Starting phenix.real_space_refine on Wed Mar 20 18:00:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/03_2024/6hdd_0204.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/03_2024/6hdd_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_0204/03_2024/6hdd_0204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/03_2024/6hdd_0204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/03_2024/6hdd_0204.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hdd_0204/03_2024/6hdd_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 14.63, per 1000 atoms: 0.52 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: 10.33 Conformation dependent library (CDL) restraints added in 4.8 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: 2.64 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: 8.65 Time building geometry restraints manager: 11.26 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: 0.980 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: 5.170 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 69.720 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.150 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.520 ------------------------------------------------------------------------------- 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 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 *********************** 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 : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.2112 time to fit residues: 11.0489 Evaluate side-chains 20 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 499 HIS 0.004 0.002 HIS C 101 PHE 0.047 0.003 PHE F 10 TYR 0.028 0.002 TYR A 41 ARG 0.014 0.001 ARG E 338 *********************** 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 : 0.462 Fit side-chains revert: symmetry clash REVERT: A 227 ARG cc_start: 0.3461 (OUTLIER) cc_final: 0.2794 (mpt180) outliers start: 11 outliers final: 1 residues processed: 42 average time/residue: 0.1771 time to fit residues: 9.5017 Evaluate side-chains 21 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 0.2484 moved from start: 3.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 28616 Z= 0.386 Angle : 1.279 23.171 38815 Z= 0.722 Chirality : 0.062 0.352 4466 Planarity : 0.008 0.064 5082 Dihedral : 10.076 50.700 3927 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 38.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.37 % Favored : 83.63 % Rotamer: Outliers : 1.37 % Allowed : 6.61 % Favored : 92.03 % Cbeta Deviations : 0.21 % 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: -4.47 (0.12), residues: 3591 helix: -2.38 (0.11), residues: 1561 sheet: -1.66 (0.28), residues: 308 loop : -3.86 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 394 HIS 0.007 0.002 HIS B 101 PHE 0.031 0.002 PHE C 10 TYR 0.033 0.002 TYR G 519 ARG 0.019 0.001 ARG D 514 *********************** 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 39 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 37 average time/residue: 0.1774 time to fit residues: 8.4919 Evaluate side-chains 20 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 10.0000 chunk 244 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 154 optimal weight: 0.0070 chunk 218 optimal weight: 0.2980 chunk 325 optimal weight: 0.0040 chunk 345 optimal weight: 0.1980 chunk 170 optimal weight: 0.2980 chunk 308 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.1610 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2450 moved from start: 3.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28616 Z= 0.322 Angle : 1.170 25.734 38815 Z= 0.657 Chirality : 0.060 0.354 4466 Planarity : 0.006 0.060 5082 Dihedral : 9.575 46.287 3927 Min Nonbonded Distance : 1.493 Molprobity Statistics. All-atom Clashscore : 34.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % Rotamer: Outliers : 0.46 % Allowed : 5.47 % Favored : 94.08 % 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: -4.12 (0.12), residues: 3591 helix: -1.93 (0.12), residues: 1512 sheet: -1.49 (0.28), residues: 308 loop : -3.82 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 394 HIS 0.005 0.002 HIS E 101 PHE 0.015 0.002 PHE A 10 TYR 0.021 0.002 TYR E 41 ARG 0.007 0.001 ARG D 514 *********************** 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 27 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 ASN cc_start: 0.6743 (t0) cc_final: 0.6536 (t0) REVERT: C 512 MET cc_start: 0.3545 (mmp) cc_final: 0.3300 (mmp) outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.2010 time to fit residues: 7.0655 Evaluate side-chains 20 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 10.0000 chunk 195 optimal weight: 0.0770 chunk 5 optimal weight: 30.0000 chunk 256 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 294 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 309 optimal weight: 0.0770 chunk 87 optimal weight: 9.9990 overall best weight: 1.3098 ------------------------------------------------------------------------------- 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 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN C 367 ASN C 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2450 moved from start: 3.