Starting phenix.real_space_refine on Sat Jun 28 12:59:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fne_29310/06_2025/8fne_29310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fne_29310/06_2025/8fne_29310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fne_29310/06_2025/8fne_29310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fne_29310/06_2025/8fne_29310.map" model { file = "/net/cci-nas-00/data/ceres_data/8fne_29310/06_2025/8fne_29310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fne_29310/06_2025/8fne_29310.cif" } resolution = 3.9 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= 2.062 sd= 0.266 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 10620 2.51 5 N 2964 2.21 5 O 3212 1.98 5 H 16644 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33508 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8213 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 21, 'TRANS': 503} Chain breaks: 1 Chain: "B" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8213 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 21, 'TRANS': 503} Chain breaks: 1 Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 164 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 164 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Restraints were copied for chains: D, C, H, G Time building chain proxies: 40.89, per 1000 atoms: 1.22 Number of scatterers: 33508 At special positions: 0 Unit cell: (157.626, 157.626, 75.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 3212 8.00 N 2964 7.00 C 10620 6.00 H 16644 1.00 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: 7.92 Conformation dependent library (CDL) restraints added in 2.5 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3992 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 24 sheets defined 41.6% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 36 through 56 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 173 through 196 Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.513A pdb=" N LEU A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.939A pdb=" N SER A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.509A pdb=" N ARG A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 397 through 407 removed outlier: 4.496A pdb=" N VAL A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 481 through 492 Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'B' and resid 20 through 27 removed outlier: 5.115A pdb=" N ILE B 25 " --> pdb=" O ASN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 56 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 135 through 151 Processing helix chain 'B' and resid 173 through 196 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 311 through 324 removed outlier: 3.833A pdb=" N SER B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 347 through 354 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 397 through 407 removed outlier: 4.222A pdb=" N VAL B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 481 through 492 removed outlier: 3.956A pdb=" N GLN B 492 " --> pdb=" O TRP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 530 through 543 Processing helix chain 'C' and resid 20 through 27 removed outlier: 5.116A pdb=" N ILE C 25 " --> pdb=" O ASN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 56 Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 135 through 151 Processing helix chain 'C' and resid 173 through 196 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 311 through 324 removed outlier: 3.833A pdb=" N SER C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 369 through 381 Processing helix chain 'C' and resid 397 through 407 removed outlier: 4.222A pdb=" N VAL C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 429 Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 481 through 492 removed outlier: 3.955A pdb=" N GLN C 492 " --> pdb=" O TRP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 515 Processing helix chain 'C' and resid 530 through 543 Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 36 through 56 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 135 through 151 Processing helix chain 'D' and resid 173 through 196 Processing helix chain 'D' and resid 202 through 207 removed outlier: 3.512A pdb=" N LEU D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.940A pdb=" N SER D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN D 321 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 336 removed outlier: 3.509A pdb=" N ARG D 333 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 354 Processing helix chain 'D' and resid 369 through 381 Processing helix chain 'D' and resid 397 through 407 removed outlier: 4.495A pdb=" N VAL D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 429 Processing helix chain 'D' and resid 431 through 435 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 470 through 478 Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 498 through 514 Processing helix chain 'D' and resid 530 through 543 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.524A pdb=" N GLN A 92 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE A 158 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 94 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 117 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 446 removed outlier: 6.904A pdb=" N VAL A 518 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 457 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR A 520 