Starting phenix.real_space_refine on Thu Jul 2 15:41:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tch_25812/07_2026/7tch_25812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tch_25812/07_2026/7tch_25812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tch_25812/07_2026/7tch_25812.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tch_25812/07_2026/7tch_25812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tch_25812/07_2026/7tch_25812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tch_25812/07_2026/7tch_25812.map" model { file = "/net/cci-nas-00/data/ceres_data/7tch_25812/07_2026/7tch_25812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tch_25812/07_2026/7tch_25812.cif" } resolution = 3.7 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= -0.000 sd= 0.026 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 7 5.49 5 S 39 5.16 5 C 5838 2.51 5 N 1491 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 9043 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5078 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 10, 'TRANS': 634} Chain: "B" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1922 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "C" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1922 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'I0O': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.56, per 1000 atoms: 0.17 Number of scatterers: 9043 At special positions: 0 Unit cell: (77.608, 82.84, 156.96, 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 7 15.00 O 1668 8.00 N 1491 7.00 C 5838 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: 0.79 Conformation dependent library (CDL) restraints added in 323.8 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 55.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.681A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.793A pdb=" N TYR A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.932A pdb=" N VAL A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 52 through 84 removed outlier: 3.728A pdb=" N ALA A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 96 through 138 removed outlier: 3.584A pdb=" N ILE A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 177 removed outlier: 3.907A pdb=" N VAL A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 221 removed outlier: 3.731A pdb=" N GLU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 260 removed outlier: 4.061A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 removed outlier: 4.048A pdb=" N ARG A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 288 through 326 removed outlier: 4.150A pdb=" N LEU A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.734A pdb=" N ALA A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 461 through 472 removed outlier: 4.173A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 513 through 524 removed outlier: 3.697A pdb=" N PHE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 557 removed outlier: 3.953A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.625A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 602 removed outlier: 3.896A pdb=" N ILE A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 614 through 644 removed outlier: 3.781A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 620 " --> pdb=" O MET A 616 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 622 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 77 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 116 through 132 Processing helix chain 'B' and resid 147 through 157 removed outlier: 4.043A pdb=" N ALA B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 3.511A pdb=" N ARG B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.826A 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 46 through 54 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 Processing helix chain 'C' and resid 109 through 112 removed outlier: 4.184A pdb=" N ILE C 112 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.799A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 175 through 192 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 231 through 246 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 432 through 435 removed outlier: 3.529A pdb=" N GLN A 433 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 427 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN A 362 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 363 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 404 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALA A 403 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 439 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.542A pdb=" N THR B 63 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.946A pdb=" N LYS B 11 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 22 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.583A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 165 