Starting phenix.real_space_refine on Thu Mar 14 20:25:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/03_2024/6gct_4386.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/03_2024/6gct_4386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/03_2024/6gct_4386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/03_2024/6gct_4386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/03_2024/6gct_4386.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/03_2024/6gct_4386.pdb" } resolution = 3.85 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= 0.000 sd= 0.007 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 48 5.16 5 C 6324 2.51 5 N 1605 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9672 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3214 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 16, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3214 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 16, 'TRANS': 415} Chain breaks: 1 Chain: "C" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3214 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 16, 'TRANS': 415} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.59 Number of scatterers: 9672 At special positions: 0 Unit cell: (117.392, 119.416, 82.984, 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 48 16.00 O 1695 8.00 N 1605 7.00 C 6324 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: 4.40 Conformation dependent library (CDL) restraints added in 2.0 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 75.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.789A pdb=" N ARG A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 52 " --> pdb=" O CYS A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 52' Processing helix chain 'A' and resid 52 through 76 removed outlier: 3.913A pdb=" N VAL A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.910A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.674A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 154 removed outlier: 3.618A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 removed outlier: 3.652A pdb=" N PHE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.878A pdb=" N ALA A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.823A pdb=" N SER A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 290 removed outlier: 4.113A pdb=" N TRP A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.705A pdb=" N MET A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.693A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 330 removed outlier: 3.695A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.558A pdb=" N TRP A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.529A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 4.158A pdb=" N MET A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.551A pdb=" N CYS A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 410 through 424 removed outlier: 3.553A pdb=" N THR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 removed outlier: 3.641A pdb=" N THR A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 449 through 452 removed outlier: 3.560A pdb=" N HIS A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 452' Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 459 through 487 removed outlier: 3.558A pdb=" N VAL A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 removed outlier: 3.789A pdb=" N ARG B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 52' Processing helix chain 'B' and resid 52 through 76 removed outlier: 3.912A pdb=" N VAL B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 90 through 118 removed outlier: 3.909A pdb=" N LEU B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix removed outlier: 3.674A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 154 removed outlier: 3.617A pdb=" N LEU B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.651A pdb=" N PHE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.878A pdb=" N ALA B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.823A pdb=" N SER B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 290 removed outlier: 4.114A pdb=" N TRP B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.705A pdb=" N MET B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 319 removed outlier: 3.692A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 removed outlier: 3.695A pdb=" N PHE B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.558A pdb=" N TRP B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.530A