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR A 455 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR A 522 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 453 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 446 removed outlier: 5.480A pdb=" N PHE A 387 " --> pdb=" O TRP A 529 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N VAL A 386 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET A 388 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 296 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP A 390 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 298 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 264 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL A 301 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN A 262 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN A 303 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 260 " --> pdb=" O GLN A 303 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 240 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 262 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 238 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER A 264 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE A 236 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 214 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 213 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.769A pdb=" N MET A 224 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 68 removed outlier: 4.137A pdb=" N SER B 78 " --> pdb=" O MET B 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 68 removed outlier: 4.137A pdb=" N SER B 78 " --> pdb=" O MET B 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 117 Processing sheet with id=AB1, first strand: chain 'B' and resid 444 through 446 removed outlier: 6.101A pdb=" N VAL B 518 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 457 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR B 520 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR B 455 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 522 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 444 through 446 removed outlier: 5.362A pdb=" N PHE B 387 " --> pdb=" O TRP B 529 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N VAL B 386 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET B 388 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE B 296 " --> pdb=" O MET B 388 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASP B 390 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 298 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER B 264 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 301 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN B 262 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLN B 303 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 260 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 240 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN B 262 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 238 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER B 264 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 236 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ALA B 549 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 213 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 68 removed outlier: 4.137A pdb=" N SER C 78 " --> pdb=" O MET C 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 68 removed outlier: 4.137A pdb=" N SER C 78 " --> pdb=" O MET C 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 110 through 117 Processing sheet with id=AB7, first strand: chain 'C' and resid 444 through 446 removed outlier: 6.101A pdb=" N VAL C 518 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 457 " --> pdb=" O VAL C 518 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR C 520 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 455 " --> pdb=" O TYR C 520 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 522 " --> pdb=" O LEU C 453 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 444 through 446 removed outlier: 5.362A pdb=" N PHE C 387 " --> pdb=" O TRP C 529 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N VAL C 386 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N MET C 388 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE C 296 " --> pdb=" O MET C 388 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP C 390 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 298 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER C 264 " --> pdb=" O THR C 299 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL C 301 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN C 262 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLN C 303 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU C 260 " --> pdb=" O GLN C 303 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU C 240 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN C 262 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 238 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER C 264 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 236 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ALA C 549 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 213 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 68 removed outlier: 6.524A pdb=" N GLN D 92 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE D 158 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 94 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 64 