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL B 200 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 213 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLN B 224 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE B 215 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 23 through 26 removed outlier: 3.954A pdb=" N LEU C 23 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 11 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE C 9 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 63 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE C 9 " --> pdb=" O HIS C 61 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS C 61 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 168 removed outlier: 3.656A pdb=" N VAL C 200 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 36 " --> pdb=" O MET C 199 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE C 35 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE C 214 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER C 37 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE C 216 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N MET C 39 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 213 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 224 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C 215 " --> pdb=" O TYR C 222 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1269 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: 1.19 Time building geometry restraints manager: 1.05 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: 2836 1.34 - 1.46: 1807 1.46 - 1.58: 4465 1.58 - 1.69: 12 1.69 - 1.81: 74 Bond restraints: 9194 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 6.50e+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 2.93e+00 bond pdb=" C20 I0O A 701 " pdb=" C21 I0O A 701 " ideal model delta sigma weight residual 1.540 1.513 0.027 2.00e-02 2.50e+03 1.77e+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 1.52e+00 bond pdb=" N ILE A 273 " pdb=" CA ILE A 273 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.25e-02 6.40e+03 1.47e+00 ... (remaining 9189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 12039 1.57 - 3.15: 270 3.15 - 4.72: 52 4.72 - 6.30: 9 6.30 - 7.87: 5 Bond angle restraints: 12375 Sorted by residual: angle pdb=" C ALA B 128 " pdb=" N LYS B 129 " pdb=" CA LYS B 129 " ideal model delta sigma weight residual 121.94 115.18 6.76 2.00e+00 2.50e-01 1.14e+01 angle pdb=" N ASN B 142 " pdb=" CA ASN B 142 " pdb=" C ASN B 142 " ideal model delta sigma weight residual 113.18 108.70 4.48 1.33e+00 5.65e-01 1.13e+01 angle pdb=" C ILE A 26 " pdb=" N PHE A 27 " pdb=" CA PHE A 27 " ideal model delta sigma weight residual 121.14 115.47 5.67 1.75e+00 3.27e-01 1.05e+01 angle pdb=" CB LYS A 338 " pdb=" CG LYS A 338 " pdb=" CD LYS A 338 " ideal model delta sigma weight residual 111.30 118.68 -7.38 2.30e+00 1.89e-01 1.03e+01 angle pdb=" N VAL A 325 " pdb=" CA VAL A 325 " pdb=" C VAL A 325 " ideal model delta sigma weight residual 113.39 109.41 3.98 1.47e+00 4.63e-01 7.34e+00 ... (remaining 12370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 5332 30.21 - 60.42: 194 60.42 - 90.63: 19 90.63 - 120.85: 2 120.85 - 151.06: 5 Dihedral angle restraints: 5552 sinusoidal: 2271 harmonic: 3281 Sorted by residual: dihedral pdb=" CA ILE A 273 " pdb=" C ILE A 273 " pdb=" N SER A 274 " pdb=" CA SER A 274 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" C11 I0O A 701 " pdb=" C12 I0O A 701 " pdb=" C15 I0O A 701 " pdb=" C16 I0O A 701 " ideal model delta sinusoidal sigma weight residual 23.48 -127.58 151.06 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C14 I0O A 701 " pdb=" C12 I0O A 701 " pdb=" C15 I0O A 701 " pdb=" C16 I0O A 701 " ideal model delta sinusoidal sigma weight residual 202.00 53.14 148.86 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1109 0.047 - 0.093: 250 0.093 - 0.140: 59 0.140 - 0.186: 6 0.186 - 0.233: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE A 273 " pdb=" CA ILE A 273 " pdb=" CG1 ILE A 273 " pdb=" CG2 ILE A 273 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.41e-01 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 -2.38 -0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 1423 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 I0O A 701 " -0.117 2.00e-02 2.50e+03 9.58e-02 1.15e+02 pdb=" C13 I0O A 701 " 0.021 2.00e-02 2.50e+03 pdb=" C2 I0O A 701 " 0.151 2.00e-02 2.50e+03 pdb=" C3 I0O A 701 " 0.034 2.00e-02 2.50e+03 pdb=" C4 I0O A 701 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 I0O A 701 " 0.054 2.00e-02 2.50e+03 4.51e-02 2.54e+01 pdb=" C27 I0O A 701 " -0.068 2.00e-02 2.50e+03 pdb=" C28 I0O A 701 " -0.024 2.00e-02 2.50e+03 pdb=" C29 I0O A 701 " -0.006 2.00e-02 2.50e+03 pdb=" C30 I0O A 701 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 I0O A 701 " 0.038 2.00e-02 2.50e+03 2.48e-02 7.70e+00 pdb=" C12 I0O A 701 " 0.013 2.00e-02 2.50e+03 pdb=" C14 I0O A 