pdb=" N LEU B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 4.157A pdb=" N MET B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.551A pdb=" N CYS B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 Processing helix chain 'B' and resid 410 through 424 removed outlier: 3.552A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 removed outlier: 3.642A pdb=" N THR B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 449 through 452 removed outlier: 3.562A pdb=" N HIS B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 452' Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 459 through 487 removed outlier: 3.558A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 removed outlier: 3.790A pdb=" N ARG C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN C 52 " --> pdb=" O CYS C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 52' Processing helix chain 'C' and resid 52 through 76 removed outlier: 3.912A pdb=" N VAL C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.910A pdb=" N LEU C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 97 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Proline residue: C 106 - end of helix removed outlier: 3.675A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 154 removed outlier: 3.617A pdb=" N LEU C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.651A pdb=" N PHE C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 234 through 249 removed outlier: 3.878A pdb=" N ALA C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.824A pdb=" N SER C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 290 removed outlier: 4.114A pdb=" N TRP C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.706A pdb=" N MET C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 319 removed outlier: 3.693A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 307 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 330 removed outlier: 3.695A pdb=" N PHE C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 removed outlier: 3.558A pdb=" N TRP C 338 " --> pdb=" O TYR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.530A pdb=" N LEU C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 4.158A pdb=" N MET C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU C 366 " --> pdb=" O LYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 383 Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.551A pdb=" N CYS C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 Processing helix chain 'C' and resid 410 through 424 removed outlier: 3.552A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 441 removed outlier: 3.641A pdb=" N THR C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 449 through 452 removed outlier: 3.562A pdb=" N HIS C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 452' Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 459 through 487 removed outlier: 3.557A pdb=" N VAL C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 484 " --> pdb=" O GLY C 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 203 Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 209 Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AA5, first strand: chain 'C' and resid 202 through 203 Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 209 501 hydrogen bonds defined for protein. 1440 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: 2.62 Time building geometry restraints manager: 4.69 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: 2698 1.33 - 1.45: 1748 1.45 - 1.57: 5319 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 9840 Sorted by residual: bond pdb=" CA MET C 387 " pdb=" CB MET C 387 " ideal model delta sigma weight residual 1.539 1.399 0.140 4.88e-02 4.20e+02 8.26e+00 bond pdb=" CA MET B 387 " pdb=" CB MET B 387 " ideal model delta sigma weight residual 1.539 1.399 0.140 4.88e-02 4.20e+02 8.25e+00 bond pdb=" CA MET A 387 " pdb=" CB MET A 387 " ideal model delta sigma weight residual 1.539 1.400 0.140 4.88e-02 4.20e+02 8.20e+00 bond pdb=" CB ASN C 190 " pdb=" CG ASN C 190 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.42e+00 bond pdb=" CB ASN A 190 " pdb=" CG ASN A 190 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.41e+00 ... (remaining 9835 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 191 105.44 - 112.58: 5171 112.58 - 119.72: 3674 119.72 - 126.86: 4247 126.86 - 134.00: 118 Bond angle restraints: 13401 Sorted by residual: angle pdb=" C LEU A 409 " pdb=" N ASP A 410 " pdb=" CA ASP A 410 