Starting phenix.real_space_refine on Mon Jun 23 20:23:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hdd_0204/06_2025/6hdd_0204.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hdd_0204/06_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_0204/06_2025/6hdd_0204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hdd_0204/06_2025/6hdd_0204.map" model { file = "/net/cci-nas-00/data/ceres_data/6hdd_0204/06_2025/6hdd_0204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hdd_0204/06_2025/6hdd_0204.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.51, per 1000 atoms: 0.59 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: 6.97 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 3.16 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: 9.23 Time building geometry restraints manager: 8.17 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: 0.04 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 62.000 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.610 ------------------------------------------------------------------------------- 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 : 12.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.040 0.004 TRP A 394 HIS 0.014 0.003 HIS B 101 PHE 0.073 0.004 PHE C 10 TYR 0.054 0.003 TYR D 41 ARG 0.019 0.001 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.16050 ( 913) hydrogen bonds : angle 8.80087 ( 2520) covalent geometry : bond 0.00908 (28616) covalent geometry : angle 1.35690 (38815) *********************** 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 : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.2021 time to fit residues: 10.6080 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 : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 30.0000 chunk 270 optimal weight: 6.9990 chunk 150 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 279 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 235 ASN A 239 ASN A 367 ASN A 409 GLN A 487 ASN A 516 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.046407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.038257 restraints weight = 62843.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.038885 restraints weight = 50361.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.039267 restraints weight = 42954.809| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4543 moved from start: 3.0149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.210 28616 Z= 0.454 Angle : 1.570 32.188 38815 Z= 0.878 Chirality : 0.073 0.485 4466 Planarity : 0.011 0.144 5082 Dihedral : 10.875 45.497 3927 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 45.35 Ramachandran Plot: Outliers : 1.17 % Allowed : 13.84 % Favored : 84.99 % Rotamer: Outliers : 1.82 % Allowed : 5.69 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 15.00 % Twisted General : 2.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.11), residues: 3591 helix: -2.98 (0.10), residues: 1596 sheet: -2.71 (0.22), residues: 385 loop : -4.14 (0.11), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP E 394 HIS 0.005 0.002 HIS B 101 PHE 0.047 0.003 PHE C 10 TYR 0.027 0.003 TYR B 41 ARG 0.026 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.31651 ( 913) hydrogen bonds : angle 11.22058 ( 2520) covalent geometry : bond 0.00857 (28616) covalent geometry : angle 1.57006 (38815) *********************** 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 43 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.4000 (tpt) cc_final: 0.3687 (tmm) REVERT: A 227 ARG cc_start: 0.3341 (OUTLIER) cc_final: 0.2992 (mpt180) REVERT: A 249 MET cc_start: 0.1228 (tpp) cc_final: 0.0942 (tpp) outliers start: 8 outliers final: 0 residues processed: 40 average time/residue: 0.2192 time to fit residues: 10.7982 Evaluate side-chains 20 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 141 optimal weight: 2.9990 chunk 295 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 355 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 300 optimal weight: 50.0000 chunk 288 optimal weight: 0.8980 chunk 337 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.046896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.038646 restraints weight = 63746.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.039288 restraints weight = 51629.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.039552 restraints weight = 44094.323| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4464 moved from start: 3.0483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 28616 Z= 0.364 Angle : 1.314 32.515 38815 Z= 0.732 Chirality : 0.065 0.577 4466 Planarity : 0.013 0.287 5082 Dihedral : 10.244 51.218 3927 Min Nonbonded Distance : 1.397 Molprobity Statistics. All-atom Clashscore : 41.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.76 % Favored : 83.24 % Rotamer: Outliers : 1.14 % Allowed : 7.29 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 5.00 % Twisted General : 1.