LYS cc_start: 0.7789 (tptp) cc_final: 0.7056 (tptm) REVERT: C 221 MET cc_start: 0.7214 (tmm) cc_final: 0.6968 (tmm) outliers start: 13 outliers final: 12 residues processed: 130 average time/residue: 0.0802 time to fit residues: 14.9576 Evaluate side-chains 130 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 93 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.182694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140946 restraints weight = 11738.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.138086 restraints weight = 21089.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.136161 restraints weight = 21143.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.135248 restraints weight = 19935.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134489 restraints weight = 17932.961| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9037 Z= 0.134 Angle : 0.529 10.971 12146 Z= 0.274 Chirality : 0.041 0.137 1400 Planarity : 0.003 0.042 1517 Dihedral : 4.929 59.662 1248 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.65 % Allowed : 16.08 % Favored : 82.27 % 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: -0.22 (0.27), residues: 1115 helix: 1.45 (0.23), residues: 613 sheet: -0.79 (0.65), residues: 81 loop : -2.56 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.025 0.001 TYR A 270 PHE 0.031 0.001 PHE C 82 TRP 0.021 0.003 TRP A 605 HIS 0.003 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 9037) covalent geometry : angle 0.52872 / 0.27 (12146) hydrogen bonds : bond 0.04701 / 3.02 ( 430) hydrogen bonds : angle 3.62272 / 2.57 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 226 LYS cc_start: 0.7821 (ptpt) cc_final: 0.7450 (mmtm) REVERT: A 414 LYS cc_start: 0.8491 (tptm) cc_final: 0.7589 (tptp) REVERT: B 221 MET cc_start: 0.7986 (mmp) cc_final: 0.7606 (mmt) REVERT: C 134 TYR cc_start: 0.8222 (t80) cc_final: 0.7796 (t80) REVERT: C 221 MET cc_start: 0.7248 (tmm) cc_final: 0.7008 (tmm) outliers start: 16 outliers final: 14 residues processed: 129 average time/residue: 0.0816 time to fit residues: 15.1959 Evaluate side-chains 132 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 87 optimal weight: 0.0770 chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.185290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138207 restraints weight = 11752.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134094 restraints weight = 18272.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131062 restraints weight = 17948.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129727 restraints weight = 16941.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128625 restraints weight = 15470.263| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9037 Z= 0.106 Angle : 0.507 9.652 12146 Z= 0.265 Chirality : 0.040 0.190 1400 Planarity : 0.003 0.051 1517 Dihedral : 4.880 59.342 1248 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.44 % Allowed : 16.39 % Favored : 82.16 % 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: -0.17 (0.27), residues: 1115 helix: 1.53 (0.23), residues: 612 sheet: -1.07 (0.63), residues: 85 loop : -2.53 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 122 TYR 0.022 0.001 TYR A 270 PHE 0.033 0.001 PHE B 236 TRP 0.024 0.003 TRP A 605 HIS 0.001 0.000 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9037) covalent geometry : angle 0.50713 / 0.26 (12146) hydrogen bonds : bond 0.04109 / 2.62 ( 430) hydrogen bonds : angle 3.52289 / 2.50 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 226 LYS cc_start: 0.7882 (ptpt) cc_final: 0.7418 (mmtm) REVERT: A 414 LYS cc_start: 0.8473 (tptm) cc_final: 0.7578 (tptp) REVERT: B 221 MET cc_start: 0.8035 (mmp) cc_final: 0.7612 (mmt) REVERT: C 34 GLU cc_start: 0.6861 (pm20) cc_final: 0.6539 (pm20) REVERT: C 134 TYR cc_start: 0.8201 (t80) cc_final: 0.7756 (t80) REVERT: C 217 LYS cc_start: 0.7794 (tptp) cc_final: 0.7015 (tptm) REVERT: C 221 MET cc_start: 0.7140 (tmm) cc_final: 0.6919 (tmm) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 0.0782 time to fit residues: 14.2894 Evaluate side-chains 131 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.187721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.147060 restraints weight = 11320.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145611 restraints weight = 19355.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.143107 restraints weight = 15810.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.140217 restraints weight = 17661.