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C LEU C 409 " pdb=" N ASP C 410 " pdb=" CA ASP C 410 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C LEU B 409 " pdb=" N ASP B 410 " pdb=" CA ASP B 410 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" CA LEU A 321 " pdb=" CB LEU A 321 " pdb=" CG LEU A 321 " ideal model delta sigma weight residual 116.30 130.46 -14.16 3.50e+00 8.16e-02 1.64e+01 angle pdb=" CA LEU B 321 " pdb=" CB LEU B 321 " pdb=" CG LEU B 321 " ideal model delta sigma weight residual 116.30 130.46 -14.16 3.50e+00 8.16e-02 1.64e+01 ... (remaining 13396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 5141 15.74 - 31.49: 454 31.49 - 47.23: 165 47.23 - 62.97: 21 62.97 - 78.71: 9 Dihedral angle restraints: 5790 sinusoidal: 2127 harmonic: 3663 Sorted by residual: dihedral pdb=" CA ALA C 123 " pdb=" C ALA C 123 " pdb=" N LEU C 124 " pdb=" CA LEU C 124 " ideal model delta harmonic sigma weight residual 180.00 -148.26 -31.74 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA ALA B 123 " pdb=" C ALA B 123 " pdb=" N LEU B 124 " pdb=" CA LEU B 124 " ideal model delta harmonic sigma weight residual -180.00 -148.26 -31.74 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA ALA A 123 " pdb=" C ALA A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta harmonic sigma weight residual 180.00 -148.28 -31.72 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1209 0.071 - 0.143: 392 0.143 - 0.214: 60 0.214 - 0.286: 10 0.286 - 0.357: 6 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA ASP B 410 " pdb=" N ASP B 410 " pdb=" C ASP B 410 " pdb=" CB ASP B 410 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP C 410 " pdb=" N ASP C 410 " pdb=" C ASP C 410 " pdb=" CB ASP C 410 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA ASP A 410 " pdb=" N ASP A 410 " pdb=" C ASP A 410 " pdb=" CB ASP A 410 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 1674 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 321 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.85e+00 pdb=" N PRO A 322 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 379 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 380 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 380 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 380 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 321 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 322 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.037 5.00e-02 4.00e+02 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3288 2.84 - 3.36: 10139 3.36 - 3.87: 15988 3.87 - 4.39: 18808 4.39 - 4.90: 29440 Nonbonded interactions: 77663 Sorted by model distance: nonbonded pdb=" OE1 GLU A 227 " pdb=" NH2 ARG C 202 " model vdw 2.330 2.520 nonbonded pdb=" O LEU C 119 " pdb=" NH1 ARG C 246 " model vdw 2.334 2.520 nonbonded pdb=" O LEU B 119 " pdb=" NH1 ARG B 246 " model vdw 2.334 2.520 nonbonded pdb=" O LEU A 119 " pdb=" NH1 ARG A 246 " model vdw 2.334 2.520 nonbonded pdb=" O LYS A 372 " pdb=" OG SER A 375 " model vdw 2.335 2.440 ... (remaining 77658 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.520 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.680 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.012 0.140 9840 Z= 0.752 Angle : 1.401 14.161 13401 Z= 0.698 Chirality : 0.072 0.357 1677 Planarity : 0.008 0.065 1665 Dihedral : 14.504 78.713 3438 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Rotamer: Outliers : 5.57 % Allowed : 16.42 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -6.53 (0.15), residues: 1284 helix: -4.40 (0.08), residues: 879 sheet: -3.60 (0.50), residues: 60 loop : -3.38 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 275 HIS 0.006 0.002 HIS C 316 PHE 0.023 0.003 PHE B 201 TYR 0.023 0.004 TYR C 485 ARG 0.004 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 300 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 130 TRP cc_start: 0.7754 (m100) cc_final: 0.7465 (m100) REVERT: A 248 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9065 (tt) REVERT: A 473 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 130 TRP cc_start: 0.7843 (m100) cc_final: 0.7607 (m100) REVERT: B 181 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7869 (mp) REVERT: B 263 ASN cc_start: 0.8929 (p0) cc_final: 0.8709 (p0) REVERT: B 483 GLN cc_start: 0.7767 (pp30) cc_final: 0.6904 (pp30) REVERT: C 130 TRP cc_start: 0.7865 (m100) cc_final: 0.7505 (m100) REVERT: C 186 ASP cc_start: 0.8724 (t70) cc_final: 0.8496 (t0) REVERT: C 275 TRP