Starting phenix.real_space_refine on Mon Aug 25 11:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hdd_0204/08_2025/6hdd_0204.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hdd_0204/08_2025/6hdd_0204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hdd_0204/08_2025/6hdd_0204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hdd_0204/08_2025/6hdd_0204.map" model { file = "/net/cci-nas-00/data/ceres_data/6hdd_0204/08_2025/6hdd_0204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hdd_0204/08_2025/6hdd_0204.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 17724 2.51 5 N 4837 2.21 5 O 5488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28154 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4022 Classifications: {'peptide': 515} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 491} Chain: "B" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4022 Classifications: {'peptide': 515} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 491} Chain: "C" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4022 Classifications: {'peptide': 515} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 491} Chain: "D" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4022 Classifications: {'peptide': 515} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 491} Chain: "E" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4022 Classifications: {'peptide': 515} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 491} Chain: "F" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4022 Classifications: {'peptide': 515} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 491} Chain: "G" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4022 Classifications: {'peptide': 515} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 491} Time building chain proxies: 5.84, per 1000 atoms: 0.21 Number of scatterers: 28154 At special positions: 0 Unit cell: (100.62, 161.68, 157.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 5488 8.00 N 4837 7.00 C 17724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 907.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6692 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 31 sheets defined 41.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.854A pdb=" N VAL A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 78 through 88 removed outlier: 4.240A pdb=" N ASP A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.554A pdb=" N THR A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.157A pdb=" N LYS A 107 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.524A pdb=" N LYS A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.932A pdb=" N SER A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 removed outlier: 3.536A pdb=" N ILE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.712A pdb=" N ASN A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.957A pdb=" N GLY A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASP A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.028A pdb=" N GLU A 357 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 365 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 387 through 411 removed outlier: 3.769A pdb=" N LYS A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 4.365A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 468 through 473 removed outlier: 3.763A pdb=" N LEU A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 5.061A pdb=" N TRP A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 62 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 77 through 88 removed outlier: 4.045A pdb=" N SER B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.861A pdb=" N PHE B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 133 removed outlier: 4.443A pdb=" N LEU B 118 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 154 through 165 removed outlier: 3.697A pdb=" N VAL B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.647A pdb=" N PHE B 241 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.614A pdb=" N TRP B 320 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 321 " --> pdb=" O THR B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 321' Processing helix chain 'B' and resid 339 through 355 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 386 through 410 removed outlier: 3.743A pdb=" N LYS B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 451 through 459 Processing helix chain 'B' and resid 491 through 509 removed outlier: 3.961A pdb=" N LEU B 495 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 23 through 31 removed outlier: 3.539A pdb=" N VAL C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 69 through 78 removed outlier: 4.235A pdb=" N ILE C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 88 removed outlier: 4.179A pdb=" N ASP C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 112 through 130 removed outlier: 3.861A pdb=" N ARG C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 149 Processing helix chain 'C' and resid 154 through 168 removed outlier: 4.663A pdb=" N ILE C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.710A pdb=" N ILE C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 352 removed outlier: 4.274A pdb=" N GLY C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASN C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.679A pdb=" N ILE C 356 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU C 357 " --> pdb=" O GLY C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 365 removed outlier: 4.009A pdb=" N