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138104 restraints weight = 17432.640| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9037 Z= 0.269 Angle : 0.668 8.654 12146 Z= 0.351 Chirality : 0.045 0.172 1400 Planarity : 0.004 0.050 1517 Dihedral : 5.521 58.172 1248 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.44 % Allowed : 16.70 % Favored : 81.86 % 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: -0.75 (0.26), residues: 1115 helix: 1.00 (0.23), residues: 610 sheet: -1.20 (0.62), residues: 88 loop : -2.70 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 122 TYR 0.027 0.002 TYR A 270 PHE 0.034 0.002 PHE A 258 TRP 0.025 0.003 TRP A 605 HIS 0.006 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.27 ( 9037) covalent geometry : angle 0.66794 / 0.35 (12146) hydrogen bonds : bond 0.06853 / 4.45 ( 430) hydrogen bonds : angle 4.20466 / 2.98 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.411 Fit side-chains REVERT: A 226 LYS cc_start: 0.7832 (ptpt) cc_final: 0.7434 (mmtm) REVERT: A 414 LYS cc_start: 0.8433 (tptm) cc_final: 0.7576 (tptp) REVERT: A 580 ILE cc_start: 0.9236 (pt) cc_final: 0.8741 (mp) REVERT: B 221 MET cc_start: 0.8061 (mmp) cc_final: 0.7287 (mmt) REVERT: C 34 GLU cc_start: 0.7053 (pm20) cc_final: 0.6510 (pm20) REVERT: C 134 TYR cc_start: 0.8309 (t80) cc_final: 0.7913 (t80) REVERT: C 221 MET cc_start: 0.7410 (tmm) cc_final: 0.7103 (tmm) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.0824 time to fit residues: 14.4686 Evaluate side-chains 120 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.195202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.158466 restraints weight = 11111.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156674 restraints weight = 19741.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152724 restraints weight = 18846.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150542 restraints weight = 19673.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.149019 restraints weight = 18523.697| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9037 Z= 0.117 Angle : 0.523 7.656 12146 Z= 0.277 Chirality : 0.041 0.186 1400 Planarity : 0.003 0.051 1517 Dihedral : 5.239 59.144 1248 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.24 % Allowed : 17.22 % Favored : 81.55 % 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: -0.41 (0.26), residues: 1115 helix: 1.29 (0.23), residues: 611 sheet: -0.98 (0.63), residues: 81 loop : -2.59 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.026 0.001 TYR A 270 PHE 0.025 0.001 PHE A 258 TRP 0.027 0.003 TRP A 605 HIS 0.002 0.000 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9037) covalent geometry : angle 0.52321 / 0.28 (12146) hydrogen bonds : bond 0.04713 / 3.00 ( 430) hydrogen bonds : angle 3.72641 / 2.65 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 226 LYS cc_start: 0.7809 (ptpt) cc_final: 0.7419 (mmtm) REVERT: A 291 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8498 (tt) REVERT: A 414 LYS cc_start: 0.8433 (tptm) cc_final: 0.7569 (tptp) REVERT: B 221 MET cc_start: 0.7967 (mmp) cc_final: 0.7230 (mmt) REVERT: C 34 GLU cc_start: 0.6941 (pm20) cc_final: 0.6608 (pm20) REVERT: C 134 TYR cc_start: 0.8185 (t80) cc_final: 0.7849 (t80) REVERT: C 221 MET cc_start: 0.7152 (tmm) cc_final: 0.6900 (tmm) outliers start: 12 outliers final: 10 residues processed: 134 average time/residue: 0.0822 time to fit residues: 16.0656 Evaluate side-chains 132 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.194127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.158668 restraints weight = 11207.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155504 restraints weight = 17980.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152541 restraints weight = 17360.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.151355 restraints weight = 16842.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150045 restraints weight = 14922.079| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9037 Z= 0.154 Angle : 0.575 12.386 12146 Z= 0.297 Chirality : 0.041 0.175 1400 Planarity : 0.003 0.050 1517 Dihedral : 5.248 59.388 1248 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.55 % Allowed : 17.63 % Favored : 80.82 % 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: -0.50 (0.26), residues: 1115 helix: 1.25 (0.23), residues: 610 sheet: -1.21 (0.61), residues: 86 loop : -2.65 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 122 TYR 0.027 0.001 TYR A 270 PHE 0.028 0.001 PHE C 82 TRP 0.029 0.004 TRP A 605 HIS 0.003 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 9037) covalent geometry : angle 0.57498 / 0.30 (12146) hydrogen bonds : bond 0.05177 / 3.32 ( 430) hydrogen bonds : angle 3.79240 / 2.69 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.83 seconds wall clock time: 25 minutes 19.72 seconds (1519.72 seconds total)