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.67 (0.12), residues: 3591 helix: -2.52 (0.11), residues: 1533 sheet: -2.35 (0.26), residues: 329 loop : -3.87 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 394 HIS 0.010 0.003 HIS F 456 PHE 0.020 0.003 PHE D 10 TYR 0.024 0.002 TYR F 41 ARG 0.010 0.001 ARG D 227 Details of bonding type rmsd hydrogen bonds : bond 0.27374 ( 913) hydrogen bonds : angle 10.66779 ( 2520) covalent geometry : bond 0.00652 (28616) covalent geometry : angle 1.31403 (38815) *********************** 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 35 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9227 (m110) cc_final: 0.8889 (p0) REVERT: A 185 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8783 (pm20) REVERT: A 188 MET cc_start: 0.6506 (ttp) cc_final: 0.6066 (tpp) REVERT: A 402 LYS cc_start: 0.9442 (mmtm) cc_final: 0.9180 (tmtt) REVERT: A 514 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.4820 (tpt170) outliers start: 5 outliers final: 0 residues processed: 34 average time/residue: 0.1840 time to fit residues: 8.1605 Evaluate side-chains 24 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 350 optimal weight: 8.9990 chunk 132 optimal weight: 0.0470 chunk 99 optimal weight: 0.0000 chunk 244 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 78 optimal weight: 0.0670 chunk 250 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 232 optimal weight: 0.0870 chunk 316 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 overall best weight: 0.1598 ------------------------------------------------------------------------------- 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 = 0.057445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.048186 restraints weight = 67542.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.048767 restraints weight = 56580.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.049234 restraints weight = 49274.511| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 3.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28616 Z= 0.308 Angle : 1.198 29.059 38815 Z= 0.668 Chirality : 0.057 0.310 4466 Planarity : 0.007 0.077 5082 Dihedral : 9.670 62.293 3927 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 33.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.18 % Favored : 83.43 % Rotamer: Outliers : 0.68 % Allowed : 5.24 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.12), residues: 3591 helix: -2.00 (0.12), residues: 1505 sheet: -2.36 (0.25), residues: 329 loop : -3.85 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 394 HIS 0.003 0.001 HIS G 456 PHE 0.015 0.003 PHE E 97 TYR 0.019 0.002 TYR G 519 ARG 0.011 0.001 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.24665 ( 913) hydrogen bonds : angle 9.88972 ( 2520) covalent geometry : bond 0.00543 (28616) covalent geometry : angle 1.19814 (38815) *********************** 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: 3 poor density : 30 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7510 (tmm) cc_final: 0.7147 (tmm) REVERT: A 402 LYS cc_start: 0.9216 (mmtm) cc_final: 0.8990 (tptt) outliers start: 3 outliers final: 0 residues processed: 33 average time/residue: 0.1603 time to fit residues: 7.1468 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 : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 47 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 331 optimal weight: 0.0970 chunk 311 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 201 optimal weight: 0.4980 chunk 143 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.049146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.040474 restraints weight = 79230.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.041122 restraints weight = 62863.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.041672 restraints weight = 52380.720| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 3.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.157 28616 Z= 0.303 Angle : 1.120 15.421 38815 Z= 0.643 Chirality : 0.060 0.499 4466 Planarity : 0.007 0.066 5082 Dihedral : 9.077 57.037 3927 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 32.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.98 % Favored : 84.02 % Rotamer: Outliers : 0.23 % Allowed : 4.78 % Favored : 94.99 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.13), residues: 3591 helix: -1.75 (0.13), residues: 1484 sheet: -2.23 (0.26), residues: 329 loop : -3.54 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 394 HIS 0.002 0.001 HIS A 101 PHE 0.019 0.002 PHE E 97 TYR 0.025 0.001 TYR C 41 ARG 0.005 0.001 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.22335 ( 913) hydrogen bonds : angle 9.46601 ( 2520) covalent geometry : bond 0.00557 (28616) covalent geometry : angle 1.11982 (38815) *********************** 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 30 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.6065 (tpp) cc_final: 0.5791 (tpp) REVERT: A 402 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8975 (tptt) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.1865 time to fit residues: 7.3688 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 : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 104 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 352 optimal weight: 7.9990 chunk 315 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 125 optimal weight: 40.0000 chunk 87 optimal weight: 0.3980 chunk 312 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.058950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.049948 restraints weight = 68386.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.050341 restraints weight = 59910.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.050743 restraints weight = 54416.904| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 3.