Starting phenix.real_space_refine on Sun Nov 19 21:57:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/11_2023/6hdd_0204.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/11_2023/6hdd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/11_2023/6hdd_0204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/11_2023/6hdd_0204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/11_2023/6hdd_0204.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/11_2023/6hdd_0204.pdb" } 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 Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 364": "NH1" <-> "NH2" Residue "G PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 14.36, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 11.11 Conformation dependent library (CDL) restraints added in 5.1 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: 2.72 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: 7.92 Time building geometry restraints manager: 12.00 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: 95.69 - 104.85: 560 104.85 - 114.00: 16310 114.00 - 123.15: 20123 123.15 - 132.31: 1778 132.31 - 141.46: 44 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 2.440 nonbonded pdb=" O SER G 111 " pdb=" OG1 THR G 115 " model vdw 2.243 2.440 nonbonded pdb=" O SER B 111 " pdb=" OG1 THR B 115 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR A 350 " pdb=" O GLY A 371 " model vdw 2.253 2.440 nonbonded pdb=" O ASP F 108 " pdb=" OG SER F 111 " model vdw 2.259 2.440 ... (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 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: 0.770 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: 5.210 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 69.680 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.000 ------------------------------------------------------------------------------- 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= 0.595 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.2076 time to fit residues: 10.8333 Evaluate side-chains 20 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6665 ------------------------------------------------------------------------------- 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: 0.1980 chunk 270 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 92 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 144 optimal weight: 0.0870 chunk 279 optimal weight: 0.0050 chunk 108 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 324 optimal weight: 0.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 239 ASN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2565 moved from start: 3.0322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 28616 Z= 0.539 Angle : 1.604 41.796 38815 Z= 0.871 Chirality : 0.074 0.454 4466 Planarity : 0.010 0.117 5082 Dihedral : 11.102 52.562 3927 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 48.60 Ramachandran Plot: Outliers : 1.17 % Allowed : 12.67 % Favored : 86.16 % Rotamer: Outliers : 2.51 % Allowed : 5.24 % Favored : 92.26 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 10.00 % Twisted General : 2.43 % 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: -5.18 (0.11), residues: 3591 helix: -3.09 (0.10), residues: 1715 sheet: -2.15 (0.26), residues: 322 loop : -4.11 (0.12), residues: 1554 *********************** 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 44 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.519 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 42 average time/residue: 0.1832 time to fit residues: 9.8643 Evaluate side-chains 20 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0378 time to fit residues: 0.7226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 0.0270 chunk 100 optimal weight: 30.0000 chunk 269 optimal weight: 30.0000 chunk 220 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 324 optimal weight: 0.4980 chunk 350 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 322 optimal weight: 0.2980 chunk 110 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2490 moved from start: 3.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 28616 Z= 0.389 Angle : 1.298 27.117 38815 Z= 0.726 Chirality : 0.062 0.309 4466 Planarity : 0.008 0.077 5082 Dihedral : 10.100 51.947 3927 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 38.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.57 % Favored : 83.43 % Rotamer: Outliers : 1.14 % Allowed : 6.61 % Favored : 92.26 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 5.00 % Twisted General : 1.82 % 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: -4.48 (0.12), residues: 3591 helix: -2.37 (0.11), residues: 1561 sheet: -2.00 (0.27), residues: 329 loop : -3.82 (0.13), residues: 1701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 37 average time/residue: 0.1893 time to fit residues: 9.0412 Evaluate side-chains 19 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 9.9990 chunk 244 optimal weight: 30.0000 chunk 168 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 218 optimal weight: 0.1980 chunk 325 optimal weight: 2.9990 chunk 345 optimal weight: 0.0370 chunk 170 optimal weight: 0.0470 chunk 308 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2460 moved from start: 3.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28616 Z= 0.325 Angle : 1.180 29.577 38815 Z= 0.660 Chirality : 0.065 0.714 4466 Planarity : 0.006 0.062 5082 Dihedral : 9.554 49.243 3927 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 35.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 0.23 % Allowed : 5.24 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 2.02 % 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: -4.15 (0.12), residues: 3591 helix: -2.00 (0.12), residues: 1540 sheet: -1.48 (0.29), residues: 280 loop : -3.78 (0.13), residues: 1771 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 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 fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.2244 time to fit residues: 7.9856 Evaluate side-chains 20 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 0.4980 chunk 195 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 256 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 chunk 294 optimal weight: 0.0980 chunk 238 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 309 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS C 239 ASN C 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2454 moved from start: 3.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28616 Z= 0.309 Angle : 1.129 25.867 38815 Z= 0.635 Chirality : 0.058 0.320 4466 Planarity : 0.006 0.064 5082 Dihedral : 9.225 44.831 3927 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 32.