701 " 0.003 2.00e-02 2.50e+03 pdb=" C15 I0O A 701 " -0.024 2.00e-02 2.50e+03 pdb=" C5 I0O A 701 " -0.030 2.00e-02 2.50e+03 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1819 2.78 - 3.31: 8478 3.31 - 3.84: 13693 3.84 - 4.37: 14961 4.37 - 4.90: 26923 Nonbonded interactions: 65874 Sorted by model distance: nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP B 70 " pdb=" OG1 THR B 72 " model vdw 2.249 3.040 nonbonded pdb=" O SER A 188 " pdb=" ND2 ASN B 142 " model vdw 2.265 3.120 nonbonded pdb=" O TYR B 222 " pdb=" OG1 THR B 223 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 216 " pdb=" ND1 HIS A 596 " model vdw 2.297 3.120 ... (remaining 65869 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: 1.710 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.010 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.051 9194 Z= 0.146 Angle : 0.597 7.871 12375 Z= 0.312 Chirality : 0.043 0.233 1426 Planarity : 0.004 0.096 1534 Dihedral : 16.058 151.057 3442 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.26), residues: 1129 helix: 1.83 (0.22), residues: 570 sheet: -0.31 (0.56), residues: 111 loop : -2.35 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 232 TYR 0.015 0.001 TYR A 627 PHE 0.018 0.001 PHE A 27 TRP 0.008 0.001 TRP A 605 HIS 0.002 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 9194) covalent geometry : angle 0.59694 / 0.31 (12375) hydrogen bonds : bond 0.15854 / 10.14 ( 431) hydrogen bonds : angle 5.28516 / 3.89 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.259 Fit side-chains REVERT: A 197 ILE cc_start: 0.7538 (mm) cc_final: 0.7172 (mm) REVERT: A 391 LYS cc_start: 0.8569 (pttt) cc_final: 0.8291 (ptmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.0817 time to fit residues: 18.2413 Evaluate side-chains 130 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0270 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.156673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114530 restraints weight = 11118.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112137 restraints weight = 13830.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114321 restraints weight = 12264.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114410 restraints weight = 8027.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114671 restraints weight = 7484.356| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9194 Z= 0.134 Angle : 0.549 6.561 12375 Z= 0.293 Chirality : 0.041 0.150 1426 Planarity : 0.003 0.039 1534 Dihedral : 11.498 148.985 1267 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.53 % Allowed : 7.73 % Favored : 90.74 % 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: 0.07 (0.26), residues: 1129 helix: 1.92 (0.22), residues: 592 sheet: -1.23 (0.51), residues: 117 loop : -2.46 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.016 0.001 TYR A 437 PHE 0.025 0.001 PHE A 27 TRP 0.009 0.002 TRP A 605 HIS 0.002 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9194) covalent geometry : angle 0.54896 / 0.29 (12375) hydrogen bonds : bond 0.05887 / 3.73 ( 431) hydrogen bonds : angle 4.22265 / 3.12 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.360 Fit side-chains REVERT: A 197 ILE cc_start: 0.7404 (mm) cc_final: 0.7091 (mm) REVERT: A 391 LYS cc_start: 0.8496 (pttt) cc_final: 0.8280 (ptmm) REVERT: B 58 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8130 (mt0) outliers start: 15 outliers final: 9 residues processed: 137 average time/residue: 0.1012 time to fit residues: 19.4162 Evaluate side-chains 136 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.154181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110943 restraints weight = 11065.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108792 restraints weight = 12307.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110936 restraints weight = 10578.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111259 restraints weight = 7196.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111258 restraints weight = 6664.944| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9194 Z= 0.136 Angle : 0.538 6.752 12375 Z= 0.287 Chirality : 0.041 0.145 1426 Planarity : 0.003 0.035 1534 Dihedral : 11.425 150.457 1267 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.88 % Favored : 92.03 % Rotamer: Outliers : 1.83 % Allowed : 11.29 % Favored : 86.88 % 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 (0.26), residues: 1129 helix: 1.96 (0.22), residues: 591 sheet: -1.27 (0.50), residues: 117 loop : -2.39 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.011 0.001 TYR A 584 PHE 0.023 0.001 PHE A 27 TRP 0.009 0.002 TRP A 605 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9194) covalent geometry : angle 0.53835 / 0.29 (12375) hydrogen bonds : bond 0.05785 / 3.63 ( 431) hydrogen bonds : angle 4.05242 / 2.98 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.431 Fit side-chains REVERT: A 391 LYS cc_start: 0.8617 (pttt) cc_final: 0.8366 (ptmm) REVERT: A 551 MET cc_start: 0.8115 (mmt) cc_final: 0.7595 (mpp) REVERT: B 58 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8191 (mt0) REVERT: C 218 ASP cc_start: 0.7265 (t0) cc_final: 0.6890 (t0) outliers start: 18 outliers final: 16 residues processed: 145 average time/residue: 0.0975 time to fit residues: 20.0655 Evaluate side-chains 141 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 71 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 5.9990 chunk 104 optimal weight: 0.0030 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.0010 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.159439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118090 restraints weight = 11168.