through 68 Processing sheet with id=AC3, first strand: chain 'D' and resid 111 through 117 Processing sheet with id=AC4, first strand: chain 'D' and resid 444 through 446 removed outlier: 6.904A pdb=" N VAL D 518 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU D 457 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR D 520 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR D 455 " --> pdb=" O TYR D 520 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR D 522 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU D 453 " --> pdb=" O THR D 522 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 444 through 446 removed outlier: 5.481A pdb=" N PHE D 387 " --> pdb=" O TRP D 529 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N VAL D 386 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET D 388 " --> pdb=" O PRO D 294 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE D 296 " --> pdb=" O MET D 388 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP D 390 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE D 298 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER D 264 " --> pdb=" O THR D 299 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL D 301 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN D 262 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN D 303 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU D 260 " --> pdb=" O GLN D 303 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU D 240 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN D 262 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL D 238 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER D 264 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE D 236 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA D 214 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU D 213 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.768A pdb=" N MET D 224 " --> pdb=" O ILE D 232 " (cutoff:3.500A) 864 hydrogen bonds defined for protein. 2316 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: 14.38 Time building geometry restraints manager: 9.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.93: 8 0.93 - 1.15: 16620 1.15 - 1.38: 6436 1.38 - 1.60: 10634 1.60 - 1.82: 122 Bond restraints: 33820 Sorted by residual: bond pdb=" NE2 HIS D 120 " pdb=" HE2 HIS D 120 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.66e+01 bond pdb=" NE2 HIS A 120 " pdb=" HE2 HIS A 120 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.62e+01 bond pdb=" NE2 GLN A 288 " pdb="HE22 GLN A 288 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.42e+01 bond pdb=" NE2 GLN D 288 " pdb="HE22 GLN D 288 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" NH2 ARG D 382 " pdb="HH22 ARG D 382 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 33815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.83: 60880 8.83 - 17.66: 129 17.66 - 26.50: 3 26.50 - 35.33: 2 35.33 - 44.16: 2 Bond angle restraints: 61016 Sorted by residual: angle pdb=" N TYR C 513 " pdb=" CA TYR C 513 " pdb=" HA TYR C 513 " ideal model delta sigma weight residual 110.00 65.84 44.16 3.00e+00 1.11e-01 2.17e+02 angle pdb=" N TYR B 513 " pdb=" CA TYR B 513 " pdb=" HA TYR B 513 " ideal model delta sigma weight residual 110.00 65.87 44.13 3.00e+00 1.11e-01 2.16e+02 angle pdb=" CB TYR C 513 " pdb=" CA TYR C 513 " pdb=" HA TYR C 513 " ideal model delta sigma weight residual 109.00 77.78 31.22 3.00e+00 1.11e-01 1.08e+02 angle pdb=" CB TYR B 513 " pdb=" CA TYR B 513 " pdb=" HA TYR B 513 " ideal model delta sigma weight residual 109.00 77.81 31.19 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C TYR B 513 " pdb=" CA TYR B 513 " pdb=" HA TYR B 513 " ideal model delta sigma weight residual 109.00 83.17 25.83 3.00e+00 1.11e-01 7.41e+01 ... (remaining 61011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 14928 16.91 - 33.81: 658 33.81 - 50.72: 172 50.72 - 67.62: 114 67.62 - 84.53: 16 Dihedral angle restraints: 15888 sinusoidal: 8732 harmonic: 7156 Sorted by residual: dihedral pdb=" CA SER B 543 " pdb=" C SER B 543 " pdb=" N VAL B 544 " pdb=" CA VAL B 544 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ALA D 167 " pdb=" C ALA D 167 " pdb=" N ASP D 168 " pdb=" CA ASP D 168 " ideal model delta harmonic sigma weight residual 180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA SER C 543 " pdb=" C SER C 543 " pdb=" N VAL C 544 " pdb=" CA VAL C 544 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 15885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1692 0.088 - 0.175: 693 0.175 - 0.263: 162 0.263 - 0.350: 31 0.350 - 0.438: 6 Chirality restraints: 2584 Sorted by residual: chirality pdb=" CB ILE A 158 " pdb=" CA ILE A 158 " pdb=" CG1 ILE A 158 " pdb=" CG2 ILE A 158 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CB ILE D 158 " pdb=" CA ILE D 158 " pdb=" CG1 ILE D 158 " pdb=" CG2 ILE D 158 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA ALA B 554 " pdb=" N ALA B 554 " pdb=" C ALA B 554 " pdb=" CB ALA B 554 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 2581 not shown) Planarity restraints: 5140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 38 " -0.086 9.50e-02 1.11e+02 8.92e-02 1.61e+02 pdb=" NE ARG A 38 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 38 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG A 38 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 38 " 0.124 2.00e-02 2.50e+03 pdb="HH11 ARG A 38 " -0.038 2.00e-02 2.50e+03 pdb="HH12 ARG A 38 " -0.073 2.00e-02 2.50e+03 