cc_start: 0.8221 (m100) cc_final: 0.7533 (m-10) REVERT: C 483 GLN cc_start: 0.7831 (pp30) cc_final: 0.7278 (pp30) outliers start: 57 outliers final: 18 residues processed: 324 average time/residue: 0.2034 time to fit residues: 93.0141 Evaluate side-chains 235 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 320 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 316 HIS A 367 ASN A 386 ASN A 403 GLN A 484 ASN B 154 GLN B 316 HIS B 367 ASN B 373 HIS B 403 GLN C 154 GLN C 316 HIS C 367 ASN C 386 ASN C 484 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9840 Z= 0.229 Angle : 0.820 14.480 13401 Z= 0.392 Chirality : 0.044 0.208 1677 Planarity : 0.005 0.045 1665 Dihedral : 7.418 58.488 1403 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 7.43 % Allowed : 18.96 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.69 (0.18), residues: 1284 helix: -2.95 (0.12), residues: 906 sheet: -3.41 (0.54), residues: 60 loop : -2.69 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 461 HIS 0.003 0.001 HIS A 316 PHE 0.030 0.002 PHE B 400 TYR 0.019 0.002 TYR A 276 ARG 0.004 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 275 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8142 (tm) REVERT: A 91 PHE cc_start: 0.8810 (t80) cc_final: 0.8596 (t80) REVERT: A 132 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8550 (tt) REVERT: A 248 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9070 (tt) REVERT: A 311 LEU cc_start: 0.9248 (tp) cc_final: 0.9012 (tt) REVERT: B 247 LYS cc_start: 0.8107 (tttt) cc_final: 0.7841 (ttmt) REVERT: C 275 TRP cc_start: 0.8010 (m100) cc_final: 0.7354 (m-10) REVERT: C 305 TYR cc_start: 0.8798 (t80) cc_final: 0.8581 (t80) REVERT: C 361 MET cc_start: 0.6600 (mpp) cc_final: 0.6282 (mpp) REVERT: C 388 ASP cc_start: 0.8583 (m-30) cc_final: 0.8324 (m-30) REVERT: C 482 LEU cc_start: 0.8795 (mm) cc_final: 0.8578 (mm) outliers start: 76 outliers final: 29 residues processed: 328 average time/residue: 0.1633 time to fit residues: 79.1396 Evaluate side-chains 267 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 235 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 0.0370 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9840 Z= 0.239 Angle : 0.837 13.968 13401 Z= 0.387 Chirality : 0.044 0.203 1677 Planarity : 0.005 0.044 1665 Dihedral : 6.605 57.492 1384 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 8.02 % Allowed : 22.58 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.57 (0.21), residues: 1284 helix: -2.13 (0.15), residues: 897 sheet: -3.27 (0.57), residues: 60 loop : -2.19 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 461 HIS 0.004 0.001 HIS C 316 PHE 0.022 0.002 PHE A 400 TYR 0.010 0.002 TYR B 325 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 242 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8141 (tm) REVERT: A 132 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 149 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8228 (tp) REVERT: B 149 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8422 (tp) REVERT: B 247 LYS cc_start: 0.8036 (tttt) cc_final: 0.7774 (ttmt) REVERT: B 387 MET cc_start: 0.7749 (mtp) cc_final: 0.7480 (mtp) REVERT: C 275 TRP cc_start: 0.8040 (m100) cc_final: 0.7719 (m-10) REVERT: C 305 TYR cc_start: 0.8827 (t80) cc_final: 0.8570 (t80) REVERT: B 601 GLN cc_start: 0.8122 (pm20) cc_final: 0.7838 (pm20) outliers start: 82 outliers final: 39 residues processed: 300 average time/residue: 0.1699 time to fit residues: 75.0496 Evaluate side-chains 261 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9840 Z= 0.208 Angle : 0.840 15.693 13401 Z= 0.378 Chirality : 0.044 0.195 1677 Planarity : 0.004 0.039 1665 Dihedral : 5.827 53.509 1380 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 7.33 % Allowed : 24.73 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.28 (0.22), residues: 1284 helix: -2.00 (0.15), residues: 909 sheet: -3.11 (0.59), residues: 60 loop : -1.78 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 461 HIS 0.004 0.001 HIS B 316 PHE 0.025 0.002 PHE B 400 TYR 0.013 0.001 TYR B 325 ARG 0.002 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 251 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8083 (tm) REVERT: A 132 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8625 (tt) REVERT: A 268 VAL cc_start: 0.8969 (p) cc_final: 0.8630 (t) REVERT: A 288 LYS cc_start: 0.8661 (tmmm) cc_final: 0.8183 (ttmt) REVERT: A 387 MET cc_start: 0.7730 (mtp) cc_final: 0.7510 (mtm) REVERT: B 149 