GLU C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 411 removed outlier: 3.630A pdb=" N ALA C 390 " --> pdb=" O THR C 386 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 411 " --> pdb=" O GLY C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 removed outlier: 4.029A pdb=" N LYS C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 448 Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 468 through 473 Processing helix chain 'C' and resid 493 through 507 removed outlier: 4.940A pdb=" N TRP C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 62 removed outlier: 4.252A pdb=" N VAL D 59 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 78 removed outlier: 4.148A pdb=" N ILE D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 88 removed outlier: 4.398A pdb=" N ASP D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.725A pdb=" N THR D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 133 removed outlier: 3.964A pdb=" N LEU D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 150 removed outlier: 3.762A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.106A pdb=" N VAL D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.612A pdb=" N VAL D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 4.010A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'D' and resid 283 through 287 removed outlier: 4.418A pdb=" N ALA D 286 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 386 through 410 Processing helix chain 'D' and resid 417 through 430 removed outlier: 4.046A pdb=" N ALA D 423 " --> pdb=" O GLY D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 448 Processing helix chain 'D' and resid 451 through 459 Processing helix chain 'D' and resid 492 through 509 removed outlier: 4.110A pdb=" N TRP D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 21 removed outlier: 4.088A pdb=" N GLU E 18 " --> pdb=" O ASN E 14 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE E 19 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 removed outlier: 3.655A pdb=" N SER E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 62 removed outlier: 4.108A pdb=" N VAL E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 78 through 88 removed outlier: 3.598A pdb=" N ILE E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 Processing helix chain 'E' and resid 112 through 133 removed outlier: 5.330A pdb=" N LEU E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU E 121 " --> pdb=" O TYR E 117 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 146 removed outlier: 3.526A pdb=" N MET E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 165 Processing helix chain 'E' and resid 255 through 260 removed outlier: 3.514A pdb=" N ALA E 259 " --> pdb=" O GLU E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 266 Processing helix chain 'E' and resid 289 through 294 removed outlier: 3.705A pdb=" N ARG E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 354 Processing helix chain 'E' and resid 364 through 368 removed outlier: 4.079A pdb=" N ASN E 367 " --> pdb=" O ARG E 364 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG E 368 " --> pdb=" O GLU E 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 364 through 368' Processing helix chain 'E' and resid 386 through 410 removed outlier: 3.847A pdb=" N LYS E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.640A pdb=" N LEU E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 430 Processing helix chain 'E' and resid 437 through 448 Processing helix chain 'E' and resid 451 through 459 Processing helix chain 'E' and resid 492 through 509 removed outlier: 4.544A pdb=" N TRP E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER E 509 " --> pdb=" O LEU E 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 23 through 29 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 78 through 88 removed outlier: 4.190A pdb=" N ASP F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 103 removed outlier: 4.403A pdb=" N TYR F 100 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 117 through 132 removed outlier: 4.667A pdb=" N LYS F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 removed outlier: 3.613A pdb=" N ARG F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 168 removed outlier: 4.227A pdb=" N ILE F 161 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU F 167 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 240 Processing helix chain 'F' and resid 256 through 261 Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 341 through 352 removed outlier: 4.414A pdb=" N GLY F 345 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 357 removed outlier: 3.604A pdb=" N ILE F 356 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU F 357 " --> pdb=" O GLY F 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 353 through 357' Processing helix chain 'F' and resid 363 through 370 removed outlier: 3.595A pdb=" N ARG F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 411 removed outlier: 3.827A pdb=" N LYS F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY F 411 " --> pdb=" O GLY F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 426 Processing helix chain 'F' and resid 437 through 448 Processing helix chain 'F' and resid 451 through 459 Processing helix chain 'F' and resid 468 through 473 removed outlier: 3.545A pdb=" N LEU F 472 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 504 removed outlier: 4.560A pdb=" N TRP F 499 " --> pdb=" O LEU F 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 62 removed