pdb="HH21 ARG A 38 " -0.183 2.00e-02 2.50e+03 pdb="HH22 ARG A 38 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 38 " 0.086 9.50e-02 1.11e+02 8.92e-02 1.61e+02 pdb=" NE ARG D 38 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG D 38 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG D 38 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG D 38 " -0.123 2.00e-02 2.50e+03 pdb="HH11 ARG D 38 " 0.038 2.00e-02 2.50e+03 pdb="HH12 ARG D 38 " 0.073 2.00e-02 2.50e+03 pdb="HH21 ARG D 38 " 0.183 2.00e-02 2.50e+03 pdb="HH22 ARG D 38 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 317 " 0.154 2.00e-02 2.50e+03 5.90e-02 1.04e+02 pdb=" CG PHE D 317 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE D 317 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE D 317 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE D 317 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE D 317 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE D 317 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE D 317 " -0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE D 317 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE D 317 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE D 317 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE D 317 " 0.082 2.00e-02 2.50e+03 ... (remaining 5137 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1441 2.09 - 2.72: 52528 2.72 - 3.34: 99939 3.34 - 3.97: 130828 3.97 - 4.60: 194137 Nonbonded interactions: 478873 Sorted by model distance: nonbonded pdb=" HE2 MET A 205 " pdb="HD23 LEU C 22 " model vdw 1.461 2.440 nonbonded pdb="HD23 LEU B 22 " pdb=" HE2 MET D 205 " model vdw 1.462 2.440 nonbonded pdb=" H THR A 440 " pdb=" H MET A 441 " model vdw 1.492 2.100 nonbonded pdb=" H THR D 440 " pdb=" H MET D 441 " model vdw 1.492 2.100 nonbonded pdb=" OD1 ASP A 190 " pdb=" HG SER C 29 " model vdw 1.588 2.450 ... (remaining 478868 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' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 8.000 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: 0.510 Extract box with map and model: 1.260 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 93.520 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4678 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 : 0.018 0.107 17176 Z= 0.933 Angle : 1.776 12.129 23268 Z= 1.215 Chirality : 0.099 0.438 2584 Planarity : 0.010 0.091 3088 Dihedral : 11.330 84.528 6364 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2124 helix: -0.44 (0.17), residues: 740 sheet: 0.80 (0.24), residues: 466 loop : 0.70 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.010 TRP C 139 HIS 0.010 0.002 HIS D 60 PHE 0.090 0.010 PHE D 317 TYR 0.108 0.016 TYR G 602 ARG 0.008 0.001 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.15038 ( 790) hydrogen bonds : angle 7.97763 ( 2316) covalent geometry : bond 0.01774 (17176) covalent geometry : angle 1.77556 (23268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 810 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.6632 (mm) cc_final: 0.6326 (mm) REVERT: C 550 MET cc_start: 0.5411 (pmm) cc_final: 0.5170 (pmm) REVERT: D 142 ILE cc_start: 0.6524 (mm) cc_final: 0.6214 (mm) REVERT: D 297 VAL cc_start: 0.5429 (t) cc_final: 0.5181 (t) REVERT: D 451 ILE cc_start: 0.6388 (mt) cc_final: 0.6179 (mm) outliers start: 0 outliers final: 0 residues processed: 810 average time/residue: 0.8122 time to fit residues: 926.2234 Evaluate side-chains 587 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN B 72 GLN B 505 GLN C 72 GLN C 505 GLN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN D 249 GLN D 445 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.168244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143758 restraints weight = 123747.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148763 restraints weight = 60695.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152143 restraints weight = 37420.633| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17176 Z= 0.152 Angle : 0.662 6.557 23268 Z= 0.368 Chirality : 0.045 0.383 2584 Planarity : 0.005 0.059 3088 Dihedral : 5.482 28.442 2316 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.72 % Allowed : 12.25 % Favored : 86.03 % 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: 0.84 (0.18), residues: 2124 helix: 0.88 (0.18), residues: 722 sheet: 0.13 (0.24), residues: 420 loop : 0.72 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 331 HIS 0.006 0.001 HIS D 498 PHE 0.031 0.002 PHE D 373 TYR 0.017 0.002 TYR C 315 ARG 0.006 0.001 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.05045 ( 790) hydrogen bonds : angle 6.00669 ( 2316) covalent geometry : bond 0.00322 (17176) covalent geometry : angle 0.66243 (23268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 641 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8796 (p0) cc_final: 0.8536 (p0) REVERT: A 52 GLU cc_start: 0.9088 (tp30) cc_final: 0.8789 (tp30) REVERT: A 56 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8267 (mm-40) REVERT: A 157 VAL cc_start: 0.8705 (t) cc_final: 0.8465 (t) REVERT: A 158 ILE cc_start: 0.9223 (mt) cc_final: 0.8898 (mt) REVERT: A 185 VAL cc_start: 0.9310 (m) cc_final: 0.9028 (p) REVERT: A 253 PHE cc_start: 0.7142 (m-80) cc_final: 0.6872 (m-80) REVERT: A 333 ARG cc_start: 0.9099 (tpt90) cc_final: 0.8767 (tpt90) REVERT: A 345 MET cc_start: 0.8544 (pmm) cc_final: 0.8314 (pmm) REVERT: A 397 ASN cc_start: 0.8716 (t0) cc_final: 0.8416 (t0) REVERT: A 442 PRO cc_start: 0.9054 (Cg_exo) cc_final: 0.8799 (Cg_endo) REVERT: A 447 TYR cc_start: 0.8887 (t80) cc_final: 0.8541 (t80) REVERT: A 464 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8079 (mp10) REVERT: A 500 GLU cc_start: 0.9261 (tp30) cc_final: 0.8898 (tp30) REVERT: B 32 THR cc_start: 0.6958 (t) cc_final: 0.6706 (m) REVERT: B 101 MET cc_start: 0.7905 (mtm) cc_final: 0.7329 (mtm) REVERT: B 219 PHE cc_start: 0.8150 (m-80) cc_final: 0.7794 (m-80) REVERT: B 313 GLU cc_start: 0.9112 (mp0) cc_final: 0.8745 (mp0) REVERT: B 321 ASN cc_start: 0.9279 (m-40) cc_final: 0.8604 (m110) REVERT: B 331 TRP cc_start: 0.8975 (p-90) cc_final: 0.8593 (p-90) REVERT: B 380 MET cc_start: 0.8627 (mmm) cc_final: 0.7826 (mmm) REVERT: B 443 ILE cc_start: 0.9550 (mm) cc_final: 0.9083 (mm) REVERT: C 69 ASP cc_start: 0.8009 (t0) cc_final: 0.6496 (t0) REVERT: C 101 MET cc_start: 0.7873 (mtm) cc_final: 0.7321 (mtm) REVERT: C 144 ASP cc_start: 0.9083 (m-30) cc_final: 0.8792 (m-30) REVERT: C 219 PHE cc_start: 0.8003 (m-80) cc_final: 0.7656 (m-80) REVERT: C 321 ASN cc_start: 0.9208 (m-40) cc_final: 0.8260 (m110) REVERT: C 380 MET cc_start: 0.8708 (mmm) cc_final: 0.8275 (mmm) REVERT: D 52 GLU cc_start: 0.9088 (tp30) cc_final: 0.8766 (tp30) REVERT: D 157 VAL cc_start: 0.8729 (t) cc_final: 0.8521 (t) REVERT: D 185 VAL cc_start: 0.9241 (m) cc_final: 0.8923 (p) REVERT: D 249 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7585 (pp30) REVERT: D 253 PHE cc_start: 0.7150 (m-80) cc_final: 0.6900 (m-80) REVERT: D 333 ARG cc_start: 0.9052 (tpt90) cc_final: 0.8700 (tpt90) REVERT: D 397 ASN cc_start: 0.8678 (t0) cc_final: 0.8335 (t0) REVERT: D 452 GLN cc_start: 0.8209 (tp40) cc_final: 0.7918 (tp40) REVERT: D 464 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8159 (mp10) REVERT: D 500 GLU cc_start: 0.9246 (tp30) cc_final: 0.8874 (tp30) REVERT: D 546 LEU cc_start: 0.9101 (tp) cc_final: 0.8883 (tt) outliers start: 31 outliers final: 21 residues processed: 653 average time/residue: 0.8234 time to fit residues: 787.1012 Evaluate side-chains 582 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 560 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 66 optimal weight: 0.0070 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 HIS ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128856 restraints weight = 130918.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133691 restraints weight = 61468.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137060 restraints weight = 36597.553| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17176 Z= 0.194 Angle : 0.622 5.609 23268 Z= 0.346 Chirality : 0.043 0.377 2584 Planarity : 0.005 0.063 3088 Dihedral : 5.127 24.527 2316 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.27 % Allowed : 15.08 % Favored : 81.65 % 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: 0.45 (0.18), residues: 2124 helix: 0.71 (0.18), residues: 740 sheet: -0.11 (0.23), residues: 464 loop : 0.39 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 331 HIS 0.007 0.002 HIS C 498 PHE 0.019 0.002 PHE D 373 TYR 0.016 0.002 TYR B 315 ARG 0.006 0.001 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 790) hydrogen bonds : angle 5.67001 ( 2316) covalent geometry : bond 0.00399 (17176) covalent geometry : angle 0.62164 (23268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 602 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8989 (p0) cc_final: 0.8603 (p0) REVERT: A 52 GLU cc_start: 0.9220 (tp30) cc_final: 0.8875 (tp30) REVERT: A 56 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8381 (mm-40) REVERT: A 95 VAL cc_start: 0.9010 (t) cc_final: 0.8621 (p) REVERT: A 185 VAL cc_start: 0.9192 (m) cc_final: 0.8742 (p) REVERT: A 189 ASP cc_start: 0.8204 (m-30) cc_final: 0.7964 (m-30) REVERT: A 253 PHE cc_start: 0.7467 (m-80) cc_final: 0.7224 (m-80) REVERT: A 345 MET cc_start: 0.8536 (pmm) cc_final: 0.8274 (pmm) REVERT: A 397 ASN cc_start: 0.9005 (t0) cc_final: 0.8604 (t0) REVERT: A 402 ASN cc_start: 0.8522 (m-40) cc_final: 0.8195 (m-40) REVERT: A 426 ASN cc_start: 0.8634 (m-40) cc_final: 0.8235 (m-40) REVERT: A 447 TYR cc_start: 0.8666 (t80) cc_final: 0.8036 (t80) REVERT: A 452 GLN cc_start: 0.8119 (tp40) cc_final: 0.7643 (tp-100) REVERT: A 500 GLU cc_start: 0.9359 (tp30) cc_final: 0.8918 (tp30) REVERT: A 504 ARG cc_start: 0.9660 (ttm-80) cc_final: 0.9387 (ttm-80) REVERT: A 535 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8482 (tm-30) REVERT: B 205 MET cc_start: 0.7601 (mtm) cc_final: 0.6723 (tpt) REVERT: B 224 MET cc_start: 0.7745 (ttm) cc_final: 0.7508 (ttt) REVERT: B 379 ASN cc_start: 0.8714 (m-40) cc_final: 0.8459 (m-40) REVERT: B 380 MET cc_start: 0.8814 (mmm) cc_final: 0.8436 (mmm) REVERT: C 69 ASP cc_start: 0.7033 (t0) cc_final: 0.6688 (t0) REVERT: C 72 GLN cc_start: 0.7706 (mp10) cc_final: 0.7505 (mp10) REVERT: C 144 ASP cc_start: 0.9223 (m-30) cc_final: 0.8900 (m-30) REVERT: C 174 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8466 (mm-30) REVERT: C 205 MET cc_start: 0.7802 (mtm) cc_final: 0.6824 (tpt) REVERT: C 324 ARG cc_start: 0.8355 (mtt180) cc_final: 0.8129 (mtt-85) REVERT: C 379 ASN cc_start: 0.8761 (m-40) cc_final: 0.8066 (m-40) REVERT: C 380 MET cc_start: 0.8898 (mmm) cc_final: 0.8505 (mmm) REVERT: D 33 ASP cc_start: 0.9003 (p0) cc_final: 0.8735 (p0) REVERT: D 52 GLU cc_start: 0.9159 (tp30) cc_final: 0.8719 (tp30) REVERT: D 56 GLN cc_start: 0.8727 (mm-40) cc_final: 0.7980 (mm110) REVERT: D 95 VAL cc_start: 0.9030 (t) cc_final: 0.8658 (p) REVERT: D 159 ASN cc_start: 0.8718 (t0) cc_final: 