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8331 (tp) REVERT: B 247 LYS cc_start: 0.8033 (tttt) cc_final: 0.7772 (ttmt) REVERT: B 387 MET cc_start: 0.7656 (mtp) cc_final: 0.7385 (mtp) REVERT: B 401 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9056 (mm) REVERT: B 455 LEU cc_start: 0.8297 (pt) cc_final: 0.8022 (pt) REVERT: B 470 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9055 (tt) REVERT: C 305 TYR cc_start: 0.8846 (t80) cc_final: 0.8451 (t80) REVERT: C 388 ASP cc_start: 0.8242 (m-30) cc_final: 0.7973 (m-30) REVERT: C 441 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 601 GLN cc_start: 0.8023 (pm20) cc_final: 0.7740 (pm20) outliers start: 75 outliers final: 40 residues processed: 301 average time/residue: 0.1749 time to fit residues: 76.9886 Evaluate side-chains 273 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9840 Z= 0.215 Angle : 0.839 15.043 13401 Z= 0.376 Chirality : 0.045 0.216 1677 Planarity : 0.004 0.038 1665 Dihedral : 5.603 53.343 1378 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 7.14 % Allowed : 25.71 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.89 (0.22), residues: 1284 helix: -1.69 (0.16), residues: 903 sheet: -3.00 (0.60), residues: 60 loop : -1.70 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 461 HIS 0.003 0.001 HIS B 373 PHE 0.026 0.001 PHE B 400 TYR 0.013 0.001 TYR C 325 ARG 0.001 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 240 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8029 (tm) REVERT: A 89 PHE cc_start: 0.7167 (m-80) cc_final: 0.6228 (m-80) REVERT: A 132 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 149 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8038 (tp) REVERT: A 268 VAL cc_start: 0.8986 (p) cc_final: 0.8631 (t) REVERT: A 288 LYS cc_start: 0.8673 (tmmm) cc_final: 0.8198 (ttmt) REVERT: A 334 TYR cc_start: 0.6482 (m-80) cc_final: 0.6109 (m-10) REVERT: B 90 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8721 (t) REVERT: B 149 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8362 (tp) REVERT: B 247 LYS cc_start: 0.8037 (tttt) cc_final: 0.7796 (ttmt) REVERT: B 470 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9020 (tt) REVERT: C 229 MET cc_start: 0.8132 (ppp) cc_final: 0.7761 (ptm) REVERT: C 341 VAL cc_start: 0.8382 (t) cc_final: 0.8065 (p) REVERT: C 388 ASP cc_start: 0.8252 (m-30) cc_final: 0.8028 (m-30) REVERT: C 441 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 601 GLN cc_start: 0.8000 (pm20) cc_final: 0.7799 (pm20) outliers start: 73 outliers final: 44 residues processed: 286 average time/residue: 0.1730 time to fit residues: 72.7279 Evaluate side-chains 276 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 225 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 0.0020 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9840 Z= 0.203 Angle : 0.838 14.721 13401 Z= 0.372 Chirality : 0.044 0.229 1677 Planarity : 0.004 0.035 1665 Dihedral : 5.426 52.316 1376 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 6.94 % Allowed : 26.39 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.56 (0.23), residues: 1284 helix: -1.40 (0.16), residues: 906 sheet: -2.87 (0.62), residues: 60 loop : -1.72 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 461 HIS 0.003 0.001 HIS B 316 PHE 0.027 0.001 PHE B 400 TYR 0.009 0.001 TYR B 325 ARG 0.001 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 250 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7929 (tm) REVERT: A 89 PHE cc_start: 0.7079 (m-80) cc_final: 0.6264 (m-80) REVERT: A 90 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8935 (t) REVERT: A 132 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8592 (tt) REVERT: A 149 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7957 (tp) REVERT: A 268 VAL cc_start: 0.8937 (p) cc_final: 0.8548 (t) REVERT: A 288 LYS cc_start: 0.8664 (tmmm) cc_final: 0.8203 (ttmt) REVERT: A 334 TYR cc_start: 0.6324 (m-80) cc_final: 0.6080 (m-10) REVERT: A 372 LYS cc_start: 0.8025 (tppt) cc_final: 0.7682 (tppt) REVERT: A 460 ASP cc_start: 0.7679 (t70) cc_final: 0.7066 (t0) REVERT: A 473 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: B 90 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8945 (t) REVERT: B 149 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8338 (tp) REVERT: B 247 LYS cc_start: 0.8001 (tttt) cc_final: 0.7748 (ttmt) REVERT: B 281 ILE cc_start: 0.8802 (mt) cc_final: 0.8549 (mt) REVERT: B 341 VAL cc_start: 0.8385 (t) cc_final: 0.8092 (p) REVERT: C 90 