outlier: 3.829A pdb=" N VAL G 59 " --> pdb=" O ASP G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 75 Processing helix chain 'G' and resid 78 through 88 Processing helix chain 'G' and resid 91 through 102 removed outlier: 3.904A pdb=" N PHE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 117 Processing helix chain 'G' and resid 119 through 133 Processing helix chain 'G' and resid 138 through 150 removed outlier: 3.581A pdb=" N MET G 142 " --> pdb=" O ILE G 138 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU G 147 " --> pdb=" O PHE G 143 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU G 148 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER G 150 " --> pdb=" O MET G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 165 removed outlier: 3.762A pdb=" N VAL G 158 " --> pdb=" O GLU G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.547A pdb=" N VAL G 204 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 240 removed outlier: 3.542A pdb=" N ARG G 240 " --> pdb=" O ALA G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 removed outlier: 3.887A pdb=" N ILE G 261 " --> pdb=" O ILE G 258 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN G 262 " --> pdb=" O ALA G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 365 through 370 removed outlier: 4.140A pdb=" N ARG G 369 " --> pdb=" O GLU G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 410 removed outlier: 3.688A pdb=" N LYS G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 430 removed outlier: 4.867A pdb=" N ALA G 423 " --> pdb=" O GLY G 419 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU G 428 " --> pdb=" O SER G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 448 removed outlier: 3.580A pdb=" N LYS G 441 " --> pdb=" O GLU G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 459 Processing helix chain 'G' and resid 491 through 509 removed outlier: 3.964A pdb=" N LEU G 495 " --> pdb=" O THR G 491 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP G 499 " --> pdb=" O LEU G 495 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU G 505 " --> pdb=" O THR G 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 177 removed outlier: 5.760A pdb=" N ASN A 172 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 380 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS A 174 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 382 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLU A 176 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 189 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 193 removed outlier: 3.663A pdb=" N GLU A 334 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 219 through 221 removed outlier: 3.712A pdb=" N TYR A 276 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 412 through 413 Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 515 removed outlier: 7.409A pdb=" N VAL G 43 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 515 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 53 removed outlier: 7.828A pdb=" N TYR B 41 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER C 515 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 43 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AA9, first strand: chain 'B' and resid 192 through 195 removed outlier: 3.668A pdb=" N PHE B 194 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 221 removed outlier: 7.676A pdb=" N VAL B 220 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 276 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 44 Processing sheet with id=AB3, first strand: chain 'C' and resid 174 through 177 removed outlier: 6.580A pdb=" N HIS C 174 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL C 382 " --> pdb=" O HIS C 174 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU C 176 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 189 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 219 through 221 removed outlier: 3.923A pdb=" N TYR C 276 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 326 through 327 Processing sheet with id=AB6, first strand: chain 'C' and resid 412 through 413 Processing sheet with id=AB7, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AB8, first strand: chain 'D' and resid 185 through 189 Processing sheet with id=AB9, first strand: chain 'D' and resid 192 through 193 Processing sheet with id=AC1, first strand: chain 'D' and resid 219 through 221 removed outlier: 3.653A pdb=" N MET D 249 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AC3, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'E' and resid 193 through 195 removed outlier: 4.240A pdb=" N PHE E 194 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 42 through 44 Processing sheet with id=AC6, first strand: chain 'F' and resid 174 through 180 removed outlier: 6.332A pdb=" N HIS F 174 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL F 382 " --> pdb=" O HIS F 174 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU F 176 " --> pdb=" O VAL F 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 189 through 190 removed outlier: 3.956A pdb=" N THR F 189 " --> pdb=" O ASN F 377 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 219 through 221 removed outlier: 3.875A pdb=" N TYR F 276 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 326 through 327 Processing sheet with id=AD1, first strand: chain 'F' and resid 412 through 413 Processing sheet with id=AD2, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD3, first strand: chain 'G' and resid 192 through 195 