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 28616 Z= 0.285 Angle : 1.088 15.349 38815 Z= 0.632 Chirality : 0.059 0.349 4466 Planarity : 0.006 0.065 5082 Dihedral : 8.689 47.606 3927 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 31.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.13), residues: 3591 helix: -1.62 (0.13), residues: 1456 sheet: -2.04 (0.26), residues: 329 loop : -3.60 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 394 HIS 0.002 0.001 HIS A 168 PHE 0.015 0.002 PHE D 97 TYR 0.043 0.002 TYR A 41 ARG 0.005 0.001 ARG F 338 Details of bonding type rmsd hydrogen bonds : bond 0.21727 ( 913) hydrogen bonds : angle 9.09274 ( 2520) covalent geometry : bond 0.00524 (28616) covalent geometry : angle 1.08753 (38815) *********************** 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 28 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 LYS cc_start: 0.9252 (mmtm) cc_final: 0.8992 (tptt) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2380 time to fit residues: 8.4131 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 : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 260 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 232 optimal weight: 0.0060 chunk 336 optimal weight: 0.6980 chunk 282 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 chunk 278 optimal weight: 0.0030 chunk 351 optimal weight: 50.0000 overall best weight: 1.7410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** 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 = 0.4077 r_free = 0.4077 target = 0.057007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.042588 restraints weight = 54682.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.043612 restraints weight = 42007.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.044386 restraints weight = 37770.423| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4846 moved from start: 3.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 28616 Z= 0.285 Angle : 1.127 24.100 38815 Z= 0.635 Chirality : 0.059 0.387 4466 Planarity : 0.006 0.063 5082 Dihedral : 8.627 48.194 3927 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 29.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.35 % Favored : 82.46 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.13), residues: 3591 helix: -1.24 (0.14), residues: 1358 sheet: -2.27 (0.33), residues: 259 loop : -3.31 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 394 HIS 0.002 0.000 HIS F 101 PHE 0.014 0.002 PHE E 97 TYR 0.022 0.001 TYR D 41 ARG 0.004 0.000 ARG D 227 Details of bonding type rmsd hydrogen bonds : bond 0.21226 ( 913) hydrogen bonds : angle 8.95045 ( 2520) covalent geometry : bond 0.00523 (28616) covalent geometry : angle 1.12663 (38815) *********************** 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 29 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 LYS cc_start: 0.9334 (mmtm) cc_final: 0.8912 (tptt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2587 time to fit residues: 9.1835 Evaluate side-chains 24 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 122 optimal weight: 0.6980 chunk 337 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 chunk 348 optimal weight: 0.0970 chunk 186 optimal weight: 8.9990 chunk 333 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN A 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.057986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.042941 restraints weight = 52407.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.044242 restraints weight = 45852.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.045132 restraints weight = 38284.354| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4897 moved from start: 3.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 28616 Z= 0.272 Angle : 1.176 25.946 38815 Z= 0.645 Chirality : 0.062 0.417 4466 Planarity : 0.006 0.063 5082 Dihedral : 8.437 42.649 3927 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 29.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.15 % Favored : 82.65 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.13), residues: 3591 helix: -1.18 (0.14), residues: 1379 sheet: -1.79 (0.34), residues: 238 loop : -3.33 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 394 HIS 0.002 0.000 HIS B 101 PHE 0.013 0.002 PHE G 97 TYR 0.020 0.001 TYR E 41 ARG 0.004 0.001 ARG G 514 Details of bonding type rmsd hydrogen bonds : bond 0.21135 ( 913) hydrogen bonds : angle 8.93906 ( 2520) covalent geometry : bond 0.00490 (28616) covalent geometry : angle 1.17578 (38815) *********************** 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 27 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.4953 (pmm) cc_final: 0.4588 (pmm) REVERT: A 188 MET cc_start: 0.4938 (tpp) cc_final: 0.4683 (tpp) REVERT: A 402 LYS cc_start: 0.9226 (mmtm) cc_final: 0.8948 (tptt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.2211 time to fit residues: 7.6953 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 : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 139 optimal weight: 20.0000 chunk 330 optimal weight: 0.0970 chunk 218 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 chunk 196 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 235 optimal weight: 30.0000 chunk 350 optimal weight: 8.9990 chunk 221 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 overall best weight: 1.5760 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.058449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.043205 restraints weight = 53162.