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -3.78 (0.13), residues: 3591 helix: -1.66 (0.13), residues: 1491 sheet: -1.47 (0.28), residues: 308 loop : -3.56 (0.13), residues: 1792 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2292 time to fit residues: 7.2921 Evaluate side-chains 21 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 345 optimal weight: 0.0170 chunk 286 optimal weight: 0.0030 chunk 159 optimal weight: 7.9990 chunk 28 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 181 optimal weight: 0.0370 overall best weight: 1.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2467 moved from start: 3.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 28616 Z= 0.329 Angle : 1.105 26.364 38815 Z= 0.618 Chirality : 0.056 0.332 4466 Planarity : 0.006 0.063 5082 Dihedral : 9.122 60.230 3927 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.57 % Favored : 83.43 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.62 % 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: -3.73 (0.13), residues: 3591 helix: -1.54 (0.13), residues: 1491 sheet: -1.62 (0.27), residues: 280 loop : -3.56 (0.13), residues: 1820 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 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 fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.2927 time to fit residues: 9.7708 Evaluate side-chains 22 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 0.0270 chunk 38 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 252 optimal weight: 30.0000 chunk 195 optimal weight: 0.4980 chunk 290 optimal weight: 0.0020 chunk 192 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 209 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 overall best weight: 0.4446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN C 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2406 moved from start: 3.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 28616 Z= 0.309 Angle : 1.046 24.670 38815 Z= 0.585 Chirality : 0.056 0.274 4466 Planarity : 0.006 0.061 5082 Dihedral : 8.628 47.434 3927 Min Nonbonded Distance : 1.489 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 0.23 % Allowed : 2.73 % Favored : 97.04 % 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: -3.74 (0.13), residues: 3591 helix: -1.50 (0.12), residues: 1561 sheet: -1.91 (0.31), residues: 238 loop : -3.59 (0.13), residues: 1792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 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 fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.2248 time to fit residues: 7.4399 Evaluate side-chains 19 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 218 optimal weight: 30.0000 chunk 234 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 270 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 ASN C 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2468 moved from start: 3.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 28616 Z= 0.379 Angle : 1.094 18.903 38815 Z= 0.615 Chirality : 0.060 0.462 4466 Planarity : 0.007 0.105 5082 Dihedral : 8.944 57.814 3927 Min Nonbonded Distance : 1.471 Molprobity Statistics. All-atom Clashscore : 31.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.96 % Favored : 82.85 % 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 : 2.02 % 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: -3.65 (0.13), residues: 3591 helix: -1.40 (0.12), residues: 1505 sheet: -2.41 (0.30), residues: 259 loop : -3.43 (0.13), residues: 1827 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2252 time to fit residues: 7.3012 Evaluate side-chains 20 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 5.9990 chunk 329 optimal weight: 8.9990 chunk 300 optimal weight: 40.0000 chunk 320 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 289 optimal weight: 0.9980 chunk 303 optimal weight: 30.0000 chunk 319 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2447 moved from start: 3.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 28616 Z= 0.337 Angle : 1.019 17.487 38815 Z= 0.570 Chirality : 0.058 0.424 4466 Planarity : 0.006 0.058 5082 Dihedral : 8.736 68.037 3927 Min Nonbonded Distance : 1.434 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 0.39 % Allowed : 17.15 % Favored : 82.46 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.62 % 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: -3.61 (0.13), residues: 3591 helix: -1.26 (0.13), residues: 1547 sheet: -2.32 (0.30), residues: 259 loop : -3.57 (0.13), residues: 1785 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2415 time to fit residues: 9.0352 Evaluate side-chains 19 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.9980 chunk 339 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 160 optimal weight: 0.0050 chunk 235 optimal weight: 9.9990 chunk 355 optimal weight: 9.9990 chunk 327 optimal weight: 30.0000 chunk 283 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2430 moved from start: 3.2405 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= 0.343 Angle : 1.046 18.329 38815 Z= 0.591 Chirality : 0.058 0.436 4466 Planarity : 0.006 0.054 5082 Dihedral : 8.979 68.262 3927 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 27.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.35 % Favored : 82.46 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % 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: -3.55 (0.13), residues: 3591 helix: -1.21 (0.13), residues: 1610 sheet: -2.20 (0.31), residues: 259 loop : -3.63 (0.13), residues: 1722 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1891 time to fit residues: 6.2728 Evaluate side-chains 19 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 261 optimal weight: 0.2980 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 0.0470 chunk 283 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 3.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.058060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.047850 restraints weight = 73843.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.048304 restraints weight = 66308.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.048662 restraints weight = 60465.185| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5319 moved from start: 3.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 28616 Z= 0.312 Angle : 1.007 22.850 38815 Z= 0.557 Chirality : 0.054 0.283 4466 Planarity : 0.006 0.053 5082 Dihedral : 8.618 65.920 3927 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.37 % Favored : 83.24 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.82 % 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: -3.27 (0.13), residues: 3591 helix: -1.05 (0.13), residues: 1596 sheet: -1.45 (0.28), residues: 301 loop : -3.53 (0.14), residues: 1694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.31 seconds wall clock time: 60 minutes 5.73 seconds (3605.73 seconds total)