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116970 restraints weight = 12948.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.118257 restraints weight = 11499.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118665 restraints weight = 8538.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.119340 restraints weight = 7416.001| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9194 Z= 0.101 Angle : 0.481 6.698 12375 Z= 0.258 Chirality : 0.040 0.128 1426 Planarity : 0.003 0.035 1534 Dihedral : 11.238 154.752 1267 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 1.63 % Allowed : 13.84 % Favored : 84.54 % 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: 0.35 (0.27), residues: 1129 helix: 2.17 (0.23), residues: 589 sheet: -0.96 (0.49), residues: 129 loop : -2.41 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.018 0.001 TYR A 437 PHE 0.018 0.001 PHE A 483 TRP 0.008 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 9194) covalent geometry : angle 0.48106 / 0.26 (12375) hydrogen bonds : bond 0.04487 / 2.81 ( 431) hydrogen bonds : angle 3.68327 / 2.71 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.362 Fit side-chains REVERT: A 260 SER cc_start: 0.8408 (t) cc_final: 0.8172 (t) REVERT: A 391 LYS cc_start: 0.8567 (pttt) cc_final: 0.8343 (ptmm) REVERT: B 58 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8151 (mt0) REVERT: C 125 GLU cc_start: 0.6429 (tt0) cc_final: 0.6226 (tt0) REVERT: C 218 ASP cc_start: 0.7310 (t0) cc_final: 0.6874 (t0) outliers start: 16 outliers final: 12 residues processed: 156 average time/residue: 0.0978 time to fit residues: 21.5889 Evaluate side-chains 144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.155200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113724 restraints weight = 11152.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111043 restraints weight = 12839.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112699 restraints weight = 12530.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113368 restraints weight = 8972.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113256 restraints weight = 8626.676| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9194 Z= 0.132 Angle : 0.540 9.532 12375 Z= 0.283 Chirality : 0.041 0.139 1426 Planarity : 0.003 0.034 1534 Dihedral : 11.267 159.185 1267 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.62 % Favored : 92.29 % Rotamer: Outliers : 1.93 % Allowed : 15.56 % Favored : 82.50 % 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: 0.23 (0.27), residues: 1129 helix: 2.01 (0.22), residues: 592 sheet: -1.01 (0.48), residues: 129 loop : -2.39 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 232 TYR 0.011 0.001 TYR A 584 PHE 0.023 0.001 PHE A 483 TRP 0.008 0.002 TRP A 605 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9194) covalent geometry : angle 0.53991 / 0.28 (12375) hydrogen bonds : bond 0.05398 / 3.37 ( 431) hydrogen bonds : angle 3.83790 / 2.81 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.360 Fit side-chains REVERT: A 260 SER cc_start: 0.8539 (t) cc_final: 0.8284 (t) REVERT: A 391 LYS cc_start: 0.8578 (pttt) cc_final: 0.8341 (ptmm) REVERT: A 483 PHE cc_start: 0.8476 (t80) cc_final: 0.8232 (t80) REVERT: C 125 GLU cc_start: 0.6604 (tt0) cc_final: 0.6349 (tt0) REVERT: C 218 ASP cc_start: 0.7437 (t0) cc_final: 0.6998 (t0) outliers start: 19 outliers final: 17 residues processed: 148 average time/residue: 0.0981 time to fit residues: 20.4750 Evaluate side-chains 151 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.158568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.116713 restraints weight = 11054.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116066 restraints weight = 12969.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116491 restraints weight = 11785.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.116836 restraints weight = 10141.