0.8186 (t0) REVERT: D 219 PHE cc_start: 0.7940 (m-80) cc_final: 0.7724 (m-80) REVERT: D 253 PHE cc_start: 0.7551 (m-80) cc_final: 0.7278 (m-80) REVERT: D 266 PHE cc_start: 0.9252 (p90) cc_final: 0.8732 (p90) REVERT: D 317 PHE cc_start: 0.9371 (t80) cc_final: 0.9086 (t80) REVERT: D 333 ARG cc_start: 0.9121 (tpt90) cc_final: 0.8742 (tpt90) REVERT: D 397 ASN cc_start: 0.8982 (t0) cc_final: 0.8578 (t0) REVERT: D 447 TYR cc_start: 0.8427 (t80) cc_final: 0.7783 (t80) REVERT: D 452 GLN cc_start: 0.8195 (tp40) cc_final: 0.7820 (tp-100) REVERT: D 500 GLU cc_start: 0.9370 (tp30) cc_final: 0.8950 (tp30) REVERT: D 504 ARG cc_start: 0.9675 (ttm110) cc_final: 0.9186 (ttm-80) REVERT: D 520 TYR cc_start: 0.8242 (m-80) cc_final: 0.7907 (m-80) REVERT: D 529 TRP cc_start: 0.8930 (m100) cc_final: 0.8537 (m100) REVERT: D 546 LEU cc_start: 0.9353 (tp) cc_final: 0.9101 (tt) outliers start: 59 outliers final: 47 residues processed: 627 average time/residue: 0.7150 time to fit residues: 657.0832 Evaluate side-chains 589 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 541 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain F residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 56 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 0.0970 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128747 restraints weight = 135094.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133639 restraints weight = 63411.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136997 restraints weight = 37716.289| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17176 Z= 0.150 Angle : 0.570 4.883 23268 Z= 0.310 Chirality : 0.042 0.392 2584 Planarity : 0.005 0.063 3088 Dihedral : 4.887 22.512 2316 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.88 % Allowed : 17.85 % Favored : 79.27 % 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: 0.36 (0.18), residues: 2124 helix: 0.81 (0.18), residues: 740 sheet: -0.24 (0.23), residues: 478 loop : 0.24 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 331 HIS 0.006 0.001 HIS D 498 PHE 0.018 0.002 PHE D 373 TYR 0.015 0.002 TYR B 489 ARG 0.008 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 790) hydrogen bonds : angle 5.35148 ( 2316) covalent geometry : bond 0.00322 (17176) covalent geometry : angle 0.57032 (23268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 569 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8942 (p0) cc_final: 0.8486 (p0) REVERT: A 56 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8310 (mm110) REVERT: A 72 GLN cc_start: 0.8540 (mp10) cc_final: 0.8055 (mp10) REVERT: A 95 VAL cc_start: 0.9059 (t) cc_final: 0.8682 (p) REVERT: A 345 MET cc_start: 0.8506 (pmm) cc_final: 0.8203 (pmm) REVERT: A 397 ASN cc_start: 0.9015 (t0) cc_final: 0.8694 (t0) REVERT: A 402 ASN cc_start: 0.8553 (m-40) cc_final: 0.8283 (m-40) REVERT: A 426 ASN cc_start: 0.8613 (m-40) cc_final: 0.8241 (m-40) REVERT: A 442 PRO cc_start: 0.9053 (Cg_exo) cc_final: 0.8721 (Cg_endo) REVERT: A 447 TYR cc_start: 0.8783 (t80) cc_final: 0.8111 (t80) REVERT: A 452 GLN cc_start: 0.8145 (tp40) cc_final: 0.7771 (tp-100) REVERT: A 500 GLU cc_start: 0.9318 (tp30) cc_final: 0.8896 (tp30) REVERT: A 504 ARG cc_start: 0.9641 (ttm-80) cc_final: 0.9345 (ttm-80) REVERT: A 535 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: B 205 MET cc_start: 0.7746 (mtm) cc_final: 0.7130 (tpt) REVERT: B 379 ASN cc_start: 0.8622 (m-40) cc_final: 0.8363 (m-40) REVERT: B 380 MET cc_start: 0.8799 (mmm) cc_final: 0.8277 (mmm) REVERT: B 452 GLN cc_start: 0.8348 (tp40) cc_final: 0.7705 (tp40) REVERT: C 49 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8646 (mm) REVERT: C 69 ASP cc_start: 0.6971 (t0) cc_final: 0.6642 (t0) REVERT: C 144 ASP cc_start: 0.9221 (m-30) cc_final: 0.8855 (m-30) REVERT: C 174 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8385 (mm-30) REVERT: C 205 MET cc_start: 0.7916 (mtm) cc_final: 0.6871 (tpt) REVERT: C 324 ARG cc_start: 0.8374 (mtt180) cc_final: 0.8168 (mtt-85) REVERT: C 379 ASN cc_start: 0.8694 (m-40) cc_final: 0.8049 (m-40) REVERT: C 380 MET cc_start: 0.8931 (mmm) cc_final: 0.8450 (mmm) REVERT: D 33 ASP cc_start: 0.8963 (p0) cc_final: 0.8636 (p0) REVERT: D 72 GLN cc_start: 0.8428 (mp10) cc_final: 0.7745 (mp10) REVERT: D 95 VAL cc_start: 0.9039 (t) cc_final: 0.8834 (p) REVERT: D 185 VAL cc_start: 0.9207 (m) cc_final: 0.8825 (p) REVERT: D 188 CYS cc_start: 0.9272 (m) cc_final: 0.9071 (m) REVERT: D 253 PHE cc_start: 0.7715 (m-80) cc_final: 0.7452 (m-80) REVERT: D 317 PHE cc_start: 0.9369 (t80) cc_final: 0.9059 (t80) REVERT: D 397 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8711 (t0) REVERT: D 442 PRO cc_start: 0.9195 (Cg_exo) cc_final: 0.8862 (Cg_endo) REVERT: D 452 GLN cc_start: 0.8197 (tp40) cc_final: 0.7859 (tp-100) REVERT: D 500 GLU cc_start: 0.9349 (tp30) cc_final: 0.8935 (tp30) REVERT: D 504 ARG cc_start: 0.9655 (ttm110) cc_final: 0.9153 (ttm-80) REVERT: D 546 LEU cc_start: 0.9363 (tp) cc_final: 0.9107 (tt) outliers start: 52 outliers final: 40 residues processed: 593 average time/residue: 0.6876 time to fit residues: 600.4137 Evaluate side-chains 585 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 542 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain F residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN B 73 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.149360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125679 restraints weight = 132312.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130328 restraints weight = 64708.