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28616 Z= 0.316 Angle : 1.098 24.172 38815 Z= 0.617 Chirality : 0.059 0.363 4466 Planarity : 0.006 0.063 5082 Dihedral : 9.005 46.127 3927 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 32.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.57 % Favored : 83.43 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -3.91 (0.13), residues: 3591 helix: -1.66 (0.12), residues: 1477 sheet: -1.84 (0.27), residues: 301 loop : -3.66 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 394 HIS 0.003 0.001 HIS G 101 PHE 0.017 0.002 PHE B 97 TYR 0.011 0.001 TYR F 454 ARG 0.005 0.000 ARG F 227 *********************** 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 29 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 512 MET cc_start: 0.1984 (mmp) cc_final: 0.0817 (tpt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2508 time to fit residues: 9.0030 Evaluate side-chains 23 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 0.0020 chunk 68 optimal weight: 0.1980 chunk 202 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 345 optimal weight: 30.0000 chunk 286 optimal weight: 0.3980 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 114 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 46 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 168 HIS C 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2416 moved from start: 3.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.192 28616 Z= 0.376 Angle : 1.089 23.913 38815 Z= 0.611 Chirality : 0.060 0.415 4466 Planarity : 0.006 0.061 5082 Dihedral : 8.639 46.790 3927 Min Nonbonded Distance : 1.486 Molprobity Statistics. All-atom Clashscore : 29.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.15 % Favored : 82.85 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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: -3.87 (0.13), residues: 3591 helix: -1.60 (0.13), residues: 1491 sheet: -1.81 (0.26), residues: 301 loop : -3.68 (0.13), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 394 HIS 0.009 0.002 HIS D 456 PHE 0.018 0.002 PHE A 97 TYR 0.010 0.001 TYR G 41 ARG 0.012 0.001 ARG F 514 *********************** 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 : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 512 MET cc_start: 0.1213 (mmp) cc_final: 0.0575 (tpt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.2514 time to fit residues: 8.4542 Evaluate side-chains 19 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 252 optimal weight: 0.0030 chunk 195 optimal weight: 0.0010 chunk 290 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 209 optimal weight: 0.0670 chunk 158 optimal weight: 0.4980 overall best weight: 1.7136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.2438 moved from start: 3.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 28616 Z= 0.319 Angle : 1.006 17.537 38815 Z= 0.563 Chirality : 0.055 0.277 4466 Planarity : 0.006 0.080 5082 Dihedral : 8.501 55.344 3927 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 30.46 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.96 % Favored : 82.65 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.21 % 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: -3.50 (0.13), residues: 3591 helix: -1.34 (0.13), residues: 1484 sheet: -1.81 (0.27), residues: 315 loop : -3.39 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 394 HIS 0.004 0.001 HIS B 101 PHE 0.034 0.003 PHE D 10 TYR 0.023 0.001 TYR F 519 ARG 0.008 0.000 ARG C 69 *********************** 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 23 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 512 MET cc_start: -0.0775 (mmp) cc_final: -0.1870 (tmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2683 time to fit residues: 7.6148 Evaluate side-chains 19 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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: 7.9990 chunk 205 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 234 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 32 optimal weight: 0.0000 chunk 270 optimal weight: 30.0000 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 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: 0.2405 moved from start: 3.