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117442 restraints weight = 8575.594| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9194 Z= 0.107 Angle : 0.506 7.869 12375 Z= 0.267 Chirality : 0.040 0.134 1426 Planarity : 0.003 0.033 1534 Dihedral : 11.062 166.885 1267 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.73 % Favored : 93.18 % Rotamer: Outliers : 2.03 % Allowed : 16.68 % Favored : 81.28 % 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: 0.35 (0.27), residues: 1129 helix: 2.13 (0.22), residues: 589 sheet: -0.84 (0.49), residues: 124 loop : -2.35 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.020 0.001 TYR A 437 PHE 0.017 0.001 PHE A 27 TRP 0.008 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 9194) covalent geometry : angle 0.50644 / 0.27 (12375) hydrogen bonds : bond 0.04659 / 2.90 ( 431) hydrogen bonds : angle 3.65697 / 2.70 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.289 Fit side-chains REVERT: A 260 SER cc_start: 0.8478 (t) cc_final: 0.8257 (t) REVERT: B 58 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8015 (mt0) REVERT: C 218 ASP cc_start: 0.7446 (t0) cc_final: 0.7043 (t0) outliers start: 20 outliers final: 15 residues processed: 150 average time/residue: 0.0929 time to fit residues: 19.9180 Evaluate side-chains 146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 92 optimal weight: 4.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.153405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.111745 restraints weight = 11317.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.107934 restraints weight = 12047.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109332 restraints weight = 12349.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.109736 restraints weight = 9775.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110166 restraints weight = 8032.948| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9194 Z= 0.148 Angle : 0.559 8.235 12375 Z= 0.293 Chirality : 0.041 0.145 1426 Planarity : 0.003 0.034 1534 Dihedral : 10.800 175.636 1267 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.71 % Favored : 92.21 % Rotamer: Outliers : 1.83 % Allowed : 17.80 % Favored : 80.37 % 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: 0.18 (0.26), residues: 1129 helix: 1.96 (0.22), residues: 592 sheet: -1.19 (0.52), residues: 112 loop : -2.29 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 565 TYR 0.010 0.001 TYR A 584 PHE 0.022 0.001 PHE A 27 TRP 0.008 0.002 TRP A 605 HIS 0.002 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9194) covalent geometry : angle 0.55886 / 0.29 (12375) hydrogen bonds : bond 0.05806 / 3.61 ( 431) hydrogen bonds : angle 3.88380 / 2.85 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.324 Fit side-chains REVERT: A 260 SER cc_start: 0.8627 (t) cc_final: 0.8409 (t) REVERT: A 483 PHE cc_start: 0.8561 (t80) cc_final: 0.8174 (t80) REVERT: B 58 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8109 (mt0) REVERT: C 218 ASP cc_start: 0.7563 (t0) cc_final: 0.7162 (t0) outliers start: 18 outliers final: 15 residues processed: 149 average time/residue: 0.0948 time to fit residues: 20.0302 Evaluate side-chains 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 86 optimal weight: 0.0020 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.155785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113952 restraints weight = 11056.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111381 restraints weight = 11876.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.112547 restraints weight = 12098.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113751 restraints weight = 9231.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113431 restraints weight = 7953.707| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9194 Z= 0.122 Angle : 0.547 9.243 12375 Z= 0.285 Chirality : 0.040 0.142 1426 Planarity : 0.003 0.032 1534 Dihedral : 10.301 172.419 1267 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 1.93 % Allowed : 18.72 % Favored : 79.35 % 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: 0.23 (0.27), residues: 1129 helix: 2.00 (0.22), residues: 592 sheet: -1.08 (0.53), residues: 112 loop : -2.29 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.011 0.001 TYR A 584 PHE 0.019 0.001 PHE A 27 TRP 0.008 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9194) covalent geometry : angle 0.54706 / 0.29 (12375) hydrogen bonds : bond 0.05186 / 3.23 ( 431) hydrogen bonds : angle 3.77619 / 2.79 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.348 Fit side-chains REVERT: A 260 SER cc_start: 0.8578 (t) cc_final: 0.8365 (t) REVERT: B 58 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8097 (mt0) REVERT: B 138 ASP cc_start: 0.8421 (p0) cc_final: 0.8205 (p0) REVERT: C 218 ASP cc_start: 0.7571 (t0) cc_final: 0.7200 (t0) outliers start: 19 outliers final: 17 residues processed: 148 average time/residue: 0.0914 time to fit residues: 19.1834 Evaluate side-chains 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.155552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113086 restraints weight = 11114.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111557 restraints weight = 13545.