removed outlier: 3.611A pdb=" N GLU G 334 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE G 194 " --> pdb=" O ILE G 332 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 247 through 250 913 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6719 1.33 - 1.45: 5587 1.45 - 1.57: 16114 1.57 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 28616 Sorted by residual: bond pdb=" C ILE G 133 " pdb=" N GLN G 134 " ideal model delta sigma weight residual 1.330 1.448 -0.118 1.47e-02 4.63e+03 6.44e+01 bond pdb=" CA ASP G 479 " pdb=" CB ASP G 479 " ideal model delta sigma weight residual 1.527 1.449 0.078 2.48e-02 1.63e+03 1.00e+01 bond pdb=" CB VAL A 31 " pdb=" CG2 VAL A 31 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.66e+00 bond pdb=" C ILE E 133 " pdb=" N GLN E 134 " ideal model delta sigma weight residual 1.327 1.257 0.070 2.31e-02 1.87e+03 9.24e+00 bond pdb=" CB TRP A 499 " pdb=" CG TRP A 499 " ideal model delta sigma weight residual 1.498 1.408 0.090 3.10e-02 1.04e+03 8.36e+00 ... (remaining 28611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 38051 4.13 - 8.26: 684 8.26 - 12.39: 75 12.39 - 16.52: 4 16.52 - 20.65: 1 Bond angle restraints: 38815 Sorted by residual: angle pdb=" N ILE C 19 " pdb=" CA ILE C 19 " pdb=" C ILE C 19 " ideal model delta sigma weight residual 113.71 104.57 9.14 9.50e-01 1.11e+00 9.26e+01 angle pdb=" C ILE G 133 " pdb=" N GLN G 134 " pdb=" CA GLN G 134 " ideal model delta sigma weight residual 120.68 134.07 -13.39 1.52e+00 4.33e-01 7.76e+01 angle pdb=" N VAL D 24 " pdb=" CA VAL D 24 " pdb=" C VAL D 24 " ideal model delta sigma weight residual 112.17 104.24 7.93 9.50e-01 1.11e+00 6.97e+01 angle pdb=" N GLY G 218 " pdb=" CA GLY G 218 " pdb=" C GLY G 218 " ideal model delta sigma weight residual 111.36 118.93 -7.57 1.17e+00 7.31e-01 4.18e+01 angle pdb=" C SER E 151 " pdb=" N ASN E 152 " pdb=" CA ASN E 152 " ideal model delta sigma weight residual 122.46 131.06 -8.60 1.41e+00 5.03e-01 3.72e+01 ... (remaining 38810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 15940 17.10 - 34.19: 1260 34.19 - 51.29: 161 51.29 - 68.39: 12 68.39 - 85.49: 29 Dihedral angle restraints: 17402 sinusoidal: 6979 harmonic: 10423 Sorted by residual: dihedral pdb=" CA GLY F 415 " pdb=" C GLY F 415 " pdb=" N ILE F 416 " pdb=" CA ILE F 416 " ideal model delta harmonic sigma weight residual 180.00 -132.33 -47.67 0 5.00e+00 4.00e-02 9.09e+01 dihedral pdb=" CA GLY C 415 " pdb=" C GLY C 415 " pdb=" N ILE C 416 " pdb=" CA ILE C 416 " ideal model delta harmonic sigma weight residual -180.00 -135.64 -44.36 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA TYR E 229 " pdb=" C TYR E 229 " pdb=" N PRO E 230 " pdb=" CA PRO E 230 " ideal model delta harmonic sigma weight residual -180.00 -136.37 -43.63 0 5.00e+00 4.00e-02 7.61e+01 ... (remaining 17399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3681 0.094 - 0.187: 679 0.187 - 0.281: 82 0.281 - 0.374: 14 0.374 - 0.468: 10 Chirality restraints: 4466 Sorted by residual: chirality pdb=" CB VAL F 511 " pdb=" CA VAL F 511 " pdb=" CG1 VAL F 511 " pdb=" CG2 VAL F 511 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CB ILE F 8 " pdb=" CA ILE F 8 " pdb=" CG1 ILE F 8 " pdb=" CG2 ILE F 8 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CB VAL A 511 " pdb=" CA VAL A 511 " pdb=" CG1 VAL A 511 " pdb=" CG2 VAL A 511 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 4463 not shown) Planarity restraints: 5082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 10 " 0.033 2.00e-02 2.50e+03 3.30e-02 1.90e+01 pdb=" CG PHE C 10 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE C 10 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE C 10 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 10 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 10 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 10 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 10 " 0.022 2.00e-02 2.50e+03 2.97e-02 1.55e+01 pdb=" CG PHE A 10 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 10 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 10 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 10 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 10 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 10 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 10 " 0.031 2.00e-02 2.50e+03 2.56e-02 1.14e+01 pdb=" CG PHE B 10 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE B 10 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 10 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 10 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 10 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 10 " 0.007 2.00e-02 2.50e+03 ... (remaining 5079 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4189 2.76 - 3.29: 28662 3.29 - 3.83: 47897 3.83 - 4.36: 56361 4.36 - 4.90: 89792 Nonbonded interactions: 226901 Sorted by model distance: nonbonded pdb=" O SER E 111 " pdb=" OG1 THR E 115 " model vdw 2.220 3.040 nonbonded pdb=" O SER G 111 " pdb=" OG1 THR G 115 " model vdw 2.243 3.040 nonbonded pdb=" O SER B 111 " pdb=" OG1 THR B 115 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR A 350 " pdb=" O GLY A 371 " model vdw 2.253 3.040 nonbonded pdb=" O ASP F 108 " pdb=" OG SER F 111 " model vdw 2.259 3.040 ... (remaining 226896 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.290 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4364 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 : 0.009 0.118 28616 Z= 0.414 Angle : 1.357 20.650 38815 Z= 0.740 Chirality : 0.075 0.468 4466 Planarity : 0.008 0.079 5082 Dihedral : 12.602 85.486 10710 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 18.30 % Favored : 81.57 % Rotamer: Outliers : 1.07 % Allowed : 6.31 % Favored : 92.