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28616 Z= 0.299 Angle : 0.976 14.819 38815 Z= 0.552 Chirality : 0.055 0.325 4466 Planarity : 0.006 0.059 5082 Dihedral : 8.225 53.297 3927 Min Nonbonded Distance : 1.489 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 15.20 % Favored : 84.41 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -3.43 (0.13), residues: 3591 helix: -1.28 (0.13), residues: 1561 sheet: -2.00 (0.33), residues: 259 loop : -3.34 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 394 HIS 0.003 0.001 HIS C 101 PHE 0.024 0.002 PHE B 65 TYR 0.026 0.001 TYR G 41 ARG 0.008 0.001 ARG F 61 *********************** 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 24 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.7062 (mpp) cc_final: 0.6640 (mmp) REVERT: C 512 MET cc_start: -0.1303 (mmp) cc_final: -0.2218 (tmm) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2407 time to fit residues: 7.1590 Evaluate side-chains 18 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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: 1.9990 chunk 329 optimal weight: 30.0000 chunk 300 optimal weight: 30.0000 chunk 320 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 139 optimal weight: 0.0070 chunk 251 optimal weight: 0.0870 chunk 98 optimal weight: 0.0060 chunk 289 optimal weight: 4.9990 chunk 303 optimal weight: 30.0000 chunk 319 optimal weight: 10.0000 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN C 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2370 moved from start: 3.2718 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= 0.300 Angle : 0.963 15.618 38815 Z= 0.543 Chirality : 0.053 0.295 4466 Planarity : 0.006 0.058 5082 Dihedral : 8.233 58.683 3927 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.57 % Favored : 83.24 % Rotamer: Outliers : 0.23 % Allowed : 1.82 % Favored : 97.95 % Cbeta Deviations : 0.00 % 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: -3.42 (0.13), residues: 3591 helix: -1.20 (0.12), residues: 1631 sheet: -2.17 (0.32), residues: 273 loop : -3.47 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 394 HIS 0.003 0.001 HIS C 101 PHE 0.031 0.002 PHE A 10 TYR 0.032 0.001 TYR E 41 ARG 0.009 0.001 ARG D 514 *********************** 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 20 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.7046 (mpp) cc_final: 0.6566 (mmp) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1760 time to fit residues: 5.0683 Evaluate side-chains 18 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 7.9990 chunk 339 optimal weight: 0.0870 chunk 206 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 235 optimal weight: 0.6980 chunk 355 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 29 optimal weight: 40.0000 chunk 218 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 overall best weight: 1.3160 ------------------------------------------------------------------------------- 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 71 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2362 moved from start: 3.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 28616 Z= 0.361 Angle : 0.983 12.538 38815 Z= 0.559 Chirality : 0.053 0.273 4466 Planarity : 0.007 0.078 5082 Dihedral : 8.230 57.480 3927 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 26.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.18 % Favored : 83.63 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.54 % Cbeta Deviations : 0.00 % 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: -3.32 (0.13), residues: 3591 helix: -1.03 (0.13), residues: 1603 sheet: -1.89 (0.32), residues: 259 loop : -3.52 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 394 HIS 0.003 0.001 HIS C 101 PHE 0.031 0.002 PHE A 10 TYR 0.028 0.001 TYR A 41 ARG 0.007 0.001 ARG B 69 ********************** 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 19 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: C 482 MET cc_start: 0.7109 (mpp) cc_final: 0.6621 (mmp) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.1325 time to fit residues: 4.0233 Evaluate side-chains 15 residues out of total 439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 0.6980 chunk 301 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 283 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 291 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 71 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.3841 r_free = 0.3841 target = 0.060684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.048537 restraints weight = 70848.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.048756 restraints weight = 67395.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.048947 restraints weight = 64706.091| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 3.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 28616 Z= 0.319 Angle : 0.965 11.539 38815 Z= 0.548 Chirality : 0.052 0.236 4466 Planarity : 0.007 0.070 5082 Dihedral : 8.064 56.630 3927 Min Nonbonded Distance : 1.496 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 17.15 % Favored : 82.65 % 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 : 1.01 % 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: -3.09 (0.14), residues: 3591 helix: -0.85 (0.13), residues: 1568 sheet: -1.84 (0.31), residues: 273 loop : -3.34 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 394 HIS 0.003 0.001 HIS C 101 PHE 0.026 0.002 PHE E 10 TYR 0.040 0.002 TYR D 41 ARG 0.008 0.001 ARG G 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3098.30 seconds wall clock time: 60 minutes 23.83 seconds (3623.83 seconds total)