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112585 restraints weight = 12067.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.112690 restraints weight = 10217.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113023 restraints weight = 8523.411| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9194 Z= 0.121 Angle : 0.546 8.457 12375 Z= 0.283 Chirality : 0.040 0.146 1426 Planarity : 0.003 0.032 1534 Dihedral : 9.929 164.287 1267 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.44 % Favored : 92.47 % Rotamer: Outliers : 1.73 % Allowed : 18.72 % Favored : 79.55 % 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: 0.24 (0.27), residues: 1129 helix: 1.98 (0.22), residues: 593 sheet: -0.75 (0.51), residues: 124 loop : -2.41 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.011 0.001 TYR A 584 PHE 0.019 0.001 PHE A 27 TRP 0.008 0.002 TRP A 605 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9194) covalent geometry : angle 0.54620 / 0.28 (12375) hydrogen bonds : bond 0.05126 / 3.20 ( 431) hydrogen bonds : angle 3.77834 / 2.80 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.336 Fit side-chains REVERT: A 260 SER cc_start: 0.8523 (t) cc_final: 0.8310 (t) REVERT: A 425 LYS cc_start: 0.7240 (tppt) cc_final: 0.7000 (tppt) REVERT: B 238 ASP cc_start: 0.7978 (t0) cc_final: 0.7739 (t0) REVERT: C 218 ASP cc_start: 0.7597 (t0) cc_final: 0.7282 (t0) outliers start: 17 outliers final: 17 residues processed: 149 average time/residue: 0.0865 time to fit residues: 18.1345 Evaluate side-chains 153 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 0.0060 chunk 54 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.156860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115031 restraints weight = 11095.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.112342 restraints weight = 12000.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.114008 restraints weight = 11599.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115079 restraints weight = 8925.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.114984 restraints weight = 7775.989| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9194 Z= 0.117 Angle : 0.559 10.028 12375 Z= 0.288 Chirality : 0.040 0.145 1426 Planarity : 0.003 0.032 1534 Dihedral : 9.725 164.287 1267 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.91 % Favored : 93.00 % Rotamer: Outliers : 1.73 % Allowed : 19.13 % Favored : 79.15 % 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: 0.24 (0.27), residues: 1129 helix: 1.97 (0.22), residues: 598 sheet: -0.70 (0.51), residues: 124 loop : -2.47 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.011 0.001 TYR A 584 PHE 0.027 0.001 PHE A 501 TRP 0.008 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9194) covalent geometry : angle 0.55948 / 0.29 (12375) hydrogen bonds : bond 0.04855 / 3.03 ( 431) hydrogen bonds : angle 3.72445 / 2.77 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.328 Fit side-chains REVERT: A 260 SER cc_start: 0.8553 (t) cc_final: 0.8341 (t) REVERT: A 359 LEU cc_start: 0.8835 (mm) cc_final: 0.8544 (mm) REVERT: A 425 LYS cc_start: 0.7352 (tppt) cc_final: 0.7084 (tppt) REVERT: B 58 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8103 (mt0) REVERT: C 125 GLU cc_start: 0.6414 (tt0) cc_final: 0.6190 (tt0) REVERT: C 218 ASP cc_start: 0.7629 (t0) cc_final: 0.7306 (t0) outliers start: 17 outliers final: 15 residues processed: 152 average time/residue: 0.0944 time to fit residues: 20.0523 Evaluate side-chains 153 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.154938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.112715 restraints weight = 10947.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110430 restraints weight = 12709.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111863 restraints weight = 11584.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.112531 restraints weight = 9363.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.112478 restraints weight = 7870.385| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9194 Z= 0.134 Angle : 0.573 9.065 12375 Z= 0.299 Chirality : 0.041 0.154 1426 Planarity : 0.003 0.032 1534 Dihedral : 9.685 164.777 1267 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.71 % Favored : 92.21 % Rotamer: Outliers : 1.93 % Allowed : 18.92 % Favored : 79.15 % 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: 0.21 (0.26), residues: 1129 helix: 1.95 (0.22), residues: 593 sheet: -0.71 (0.51), residues: 124 loop : -2.44 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.011 0.001 TYR A 584 PHE 0.026 0.001 PHE A 501 TRP 0.008 0.002 TRP A 605 HIS 0.002 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 9194) covalent geometry : angle 0.57346 / 0.30 (12375) hydrogen bonds : bond 0.05383 / 3.35 ( 431) hydrogen bonds : angle 3.86597 / 2.86 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1521.59 seconds wall clock time: 27 minutes 11.66 seconds (1631.66 seconds total)