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 2.14 % Twisted General : 1.13 % 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 aren not related in a simple way. whole: -6.11 (0.10), residues: 3591 helix: -3.88 (0.08), residues: 1528 sheet: -3.24 (0.27), residues: 293 loop : -4.44 (0.11), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 17 TYR 0.054 0.003 TYR D 41 PHE 0.073 0.004 PHE C 10 TRP 0.040 0.004 TRP A 394 HIS 0.014 0.003 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00908 (28616) covalent geometry : angle 1.35690 (38815) hydrogen bonds : bond 0.16050 ( 913) hydrogen bonds : angle 8.80087 ( 2520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.0980 time to fit residues: 5.0916 Evaluate side-chains 20 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.0060 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0060 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.0370 chunk 298 optimal weight: 0.4980 overall best weight: 0.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 239 ASN A 367 ASN A 409 GLN A 487 ASN A 516 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.046941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.038662 restraints weight = 62891.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.039300 restraints weight = 51245.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.039728 restraints weight = 43517.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.039957 restraints weight = 38624.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.040249 restraints weight = 34742.605| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4462 moved from start: 3.0250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.221 28616 Z= 0.460 Angle : 1.588 37.730 38815 Z= 0.877 Chirality : 0.073 0.478 4466 Planarity : 0.011 0.139 5082 Dihedral : 10.863 45.927 3927 Min Nonbonded Distance : 1.277 Molprobity Statistics. All-atom Clashscore : 43.52 Ramachandran Plot: Outliers : 0.78 % Allowed : 13.65 % Favored : 85.58 % Rotamer: Outliers : 1.82 % Allowed : 6.38 % Favored : 91.80 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 10.00 % Twisted General : 2.23 % 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 aren not related in a simple way. whole: -5.09 (0.11), residues: 3591 helix: -2.98 (0.10), residues: 1610 sheet: -2.21 (0.25), residues: 322 loop : -4.06 (0.12), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG B 514 TYR 0.035 0.003 TYR F 41 PHE 0.043 0.003 PHE G 10 TRP 0.023 0.004 TRP F 499 HIS 0.004 0.002 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00886 (28616) covalent geometry : angle 1.58838 (38815) hydrogen bonds : bond 0.31791 ( 913) hydrogen bonds : angle 11.18559 ( 2520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.3840 (tpt) cc_final: 0.3120 (tmm) REVERT: A 188 MET cc_start: 0.5881 (ttm) cc_final: 0.5182 (tpp) REVERT: A 227 ARG cc_start: 0.3226 (OUTLIER) cc_final: 0.2850 (mpt180) REVERT: A 249 MET cc_start: 0.0996 (tpp) cc_final: 0.0741 (tpp) outliers start: 8 outliers final: 0 residues processed: 39 average time/residue: 0.1079 time to fit residues: 5.0923 Evaluate side-chains 19 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 188 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 337 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 265 optimal weight: 0.0770 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.048146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.039846 restraints weight = 84032.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.040464 restraints weight = 68166.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.040977 restraints weight = 57584.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.041389 restraints weight = 49935.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.041726 restraints weight = 44466.622| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4352 moved from start: 3.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 28616 Z= 0.330 Angle : 1.284 33.876 38815 Z= 0.711 Chirality : 0.064 0.536 4466 Planarity : 0.011 0.224 5082 Dihedral : 10.107 50.968 3927 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 37.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 0.91 % Allowed : 6.83 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 5.00 % Twisted General : 1.42 % 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 aren not related in a simple way. whole: -4.56 (0.12), residues: 3591 helix: -2.48 (0.11), residues: 1554 sheet: -2.24 (0.27), residues: 329 loop : -3.77 (0.13), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 227 TYR 0.022 0.002 TYR D 519 PHE 0.016 0.002 PHE E 112 TRP 0.021 0.003 TRP E 394 HIS 0.009 0.003 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00586 (28616) covalent geometry : angle 1.28353 (38815) hydrogen bonds : bond 0.26896 ( 913) hydrogen bonds : angle 10.51389 ( 2520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9344 (m110) cc_final: 0.8983 (p0) REVERT: A 15 ASP cc_start: 0.7968 (m-30) cc_final: 0.7727 (m-30) REVERT: A 185 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8806 (pm20) REVERT: A 402 LYS cc_start: 0.9408 (mmtm) cc_final: 0.9060 (tptt) outliers start: 4 outliers final: 0 residues processed: 32 average time/residue: 0.0676 time to fit residues: 2.8873 Evaluate side-chains 23 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 226 optimal weight: 0.6980 chunk 330 optimal weight: 0.8980 chunk 225 optimal weight: 0.2980 chunk 316 optimal weight: 0.2980 chunk 209 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 277 optimal weight: 0.3980 chunk 227 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 48 optimal weight: 40.0000 chunk 111 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.049535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.041420 restraints weight = 62621.