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133507 restraints weight = 39843.430| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17176 Z= 0.181 Angle : 0.573 5.844 23268 Z= 0.315 Chirality : 0.042 0.383 2584 Planarity : 0.005 0.072 3088 Dihedral : 4.811 23.012 2316 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.60 % Allowed : 18.51 % Favored : 77.88 % 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: 0.14 (0.18), residues: 2124 helix: 0.66 (0.18), residues: 744 sheet: -0.50 (0.23), residues: 468 loop : 0.15 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 331 HIS 0.006 0.001 HIS B 498 PHE 0.019 0.002 PHE D 533 TYR 0.017 0.002 TYR C 489 ARG 0.009 0.001 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 790) hydrogen bonds : angle 5.31603 ( 2316) covalent geometry : bond 0.00375 (17176) covalent geometry : angle 0.57254 (23268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 555 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8299 (mm110) REVERT: A 72 GLN cc_start: 0.8550 (mp10) cc_final: 0.8155 (mp10) REVERT: A 95 VAL cc_start: 0.9063 (t) cc_final: 0.8684 (p) REVERT: A 144 ASP cc_start: 0.8075 (m-30) cc_final: 0.7856 (m-30) REVERT: A 185 VAL cc_start: 0.9172 (m) cc_final: 0.8870 (p) REVERT: A 266 PHE cc_start: 0.9224 (p90) cc_final: 0.8722 (p90) REVERT: A 397 ASN cc_start: 0.9061 (t0) cc_final: 0.8750 (t0) REVERT: A 402 ASN cc_start: 0.8609 (m-40) cc_final: 0.8369 (m-40) REVERT: A 442 PRO cc_start: 0.9202 (Cg_exo) cc_final: 0.8888 (Cg_endo) REVERT: A 447 TYR cc_start: 0.8756 (t80) cc_final: 0.7910 (t80) REVERT: A 452 GLN cc_start: 0.8194 (tp40) cc_final: 0.7634 (tp-100) REVERT: A 500 GLU cc_start: 0.9442 (tp30) cc_final: 0.9006 (tp30) REVERT: A 504 ARG cc_start: 0.9677 (ttm-80) cc_final: 0.9382 (ttm-80) REVERT: A 529 TRP cc_start: 0.9059 (m100) cc_final: 0.8774 (m100) REVERT: A 535 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: B 103 ASN cc_start: 0.8183 (t0) cc_final: 0.7915 (t0) REVERT: B 174 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8201 (mm-30) REVERT: B 205 MET cc_start: 0.7972 (mtm) cc_final: 0.7571 (tpt) REVERT: B 379 ASN cc_start: 0.8738 (m-40) cc_final: 0.8463 (m-40) REVERT: B 380 MET cc_start: 0.8922 (mmm) cc_final: 0.8389 (mmm) REVERT: C 69 ASP cc_start: 0.6967 (t0) cc_final: 0.6650 (t0) REVERT: C 72 GLN cc_start: 0.7570 (mp10) cc_final: 0.7344 (mp10) REVERT: C 144 ASP cc_start: 0.9218 (m-30) cc_final: 0.8823 (m-30) REVERT: C 195 ARG cc_start: 0.9499 (mmm160) cc_final: 0.9014 (tpp80) REVERT: C 205 MET cc_start: 0.8104 (mtm) cc_final: 0.7308 (tpt) REVERT: C 379 ASN cc_start: 0.8782 (m-40) cc_final: 0.8538 (m-40) REVERT: C 380 MET cc_start: 0.9009 (mmm) cc_final: 0.8326 (mmm) REVERT: C 452 GLN cc_start: 0.8764 (tp40) cc_final: 0.8267 (tp40) REVERT: D 56 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8383 (mm110) REVERT: D 72 GLN cc_start: 0.8289 (mp10) cc_final: 0.7636 (mp10) REVERT: D 95 VAL cc_start: 0.9113 (t) cc_final: 0.8872 (p) REVERT: D 144 ASP cc_start: 0.8355 (m-30) cc_final: 0.8153 (m-30) REVERT: D 157 VAL cc_start: 0.9026 (m) cc_final: 0.8807 (t) REVERT: D 158 ILE cc_start: 0.9032 (mt) cc_final: 0.8824 (mp) REVERT: D 188 CYS cc_start: 0.9370 (m) cc_final: 0.9119 (m) REVERT: D 253 PHE cc_start: 0.7776 (m-80) cc_final: 0.7540 (m-80) REVERT: D 266 PHE cc_start: 0.9190 (p90) cc_final: 0.8731 (p90) REVERT: D 345 MET cc_start: 0.8608 (pmm) cc_final: 0.8350 (pmm) REVERT: D 402 ASN cc_start: 0.8401 (m-40) cc_final: 0.8102 (m110) REVERT: D 452 GLN cc_start: 0.8154 (tp40) cc_final: 0.7711 (tp-100) REVERT: D 500 GLU cc_start: 0.9451 (tp30) cc_final: 0.9100 (tp30) REVERT: D 504 ARG cc_start: 0.9679 (ttm110) cc_final: 0.9460 (ttm-80) REVERT: D 546 LEU cc_start: 0.9451 (tp) cc_final: 0.9199 (tp) outliers start: 65 outliers final: 58 residues processed: 585 average time/residue: 0.6777 time to fit residues: 582.7434 Evaluate side-chains 594 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 535 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain F residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 183 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124006 restraints weight = 135020.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128618 restraints weight = 65380.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131810 restraints weight = 39802.102| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.7817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17176 Z= 0.180 Angle : 0.577 6.159 23268 Z= 0.317 Chirality : 0.042 0.382 2584 Planarity : 0.005 0.079 3088 Dihedral : 4.759 19.810 2316 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.71 % Allowed : 19.68 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2124 helix: 0.56 (0.19), residues: 744 sheet: -0.70 (0.23), residues: 458 loop : 0.04 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 331 HIS 0.006 0.001 HIS B 498 PHE 0.023 0.002 PHE A 373 TYR 0.029 0.002 TYR C 489 ARG 0.008 0.001 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 790) hydrogen bonds : angle 5.26624 ( 2316) covalent geometry : bond 0.00379 (17176) covalent geometry : angle 0.57660 (23268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 555 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8789 (t0) cc_final: 0.8392 (t0) REVERT: A 72 GLN cc_start: 0.8610 (mp10) cc_final: 0.8259 (mp10) REVERT: A 95 VAL cc_start: 0.9152 (t) cc_final: 0.8814 (p) REVERT: A 144 ASP cc_start: 0.8139 (m-30) cc_final: 0.7894 (m-30) REVERT: A 185 VAL cc_start: 0.9136 (m) cc_final: 