Starting phenix.real_space_refine on Wed Sep 25 05:41:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/09_2024/6gct_4386.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/09_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_4386/09_2024/6gct_4386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/09_2024/6gct_4386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/09_2024/6gct_4386.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gct_4386/09_2024/6gct_4386.cif" } 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. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9672 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: C, B Time building chain proxies: 6.04, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.2 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: 1.22 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: 2.84 Time building geometry restraints manager: 2.94 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: 0.00 - 2.83: 12746 2.83 - 5.66: 522 5.66 - 8.50: 115 8.50 - 11.33: 9 11.33 - 14.16: 9 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 3.120 nonbonded pdb=" O LEU C 119 " pdb=" NH1 ARG C 246 " model vdw 2.334 3.120 nonbonded pdb=" O LEU B 119 " pdb=" NH1 ARG B 246 " model vdw 2.334 3.120 nonbonded pdb=" O LEU A 119 " pdb=" NH1 ARG A 246 " model vdw 2.334 3.120 nonbonded pdb=" O LYS A 372 " pdb=" OG SER A 375 " model vdw 2.335 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.010 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- 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 : 1.208 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: 0.1963 time to fit residues: 91.0302 Evaluate side-chains 235 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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: 3.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.0060 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- 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 373 HIS A 386 ASN A 403 GLN A 484 ASN B 154 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN B 373 HIS B 403 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 316 HIS C 367 ASN C 386 ASN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9840 Z= 0.249 Angle : 0.840 14.432 13401 Z= 0.406 Chirality : 0.045 0.202 1677 Planarity : 0.006 0.045 1665 Dihedral : 7.452 57.682 1403 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 7.62 % Allowed : 18.67 % Favored : 73.70 % 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: -4.59 (0.19), residues: 1284 helix: -2.92 (0.13), residues: 888 sheet: -3.58 (0.52), residues: 60 loop : -2.52 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 461 HIS 0.005 0.002 HIS A 316 PHE 0.031 0.002 PHE B 400 TYR 0.019 0.002 TYR A 276 ARG 0.003 0.001 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 356 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 278 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8133 (tm) REVERT: A 91 PHE cc_start: 0.8852 (t80) cc_final: 0.8647 (t80) REVERT: A 132 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8576 (tt) REVERT: A 246 ARG cc_start: 0.8122 (tmm-80) cc_final: 0.7915 (tmm-80) REVERT: A 248 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9037 (tt) REVERT: A 256 ILE cc_start: 0.9122 (mp) cc_final: 0.8893 (mp) REVERT: A 311 LEU cc_start: 0.9264 (tp) cc_final: 0.9031 (tt) REVERT: A 392 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9134 (mm) REVERT: B 247 LYS cc_start: 0.8061 (tttt) cc_final: 0.7811 (ttmt) REVERT: C 275 TRP cc_start: 0.8035 (m100) cc_final: 0.7354 (m-10) REVERT: C 387 MET cc_start: 0.8249 (mtp) cc_final: 0.7954 (mtp) REVERT: C 388 ASP cc_start: 0.8649 (m-30) cc_final: 0.8378 (m-30) REVERT: C 413 LYS cc_start: 0.9094 (ttmp) cc_final: 0.8877 (ttpt) REVERT: C 464 ASP cc_start: 0.7844 (p0) cc_final: 0.7621 (p0) REVERT: C 482 LEU cc_start: 0.8843 (mm) cc_final: 0.8639 (mm) outliers start: 78 outliers final: 26 residues processed: 335 average time/residue: 0.1773 time to fit residues: 86.2386 Evaluate side-chains 257 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 392 LEU 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 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 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: 7.9990 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 94 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN C 386 ASN C 394 GLN C 484 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9840 Z= 0.216 Angle : 0.844 14.318 13401 Z= 0.389 Chirality : 0.045 0.197 1677 Planarity : 0.005 0.043 1665 Dihedral : 6.527 54.987 1384 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 7.43 % Allowed : 23.75 % Favored : 68.82 % 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: -3.60 (0.21), residues: 1284 helix: -2.24 (0.15), residues: 867 sheet: -3.40 (0.56), residues: 60 loop : -1.95 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 461 HIS 0.003 0.001 HIS A 373 PHE 0.031 0.002 PHE B 400 TYR 0.028 