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.041952 restraints weight = 52864.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.042229 restraints weight = 46294.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.042565 restraints weight = 42421.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.042796 restraints weight = 39024.918| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4408 moved from start: 3.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 28616 Z= 0.293 Angle : 1.091 15.129 38815 Z= 0.633 Chirality : 0.055 0.263 4466 Planarity : 0.007 0.066 5082 Dihedral : 9.526 49.600 3927 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 31.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 0.23 % Allowed : 6.38 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.82 % 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 aren not related in a simple way. whole: -4.13 (0.13), residues: 3591 helix: -1.97 (0.12), residues: 1491 sheet: -2.08 (0.26), residues: 329 loop : -3.65 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 227 TYR 0.014 0.001 TYR E 454 PHE 0.023 0.002 PHE D 65 TRP 0.033 0.003 TRP G 394 HIS 0.002 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00534 (28616) covalent geometry : angle 1.09074 (38815) hydrogen bonds : bond 0.23495 ( 913) hydrogen bonds : angle 9.88252 ( 2520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9131 (m110) cc_final: 0.8752 (p0) REVERT: A 402 LYS cc_start: 0.9369 (mmtm) cc_final: 0.9054 (tptt) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0784 time to fit residues: 3.2916 Evaluate side-chains 20 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 202 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 184 optimal weight: 0.0670 chunk 192 optimal weight: 7.9990 chunk 308 optimal weight: 0.0270 chunk 298 optimal weight: 10.0000 chunk 63 optimal weight: 0.0060 chunk 286 optimal weight: 6.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS A 203 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.049730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.041681 restraints weight = 62943.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.042210 restraints weight = 53494.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.042569 restraints weight = 47097.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.042791 restraints weight = 42734.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.042995 restraints weight = 39994.395| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4454 moved from start: 3.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28616 Z= 0.276 Angle : 1.100 13.963 38815 Z= 0.640 Chirality : 0.059 0.458 4466 Planarity : 0.007 0.066 5082 Dihedral : 9.104 50.417 3927 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 31.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.40 % Favored : 84.41 % Rotamer: Outliers : 0.68 % Allowed : 4.10 % Favored : 95.22 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 0.81 % 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 aren not related in a simple way. whole: -4.01 (0.13), residues: 3591 helix: -1.74 (0.12), residues: 1477 sheet: -1.93 (0.26), residues: 329 loop : -3.73 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 227 TYR 0.036 0.002 TYR A 41 PHE 0.018 0.002 PHE A 194 TRP 0.031 0.002 TRP B 394 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00475 (28616) covalent geometry : angle 1.10009 (38815) hydrogen bonds : bond 0.21567 ( 913) hydrogen bonds : angle 9.24152 ( 2520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.4893 (pmm) cc_final: 0.4266 (pmm) REVERT: A 402 LYS cc_start: 0.9335 (mmtm) cc_final: 0.9039 (tptt) outliers start: 3 outliers final: 0 residues processed: 29 average time/residue: 0.0771 time to fit residues: 2.9166 Evaluate side-chains 20 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 50 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 325 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 265 optimal weight: 0.6980 chunk 207 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 292 optimal weight: 0.1980 chunk 191 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.051013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.042870 restraints weight = 75537.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.043469 restraints weight = 61676.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.043940 restraints weight = 52513.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.044351 restraints weight = 46358.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.044663 restraints weight = 41230.442| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 moved from start: 3.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28616 Z= 0.274 Angle : 1.080 16.606 38815 Z= 0.623 Chirality : 0.058 0.369 4466 Planarity : 0.006 0.064 5082 Dihedral : 8.848 47.586 3927 Min Nonbonded Distance : 1.565 Molprobity Statistics. All-atom Clashscore : 27.