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8921 (t) REVERT: C 229 MET cc_start: 0.8256 (ppp) cc_final: 0.7991 (ptm) REVERT: C 341 VAL cc_start: 0.8322 (t) cc_final: 0.8031 (p) REVERT: C 388 ASP cc_start: 0.8141 (m-30) cc_final: 0.7935 (m-30) outliers start: 71 outliers final: 42 residues processed: 297 average time/residue: 0.1699 time to fit residues: 73.7511 Evaluate side-chains 279 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 GLN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9840 Z= 0.205 Angle : 0.846 14.899 13401 Z= 0.375 Chirality : 0.045 0.308 1677 Planarity : 0.004 0.034 1665 Dihedral : 5.316 52.384 1376 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 7.23 % Allowed : 27.08 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.37 (0.23), residues: 1284 helix: -1.26 (0.16), residues: 897 sheet: -2.74 (0.63), residues: 60 loop : -1.64 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 461 HIS 0.003 0.001 HIS B 316 PHE 0.030 0.001 PHE B 400 TYR 0.010 0.001 TYR B 325 ARG 0.001 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 245 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7936 (tm) REVERT: A 89 PHE cc_start: 0.6953 (m-80) cc_final: 0.6159 (m-80) REVERT: A 90 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8967 (t) REVERT: A 132 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8587 (tt) REVERT: A 149 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7960 (tp) REVERT: A 288 LYS cc_start: 0.8639 (tmmm) cc_final: 0.8354 (ttpt) REVERT: A 362 LYS cc_start: 0.8075 (tptt) cc_final: 0.7860 (tppt) REVERT: A 372 LYS cc_start: 0.8105 (tppt) cc_final: 0.7782 (tppt) REVERT: B 90 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8897 (t) REVERT: B 149 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 247 LYS cc_start: 0.7981 (tttt) cc_final: 0.7779 (ttmt) REVERT: B 341 VAL cc_start: 0.8380 (t) cc_final: 0.8111 (p) REVERT: B 470 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 89 PHE cc_start: 0.6880 (m-80) cc_final: 0.6419 (m-80) REVERT: C 90 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8909 (t) REVERT: C 323 LEU cc_start: 0.8655 (tt) cc_final: 0.8448 (mp) REVERT: C 341 VAL cc_start: 0.8338 (t) cc_final: 0.8034 (p) REVERT: C 388 ASP cc_start: 0.8110 (m-30) cc_final: 0.7868 (m-30) outliers start: 74 outliers final: 48 residues processed: 294 average time/residue: 0.1700 time to fit residues: 73.2312 Evaluate side-chains 291 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 235 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.0770 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9840 Z= 0.198 Angle : 0.850 14.823 13401 Z= 0.376 Chirality : 0.045 0.217 1677 Planarity : 0.004 0.035 1665 Dihedral : 5.233 52.537 1376 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.65 % Allowed : 27.08 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.23 (0.23), residues: 1284 helix: -1.15 (0.17), residues: 897 sheet: -2.68 (0.64), residues: 60 loop : -1.60 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 461 HIS 0.003 0.001 HIS C 316 PHE 0.049 0.001 PHE B 400 TYR 0.021 0.001 TYR C 325 ARG 0.001 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 251 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6761 (m-80) cc_final: 0.6156 (m-80) REVERT: A 90 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8973 (t) REVERT: A 132 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8572 (tt) REVERT: A 149 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 275 TRP cc_start: 0.7738 (m100) cc_final: 0.7280 (m-10) REVERT: A 288 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8255 (ttpt) REVERT: A 372 LYS cc_start: 0.8091 (tppt) cc_final: 0.7812 (tppt) REVERT: B 90 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8948 (t) REVERT: B 149 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8368 (tp) REVERT: B 323 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8602 (tt) REVERT: B 341 VAL cc_start: 0.8393 (t) cc_final: 0.8119 (p) REVERT: B 482 LEU cc_start: 0.9011 (mm) cc_final: 0.8802 (mm) REVERT: C 89 PHE cc_start: 0.6882 (m-80) cc_final: 0.6434 (m-80) REVERT: C 90 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8897 (t) REVERT: C 341 VAL cc_start: 0.8313 (t) cc_final: 0.8000 (p) REVERT: C 388 ASP cc_start: 0.8138 (m-30) cc_final: 0.7879 (m-30) outliers start: 68 outliers final: 46 residues processed: 294 average time/residue: 0.1736 time to fit residues: 74.6615 Evaluate side-chains 284 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 230 