0.002 TYR C 305 ARG 0.002 0.000 ARG A 330 *********************** 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 330 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 254 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8139 (tm) REVERT: A 132 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8612 (tt) REVERT: A 149 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8091 (tp) REVERT: B 247 LYS cc_start: 0.8175 (tttt) cc_final: 0.7795 (ttmt) REVERT: C 275 TRP cc_start: 0.7976 (m100) cc_final: 0.7677 (m-10) REVERT: C 305 TYR cc_start: 0.8780 (t80) cc_final: 0.8482 (t80) REVERT: C 441 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8169 (mt) outliers start: 76 outliers final: 31 residues processed: 307 average time/residue: 0.1673 time to fit residues: 75.9186 Evaluate side-chains 261 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 226 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 422 THR Chi-restraints excluded: chain B residue 54 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 145 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 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 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 441 ILE 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: 9.9990 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 33 optimal weight: 0.0170 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN C 394 GLN C 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4012 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= 0.202 Angle : 0.833 15.320 13401 Z= 0.377 Chirality : 0.044 0.259 1677 Planarity : 0.004 0.040 1665 Dihedral : 5.745 54.942 1380 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.74 % Allowed : 25.22 % Favored : 68.04 % 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: -3.12 (0.22), residues: 1284 helix: -1.93 (0.15), residues: 894 sheet: -3.21 (0.58), residues: 60 loop : -1.53 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 461 HIS 0.003 0.001 HIS A 373 PHE 0.032 0.001 PHE B 400 TYR 0.019 0.001 TYR C 305 ARG 0.003 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 321 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 252 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8103 (tm) REVERT: A 132 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8611 (tt) REVERT: A 149 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (tp) REVERT: A 392 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9153 (mm) REVERT: B 247 LYS cc_start: 0.8144 (tttt) cc_final: 0.7794 (ttmt) REVERT: B 341 VAL cc_start: 0.8403 (t) cc_final: 0.8119 (p) REVERT: B 455 LEU cc_start: 0.8179 (pt) cc_final: 0.7937 (pt) REVERT: C 149 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8257 (tp) REVERT: C 305 TYR cc_start: 0.8791 (t80) cc_final: 0.8461 (t80) REVERT: C 387 MET cc_start: 0.7856 (mtt) cc_final: 0.7643 (mtp) REVERT: C 413 LYS cc_start: 0.9047 (ttmp) cc_final: 0.8840 (ttpt) outliers start: 69 outliers final: 34 residues processed: 297 average time/residue: 0.1700 time to fit residues: 74.4118 Evaluate side-chains 265 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 226 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 149 LEU Chi-restraints excluded: chain A residue 151 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 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 145 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 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 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 149 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 226 VAL 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 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: 0.9990 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 386 ASN C 394 GLN C 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9840 Z= 0.243 Angle : 0.854 14.363 13401 Z= 0.391 Chirality : 0.046 0.199 1677 Planarity : 0.004 0.038 1665 Dihedral : 5.461 31.320 1376 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.94 % Allowed : 25.90 % 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: -2.81 (0.22), residues: 1284 helix: -1.69 (0.16), residues: 897 sheet: -3.11 (0.60), residues: 60 loop : -1.43 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 461 HIS 0.004 0.001 HIS B 316 PHE 0.032 0.002 PHE B 400 TYR 0.013 0.002 TYR C 305 ARG 0.003 0.000 ARG A 246 *********************** 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 308 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 237 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8054 (tm) REVERT: A 89 PHE cc_start: 0.7166 (m-80) cc_final: 0.6243 (m-80) REVERT: A 90 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.8980 (t) REVERT: A 132 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8622 (tt) REVERT: A 149 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8102 (tp) REVERT: A 268 VAL cc_start: 0.9035 (p) cc_final: 0.8745 (t) REVERT: A 334 TYR cc_start: 0.6613 (m-80) cc_final: 0.6186 (m-10) REVERT: A 473 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: B 90 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8764 (t) REVERT: B 413 LYS cc_start: 0.9003 (ttmp) cc_final: 0.8796 (ttmt) REVERT: B 455 LEU cc_start: 0.8266 (pt) cc_final: 0.8003 (pt) REVERT: C 90 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8927 (t) REVERT: C 305 TYR cc_start: 0.8810 (t80) cc_final: 0.8458 (t80) REVERT: C 341 VAL cc_start: 0.8341 (t) cc_final: 0.7963 (p) REVERT: C 441 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8420 (mt) outliers start: 71 outliers final: 36 residues processed: 284 average time/residue: 0.1728 time to fit residues: 71.9556 Evaluate side-chains 263 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 337 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 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 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 337 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU 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 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 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 Chi-restraints excluded: chain C residue 431 ILE 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: 0.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN C 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9840 Z= 0.210 Angle : 0.867 15.248 13401 Z= 0.390 Chirality : 0.046 0.288 1677 Planarity : 0.004 0.036 1665 Dihedral : 5.300 32.600 1374 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.74 % Allowed : 26.98 % 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: -2.71 (0.22), residues: 1284 helix: -1.61 (0.16), residues: 903 sheet: -2.98 (0.60), residues: 60 loop : -1.42 (0.37), residues: 321 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 0.035 0.001 PHE B 400 TYR 0.011 0.001 TYR C 305 ARG 0.003 0.000 ARG A 246 *********************** 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 310 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 241 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7956 (tm) REVERT: A 89 PHE cc_start: 0.7045 (m-80) cc_final: 0.6233 (m-80) REVERT: A 90 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8968 (t) REVERT: A 132 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8568 (tt) REVERT: A 334 TYR cc_start: 0.6439 (m-80) cc_final: 0.6176 (m-10) REVERT: B 90 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8734 (t) REVERT: B 281 ILE cc_start: 0.8805 (mt) cc_final: 0.8545 (mt) REVERT: B 341 VAL cc_start: 0.8370 (t) cc_final: 0.8083 (p) REVERT: B 413 LYS cc_start: 0.8992 (ttmp) cc_final: 0.8677 (ttmt) REVERT: C 341 VAL cc_start: 0.8270 (t) cc_final: 0.7912 (p) REVERT: C 387 MET cc_start: 0.8143 (mtp) cc_final: 0.7878 (mtt) REVERT: C 388 ASP cc_start: 0.8418 (m-30) cc_final: 0.8120 (m-30) REVERT: C 471 ASN cc_start: 0.8150 (t160) cc_final: 0.7922 (t0) outliers start: 69 outliers final: 42 residues processed: 286 average time/residue: 0.1702 time to fit residues: 71.6674 Evaluate side-chains 274 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 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 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 81 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 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 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 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 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 392 LEU Chi-restraints excluded: chain C residue 431 ILE 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: 1.9990 chunk 71 optimal weight: 0.0570 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 386 ASN C 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9840 Z= 0.220 Angle : 0.884 14.798 13401 Z= 0.395 Chirality : 0.047 0.284 1677 Planarity : 0.004 0.035 1665 Dihedral : 5.231 31.100 1374 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.26 % Allowed : 27.57 % Favored : 66.18 % 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: -2.50 (0.22), residues: 1284 helix: -1.39 (0.16), residues: 894 sheet: -2.95 (0.60), residues: 60 loop : -1.54 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 461 HIS 0.003 0.001 HIS B 316 PHE 0.027 0.001 PHE A 400 TYR 0.010 0.001 TYR C 305 ARG 0.003 0.000 ARG A 246 *********************** 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 314 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 250 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7950 (tm) REVERT: A 89 PHE cc_start: 0.6964 (m-80) cc_final: 0.6207 (m-80) REVERT: A 90 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8959 (t) REVERT: A 132 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 151 LEU cc_start: 0.9072 (pt) cc_final: 0.8558 (pp) REVERT: A 334 TYR cc_start: 0.6361 (m-80) cc_final: 0.6101 (m-10) REVERT: A 372 LYS cc_start: 0.7995 (tppt) cc_final: 0.7756 (tppt) REVERT: A 387 MET cc_start: 0.7820 (mtm) cc_final: 0.7527 (mtp) REVERT: B 90 