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.044361 restraints weight = 47465.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.043985 restraints weight = 47426.530| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4991 moved from start: 3.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 28616 Z= 0.275 Angle : 1.107 21.838 38815 Z= 0.622 Chirality : 0.058 0.331 4466 Planarity : 0.006 0.062 5082 Dihedral : 8.532 43.954 3927 Min Nonbonded Distance : 1.487 Molprobity Statistics. All-atom Clashscore : 30.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.74 % Favored : 82.07 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.13), residues: 3591 helix: -1.13 (0.14), residues: 1484 sheet: -1.77 (0.33), residues: 238 loop : -3.36 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 394 HIS 0.002 0.001 HIS A 101 PHE 0.011 0.001 PHE C 194 TYR 0.037 0.002 TYR D 41 ARG 0.004 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.21416 ( 913) hydrogen bonds : angle 8.93390 ( 2520) covalent geometry : bond 0.00486 (28616) covalent geometry : angle 1.10736 (38815) *********************** 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 28 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 398 GLU cc_start: 0.8898 (mp0) cc_final: 0.8659 (mp0) REVERT: A 402 LYS cc_start: 0.9297 (mmtm) cc_final: 0.8943 (tptt) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1723 time to fit residues: 6.4631 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 : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 133 optimal weight: 0.0270 chunk 292 optimal weight: 30.0000 chunk 327 optimal weight: 0.1980 chunk 239 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 240 optimal weight: 40.0000 chunk 163 optimal weight: 0.7980 chunk 181 optimal weight: 0.0070 chunk 214 optimal weight: 3.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.059586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.044219 restraints weight = 52695.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.044735 restraints weight = 48224.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.044924 restraints weight = 45956.825| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 moved from start: 3.1911 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= 0.263 Angle : 1.087 20.408 38815 Z= 0.611 Chirality : 0.060 0.534 4466 Planarity : 0.006 0.061 5082 Dihedral : 8.241 39.998 3927 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 28.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.18 % Favored : 83.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.13), residues: 3591 helix: -1.37 (0.13), residues: 1666 sheet: -1.30 (0.29), residues: 308 loop : -3.73 (0.13), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 394 HIS 0.002 0.001 HIS C 168 PHE 0.012 0.001 PHE D 97 TYR 0.049 0.002 TYR F 41 ARG 0.004 0.001 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.21436 ( 913) hydrogen bonds : angle 8.88145 ( 2520) covalent geometry : bond 0.00475 (28616) covalent geometry : angle 1.08701 (38815) ********************** 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 26 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.504 Fit side-chains REVERT: A 398 GLU cc_start: 0.8894 (mp0) cc_final: 0.8653 (mp0) REVERT: A 402 LYS cc_start: 0.9321 (mmtm) cc_final: 0.8968 (tptt) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1822 time to fit residues: 6.4558 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 : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 317 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 246 optimal weight: 0.0870 chunk 245 optimal weight: 10.0000 chunk 252 optimal weight: 0.0050 chunk 133 optimal weight: 0.0570 chunk 119 optimal weight: 10.0000 chunk 311 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.3892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 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 = 0.4173 r_free = 0.4173 target = 0.060349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.044621 restraints weight = 52654.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.045196 restraints weight = 43516.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.045570 restraints weight = 35256.262| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4964 moved from start: 3.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 28616 Z= 0.271 Angle : 1.093 20.273 38815 Z= 0.610 Chirality : 0.058 0.429 4466 Planarity : 0.007 0.100 5082 Dihedral : 8.282 40.150 3927 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 28.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.35 % Favored : 82.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.13), residues: 3591 helix: -1.26 (0.13), residues: 1666 sheet: -1.21 (0.29), residues: 308 loop : -3.68 (0.13), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 394 HIS 0.002 0.000 HIS A 101 PHE 0.011 0.001 PHE G 97 TYR 0.082 0.002 TYR D 41 ARG 0.016 0.001 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.21102 ( 913) hydrogen bonds : angle 8.77769 ( 2520) covalent geometry : bond 0.00489 (28616) covalent geometry : angle 1.09348 (38815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4613.35 seconds wall clock time: 82 minutes 43.70 seconds (4963.70 seconds total)