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.0980 chunk 115 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 76 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9840 Z= 0.201 Angle : 0.881 14.850 13401 Z= 0.388 Chirality : 0.046 0.246 1677 Planarity : 0.004 0.037 1665 Dihedral : 4.897 28.349 1372 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.77 % Allowed : 28.54 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.21 (0.23), residues: 1284 helix: -1.13 (0.16), residues: 900 sheet: -2.60 (0.65), residues: 60 loop : -1.65 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 461 HIS 0.002 0.001 HIS B 316 PHE 0.047 0.001 PHE B 400 TYR 0.020 0.001 TYR C 325 ARG 0.001 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 238 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6758 (m-80) cc_final: 0.6177 (m-80) REVERT: A 90 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8974 (t) REVERT: A 132 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8581 (tt) REVERT: A 149 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7871 (tp) REVERT: A 275 TRP cc_start: 0.7637 (m100) cc_final: 0.7193 (m-10) REVERT: A 288 LYS cc_start: 0.8576 (tmmm) cc_final: 0.8200 (ttmt) REVERT: A 372 LYS cc_start: 0.8115 (tppt) cc_final: 0.7847 (tppt) REVERT: B 149 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 323 LEU cc_start: 0.8913 (mp) cc_final: 0.8702 (tt) REVERT: B 341 VAL cc_start: 0.8384 (t) cc_final: 0.8117 (p) REVERT: C 89 PHE cc_start: 0.6847 (m-80) cc_final: 0.6430 (m-80) REVERT: C 90 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8913 (t) REVERT: C 341 VAL cc_start: 0.8347 (t) cc_final: 0.8066 (p) REVERT: C 388 ASP cc_start: 0.8090 (m-30) cc_final: 0.7842 (m-30) outliers start: 59 outliers final: 45 residues processed: 279 average time/residue: 0.1778 time to fit residues: 72.2823 Evaluate side-chains 281 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9840 Z= 0.210 Angle : 0.898 15.576 13401 Z= 0.394 Chirality : 0.047 0.302 1677 Planarity : 0.004 0.038 1665 Dihedral : 4.882 30.461 1372 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.67 % Allowed : 28.74 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.15 (0.23), residues: 1284 helix: -1.09 (0.16), residues: 900 sheet: -2.57 (0.65), residues: 60 loop : -1.61 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 461 HIS 0.002 0.001 HIS C 316 PHE 0.042 0.002 PHE B 400 TYR 0.018 0.001 TYR C 325 ARG 0.002 0.000 ARG C 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6778 (m-80) cc_final: 0.6191 (m-80) REVERT: A 90 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8984 (t) REVERT: A 132 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 149 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 288 LYS cc_start: 0.8532 (tmmm) cc_final: 0.8172 (ttmt) REVERT: A 372 LYS cc_start: 0.8100 (tppt) cc_final: 0.7842 (tppt) REVERT: B 323 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8688 (tt) REVERT: B 334 TYR cc_start: 0.6411 (m-80) cc_final: 0.5898 (m-10) REVERT: B 341 VAL cc_start: 0.8382 (t) cc_final: 0.8127 (p) REVERT: C 89 PHE cc_start: 0.6812 (m-80) cc_final: 0.6440 (m-80) REVERT: C 90 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8866 (t) REVERT: C 323 LEU cc_start: 0.8595 (tt) cc_final: 0.8380 (mp) REVERT: C 341 VAL cc_start: 0.8325 (t) cc_final: 0.8057 (p) outliers start: 58 outliers final: 49 residues processed: 271 average time/residue: 0.1730 time to fit residues: 68.7493 Evaluate side-chains 279 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 15 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088815 restraints weight = 20529.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088102 restraints weight = 21500.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089427 restraints weight = 20146.049| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9840 Z= 0.229 Angle : 0.914 14.970 13401 Z= 0.403 Chirality : 0.049 0.305 1677 Planarity : 0.004 0.039 1665 Dihedral : 4.949 31.238 1372 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.96 % Allowed : 28.74 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.09 (0.23), residues: 1284 helix: -1.09 (0.17), residues: 894 sheet: -2.52 (0.64), residues: 60 loop : -1.44 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 461 HIS 0.003 0.001 HIS C 316 PHE 0.042 0.002 PHE B 400 TYR 0.018 0.001 TYR C 325 ARG 0.002 0.000 ARG C 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.16 seconds wall clock time: 39 minutes 28.20 seconds (2368.20 seconds total)