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8706 (t) REVERT: B 341 VAL cc_start: 0.8393 (t) cc_final: 0.8115 (p) REVERT: B 400 PHE cc_start: 0.8757 (t80) cc_final: 0.8372 (t80) REVERT: B 455 LEU cc_start: 0.8165 (pt) cc_final: 0.7909 (pt) REVERT: C 89 PHE cc_start: 0.6903 (m-80) cc_final: 0.6435 (m-80) REVERT: C 90 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8880 (t) REVERT: C 323 LEU cc_start: 0.8687 (tt) cc_final: 0.8464 (mp) REVERT: C 341 VAL cc_start: 0.8321 (t) cc_final: 0.7960 (p) REVERT: C 388 ASP cc_start: 0.8518 (m-30) cc_final: 0.8273 (m-30) outliers start: 64 outliers final: 44 residues processed: 290 average time/residue: 0.1732 time to fit residues: 73.5027 Evaluate side-chains 278 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 132 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 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 81 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 145 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE 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 342 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 54 LEU 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 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 ILE 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 342 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.0570 chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 ASN C 407 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: 0.8233 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9840 Z= 0.212 Angle : 0.888 14.644 13401 Z= 0.396 Chirality : 0.047 0.235 1677 Planarity : 0.004 0.034 1665 Dihedral : 5.083 32.787 1372 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.77 % Allowed : 28.25 % Favored : 65.98 % 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: -2.33 (0.23), residues: 1284 helix: -1.25 (0.16), residues: 891 sheet: -2.87 (0.60), residues: 60 loop : -1.53 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 461 HIS 0.002 0.001 HIS B 316 PHE 0.028 0.001 PHE A 400 TYR 0.012 0.001 TYR B 325 ARG 0.003 0.000 ARG A 246 *********************** 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 303 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6835 (m-80) cc_final: 0.6201 (m-80) REVERT: A 90 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8963 (t) REVERT: A 132 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8586 (tt) REVERT: B 90 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8901 (t) REVERT: B 341 VAL cc_start: 0.8383 (t) cc_final: 0.8116 (p) REVERT: B 400 PHE cc_start: 0.8661 (t80) cc_final: 0.8299 (t80) REVERT: B 455 LEU cc_start: 0.8126 (pt) cc_final: 0.7868 (pt) REVERT: C 89 PHE cc_start: 0.6902 (m-80) cc_final: 0.6492 (m-80) REVERT: C 90 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8879 (t) REVERT: C 323 LEU cc_start: 0.8669 (tt) cc_final: 0.8445 (mp) REVERT: C 341 VAL cc_start: 0.8302 (t) cc_final: 0.7928 (p) outliers start: 59 outliers final: 45 residues processed: 283 average time/residue: 0.1690 time to fit residues: 70.6152 Evaluate side-chains 274 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 225 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 457 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 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 141 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 ILE 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 342 THR Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU 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 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 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 342 THR Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 431 ILE 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: 0.9990 chunk 115 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 0.0770 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 386 ASN ** 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: 0.8214 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9840 Z= 0.218 Angle : 0.914 14.879 13401 Z= 0.407 Chirality : 0.047 0.323 1677 Planarity : 0.004 0.034 1665 Dihedral : 4.925 18.360 1371 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.87 % Allowed : 28.84 % 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: -2.22 (0.23), residues: 1284 helix: -1.17 (0.16), residues: 891 sheet: -2.76 (0.61), residues: 60 loop : -1.52 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 461 HIS 0.003 0.001 HIS A 316 PHE 0.028 0.001 PHE A 400 TYR 0.009 0.001 TYR C 305 ARG 0.003 0.000 ARG A 246 *********************** 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 298 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 238 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6762 (m-80) cc_final: 0.6180 (m-80) REVERT: A 90 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8939 (t) REVERT: A 132 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8567 (tt) REVERT: A 362 LYS cc_start: 0.8066 (tptt) cc_final: 