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.35 % Favored : 82.65 % Rotamer: Outliers : 0.23 % Allowed : 3.87 % Favored : 95.90 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.01 % 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 aren not related in a simple way. whole: -3.80 (0.13), residues: 3591 helix: -1.61 (0.13), residues: 1456 sheet: -2.04 (0.31), residues: 238 loop : -3.47 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 227 TYR 0.029 0.001 TYR C 41 PHE 0.015 0.002 PHE A 194 TRP 0.027 0.002 TRP F 394 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00471 (28616) covalent geometry : angle 1.08022 (38815) hydrogen bonds : bond 0.21196 ( 913) hydrogen bonds : angle 8.96773 ( 2520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.4082 (OUTLIER) cc_final: 0.3868 (tpp) REVERT: A 398 GLU cc_start: 0.8861 (mp0) cc_final: 0.8594 (mp0) REVERT: A 402 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9008 (tptt) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.1106 time to fit residues: 3.9611 Evaluate side-chains 23 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 235 optimal weight: 0.0970 chunk 231 optimal weight: 0.0870 chunk 198 optimal weight: 30.0000 chunk 34 optimal weight: 0.0170 chunk 42 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 chunk 58 optimal weight: 0.0470 chunk 120 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 overall best weight: 0.1892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN A 409 GLN A 460 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.058942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.044132 restraints weight = 53362.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.045305 restraints weight = 40636.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.045224 restraints weight = 36547.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.045695 restraints weight = 34336.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.045852 restraints weight = 32911.274| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4910 moved from start: 3.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28616 Z= 0.275 Angle : 1.077 13.513 38815 Z= 0.621 Chirality : 0.058 0.372 4466 Planarity : 0.006 0.062 5082 Dihedral : 8.558 46.179 3927 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.74 % Favored : 82.07 % Rotamer: Outliers : 0.23 % Allowed : 2.96 % Favored : 96.81 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.01 % 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 aren not related in a simple way. whole: -3.67 (0.13), residues: 3591 helix: -1.36 (0.13), residues: 1463 sheet: -1.81 (0.32), residues: 238 loop : -3.55 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 61 TYR 0.045 0.002 TYR D 41 PHE 0.016 0.002 PHE G 97 TRP 0.026 0.002 TRP G 394 HIS 0.003 0.001 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00481 (28616) covalent geometry : angle 1.07657 (38815) hydrogen bonds : bond 0.21179 ( 913) hydrogen bonds : angle 8.82404 ( 2520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LYS cc_start: 0.9303 (mmtm) cc_final: 0.8921 (tptt) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0934 time to fit residues: 3.0962 Evaluate side-chains 23 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 84 optimal weight: 0.0170 chunk 319 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 315 optimal weight: 0.0270 chunk 162 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 overall best weight: 0.9878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.059849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.044456 restraints weight = 52119.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.047086 restraints weight = 40510.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.046399 restraints weight = 33199.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.046835 restraints weight = 32626.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.047042 restraints weight = 28494.096| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4800 moved from start: 3.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28616 Z= 0.262 Angle : 1.080 14.969 38815 Z= 0.621 Chirality : 0.059 0.408 4466 Planarity : 0.006 0.061 5082 Dihedral : 8.567 47.836 3927 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.18 % Favored : 83.43 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.01 % 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 aren not related in a simple way. whole: -3.73 (0.13), residues: 3591 helix: -1.48 (0.13), residues: 1533 sheet: -1.73 (0.35), residues: 238 loop : -3.61 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 61 TYR 0.043 0.002 TYR C 41 PHE 0.013 0.001 PHE A 194 TRP 0.029 0.002 TRP F 394 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00450 (28616) covalent geometry : angle 1.07962 (38815) hydrogen bonds : bond 0.21209 ( 913) hydrogen bonds : angle 8.77647 ( 2520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LYS cc_start: 0.9221 (mmtm) cc_final: 0.8914 (tptt) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0816 time to fit residues: 2.7261 Evaluate side-chains 22 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 130 optimal weight: 0.0770 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 0.0270 chunk 20 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 152 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 134 optimal weight: 0.0060 chunk 273 optimal weight: 0.0470 chunk 68 optimal weight: 5.9990 overall best weight: 0.1910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.060485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.044962 restraints weight = 52315.