0.7834 (tppt) REVERT: B 90 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8913 (t) REVERT: B 341 VAL cc_start: 0.8386 (t) cc_final: 0.8108 (p) REVERT: B 400 PHE cc_start: 0.8636 (t80) cc_final: 0.8356 (t80) REVERT: C 89 PHE cc_start: 0.6975 (m-80) cc_final: 0.6544 (m-80) REVERT: C 90 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8866 (t) REVERT: C 323 LEU cc_start: 0.8663 (tt) cc_final: 0.8427 (mp) REVERT: C 341 VAL cc_start: 0.8273 (t) cc_final: 0.7906 (p) REVERT: C 388 ASP cc_start: 0.8461 (m-30) cc_final: 0.8164 (m-30) REVERT: C 482 LEU cc_start: 0.8903 (mm) cc_final: 0.8703 (mm) outliers start: 60 outliers final: 46 residues processed: 282 average time/residue: 0.1737 time to fit residues: 71.8550 Evaluate side-chains 277 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 227 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 342 THR 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 A residue 481 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 141 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 229 MET 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 386 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU 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 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 392 LEU Chi-restraints excluded: chain C residue 431 ILE 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: 6.9990 chunk 58 optimal weight: 0.0970 chunk 85 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9840 Z= 0.226 Angle : 0.925 14.620 13401 Z= 0.412 Chirality : 0.048 0.308 1677 Planarity : 0.004 0.035 1665 Dihedral : 4.931 18.356 1371 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.08 % Allowed : 29.81 % Favored : 65.10 % 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: -2.14 (0.23), residues: 1284 helix: -1.09 (0.16), residues: 891 sheet: -2.70 (0.62), residues: 60 loop : -1.54 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 461 HIS 0.003 0.001 HIS A 316 PHE 0.028 0.002 PHE A 400 TYR 0.010 0.001 TYR C 305 ARG 0.003 0.000 ARG A 246 ********************** 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 286 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 234 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6760 (m-80) cc_final: 0.6183 (m-80) REVERT: A 90 VAL cc_start: 0.9190 (OUTLIER) cc_final: 0.8943 (t) REVERT: A 132 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8562 (tt) REVERT: A 151 LEU cc_start: 0.9147 (pt) cc_final: 0.8735 (pp) REVERT: B 90 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8936 (t) REVERT: B 341 VAL cc_start: 0.8371 (t) cc_final: 0.8101 (p) REVERT: B 400 PHE cc_start: 0.8605 (t80) cc_final: 0.8284 (t80) REVERT: B 455 LEU cc_start: 0.8089 (pt) cc_final: 0.7853 (pt) REVERT: C 89 PHE cc_start: 0.6916 (m-80) cc_final: 0.6506 (m-80) REVERT: C 90 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8881 (t) REVERT: C 288 LYS cc_start: 0.8582 (tmmm) cc_final: 0.8295 (ttmt) REVERT: C 323 LEU cc_start: 0.8635 (tt) cc_final: 0.8399 (mp) REVERT: C 341 VAL cc_start: 0.8253 (t) cc_final: 0.7892 (p) REVERT: C 388 ASP cc_start: 0.8283 (m-30) cc_final: 0.8040 (m-30) outliers start: 52 outliers final: 45 residues processed: 271 average time/residue: 0.1791 time to fit residues: 70.8542 Evaluate side-chains 274 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 225 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 342 THR 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 A residue 481 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 141 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE 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 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 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 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 431 ILE 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: 1.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 89 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 GLN C 407 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088217 restraints weight = 20388.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088239 restraints weight = 18593.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.088520 restraints weight = 16294.595| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9840 Z= 0.247 Angle : 0.940 15.176 13401 Z= 0.421 Chirality : 0.048 0.291 1677 Planarity : 0.004 0.035 1665 Dihedral : 4.960 18.076 1371 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.18 % Allowed : 29.81 % Favored : 65.00 % 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: -2.12 (0.22), residues: 1284 helix: -1.09 (0.16), residues: 891 sheet: -2.66 (0.61), residues: 60 loop : -1.49 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 461 HIS 0.004 0.001 HIS C 316 PHE 0.029 0.002 PHE A 400 TYR 0.009 0.001 TYR C 305 ARG 0.003 0.000 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.09 seconds wall clock time: 40 minutes 20.51 seconds (2420.51 seconds total)