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.046404 restraints weight = 43691.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.047600 restraints weight = 37296.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.047812 restraints weight = 29698.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.047867 restraints weight = 28262.970| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4806 moved from start: 3.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 28616 Z= 0.267 Angle : 1.085 15.164 38815 Z= 0.615 Chirality : 0.058 0.368 4466 Planarity : 0.006 0.059 5082 Dihedral : 8.264 48.483 3927 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.79 % Favored : 84.02 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.01 % 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 aren not related in a simple way. whole: -3.54 (0.13), residues: 3591 helix: -1.31 (0.13), residues: 1589 sheet: -1.83 (0.33), residues: 238 loop : -3.53 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 227 TYR 0.028 0.002 TYR C 41 PHE 0.013 0.001 PHE E 97 TRP 0.025 0.002 TRP F 394 HIS 0.003 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00473 (28616) covalent geometry : angle 1.08547 (38815) hydrogen bonds : bond 0.20504 ( 913) hydrogen bonds : angle 8.68536 ( 2520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8864 (tptt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0945 time to fit residues: 2.8543 Evaluate side-chains 22 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 102 optimal weight: 9.9990 chunk 69 optimal weight: 0.0010 chunk 72 optimal weight: 0.4980 chunk 356 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 75 optimal weight: 0.2980 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.066473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.059270 restraints weight = 59432.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.059594 restraints weight = 53377.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.059753 restraints weight = 49162.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.060033 restraints weight = 46672.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.060153 restraints weight = 44206.573| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4119 moved from start: 3.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 28616 Z= 0.262 Angle : 1.091 14.423 38815 Z= 0.626 Chirality : 0.061 0.478 4466 Planarity : 0.006 0.058 5082 Dihedral : 8.297 48.501 3927 Min Nonbonded Distance : 1.509 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.98 % Favored : 83.82 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.21 % 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 aren not related in a simple way. whole: -3.38 (0.13), residues: 3591 helix: -1.27 (0.13), residues: 1631 sheet: -1.84 (0.33), residues: 238 loop : -3.36 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 61 TYR 0.037 0.002 TYR F 41 PHE 0.011 0.001 PHE G 97 TRP 0.023 0.002 TRP F 394 HIS 0.003 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00472 (28616) covalent geometry : angle 1.09085 (38815) hydrogen bonds : bond 0.20555 ( 913) hydrogen bonds : angle 8.69033 ( 2520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.167 Fit side-chains REVERT: A 35 MET cc_start: 0.3914 (pmm) cc_final: 0.3259 (pmm) REVERT: A 402 LYS cc_start: 0.9216 (mmtm) cc_final: 0.8846 (tptt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0920 time to fit residues: 2.9218 Evaluate side-chains 19 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 139 optimal weight: 0.0980 chunk 316 optimal weight: 0.0770 chunk 97 optimal weight: 8.9990 chunk 326 optimal weight: 0.8980 chunk 356 optimal weight: 8.9990 chunk 244 optimal weight: 0.9980 chunk 206 optimal weight: 20.0000 chunk 313 optimal weight: 0.4980 chunk 96 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 181 optimal weight: 0.4980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.054335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.040384 restraints weight = 57285.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.040982 restraints weight = 42473.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.042278 restraints weight = 36283.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.043143 restraints weight = 30101.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.043644 restraints weight = 26793.722| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4778 moved from start: 3.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 28616 Z= 0.266 Angle : 1.100 17.846 38815 Z= 0.621 Chirality : 0.059 0.398 4466 Planarity : 0.006 0.058 5082 Dihedral : 8.114 49.055 3927 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.57 % Favored : 83.24 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.21 % 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 aren not related in a simple way. whole: -3.34 (0.13), residues: 3591 helix: -1.08 (0.13), residues: 1603 sheet: -2.01 (0.33), residues: 238 loop : -3.46 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.054 0.002 TYR E 41 PHE 0.012 0.001 PHE B 97 TRP 0.020 0.002 TRP F 394 HIS 0.002 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00471 (28616) covalent geometry : angle 1.10040 (38815) hydrogen bonds : bond 0.20388 ( 913) hydrogen bonds : angle 8.64423 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2073.43 seconds wall clock time: 37 minutes 46.16 seconds (2266.16 seconds total)