0.8835 (p) REVERT: A 266 PHE cc_start: 0.9185 (p90) cc_final: 0.8750 (p90) REVERT: A 333 ARG cc_start: 0.9081 (tpt90) cc_final: 0.8728 (tpt90) REVERT: A 397 ASN cc_start: 0.9069 (t0) cc_final: 0.8795 (t0) REVERT: A 442 PRO cc_start: 0.9236 (Cg_exo) cc_final: 0.8935 (Cg_endo) REVERT: A 447 TYR cc_start: 0.8781 (t80) cc_final: 0.6891 (t80) REVERT: A 500 GLU cc_start: 0.9444 (tp30) cc_final: 0.9101 (tp30) REVERT: A 529 TRP cc_start: 0.9089 (m100) cc_final: 0.8887 (m100) REVERT: A 535 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: B 103 ASN cc_start: 0.8214 (t0) cc_final: 0.7921 (t0) REVERT: B 131 GLN cc_start: 0.8866 (mp10) cc_final: 0.8321 (mp10) REVERT: B 174 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8355 (mm-30) REVERT: B 205 MET cc_start: 0.8197 (mtm) cc_final: 0.7713 (tpt) REVERT: B 346 ARG cc_start: 0.8412 (ptt90) cc_final: 0.8143 (ptm160) REVERT: B 379 ASN cc_start: 0.8806 (m-40) cc_final: 0.8539 (m-40) REVERT: B 380 MET cc_start: 0.9009 (mmm) cc_final: 0.8340 (mmm) REVERT: B 452 GLN cc_start: 0.8668 (tp40) cc_final: 0.8115 (tp40) REVERT: B 523 ARG cc_start: 0.8460 (mtp180) cc_final: 0.8167 (mtp-110) REVERT: C 69 ASP cc_start: 0.7171 (t0) cc_final: 0.6790 (t0) REVERT: C 72 GLN cc_start: 0.7600 (mp10) cc_final: 0.7359 (mp10) REVERT: C 144 ASP cc_start: 0.9254 (m-30) cc_final: 0.8804 (m-30) REVERT: C 205 MET cc_start: 0.8230 (mtm) cc_final: 0.7426 (tpt) REVERT: C 379 ASN cc_start: 0.8826 (m-40) cc_final: 0.8571 (m-40) REVERT: C 380 MET cc_start: 0.9089 (mmm) cc_final: 0.8407 (mmm) REVERT: C 452 GLN cc_start: 0.8783 (tp40) cc_final: 0.8224 (tp40) REVERT: D 56 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8419 (mm110) REVERT: D 62 ASP cc_start: 0.8938 (t0) cc_final: 0.8567 (t0) REVERT: D 72 GLN cc_start: 0.8486 (mp10) cc_final: 0.7895 (mp10) REVERT: D 95 VAL cc_start: 0.9197 (t) cc_final: 0.8914 (p) REVERT: D 144 ASP cc_start: 0.8411 (m-30) cc_final: 0.8145 (m-30) REVERT: D 157 VAL cc_start: 0.9077 (m) cc_final: 0.8868 (t) REVERT: D 185 VAL cc_start: 0.9138 (m) cc_final: 0.8785 (p) REVERT: D 266 PHE cc_start: 0.9148 (p90) cc_final: 0.8788 (p90) REVERT: D 442 PRO cc_start: 0.9328 (Cg_exo) cc_final: 0.9029 (Cg_endo) REVERT: D 452 GLN cc_start: 0.8020 (tp40) cc_final: 0.7422 (tp-100) REVERT: D 500 GLU cc_start: 0.9478 (tp30) cc_final: 0.9069 (tp30) REVERT: D 504 ARG cc_start: 0.9682 (ttm110) cc_final: 0.9204 (ttm-80) REVERT: D 546 LEU cc_start: 0.9372 (tp) cc_final: 0.9098 (tp) outliers start: 67 outliers final: 57 residues processed: 587 average time/residue: 0.6827 time to fit residues: 585.9444 Evaluate side-chains 583 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 525 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain F residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 82 optimal weight: 0.0070 chunk 162 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 189 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 169 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.150442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126832 restraints weight = 131764.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131500 restraints weight = 64931.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134773 restraints weight = 40022.040| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.7992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17176 Z= 0.118 Angle : 0.543 6.316 23268 Z= 0.290 Chirality : 0.042 0.388 2584 Planarity : 0.005 0.084 3088 Dihedral : 4.485 19.166 2316 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.16 % Allowed : 21.51 % Favored : 75.33 % 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: 0.22 (0.18), residues: 2124 helix: 0.91 (0.18), residues: 758 sheet: -0.66 (0.23), residues: 458 loop : 0.13 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 331 HIS 0.004 0.001 HIS D 498 PHE 0.018 0.001 PHE A 373 TYR 0.025 0.001 TYR C 489 ARG 0.012 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 790) hydrogen bonds : angle 4.95179 ( 2316) covalent geometry : bond 0.00259 (17176) covalent geometry : angle 0.54302 (23268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 559 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8643 (t0) cc_final: 0.8189 (t0) REVERT: A 72 GLN cc_start: 0.8461 (mp10) cc_final: 0.8114 (mp10) REVERT: A 95 VAL cc_start: 0.9139 (t) cc_final: 0.8809 (p) REVERT: A 144 ASP cc_start: 0.8066 (m-30) cc_final: 0.7832 (m-30) REVERT: A 185 VAL cc_start: 0.9141 (m) cc_final: 0.8789 (p) REVERT: A 266 PHE cc_start: 0.9130 (p90) cc_final: 0.8779 (p90) REVERT: A 397 ASN cc_start: 0.9083 (t0) cc_final: 0.8829 (t0) REVERT: A 442 PRO cc_start: 0.9218 (Cg_exo) cc_final: 0.8948 (Cg_endo) REVERT: A 447 TYR cc_start: 0.8801 (t80) cc_final: 0.7943 (t80) REVERT: A 500 GLU cc_start: 0.9433 (tp30) cc_final: 0.9080 (tp30) REVERT: A 529 TRP cc_start: 0.9001 (m100) cc_final: 0.8638 (m100) REVERT: B 103 ASN cc_start: 0.8178 (t0) cc_final: 0.7889 (t0) REVERT: B 205 MET cc_start: 0.8256 (mtm) cc_final: 0.7752 (tpt) REVERT: B 379 ASN cc_start: 0.8730 (m-40) cc_final: 0.8480 (m-40) REVERT: B 380 MET cc_start: 0.9026 (mmm) cc_final: 0.8357 (mmm) REVERT: B 452 GLN cc_start: 0.8693 (tp40) cc_final: 0.8116 (tp40) REVERT: C 69 ASP cc_start: 0.7157 (t0) cc_final: 0.6787 (t0) REVERT: C 72 GLN cc_start: 0.7537 (mp10) cc_final: 0.7325 (mp10) REVERT: C 144 ASP cc_start: 0.9225 (m-30) cc_final: 0.8785 (m-30) REVERT: C 205 MET cc_start: 0.8198 (mtm) cc_final: 0.7351 (tpt) REVERT: C 324 ARG cc_start: 0.8621 (mtt-85) cc_final: 0.8370 (mtt-85) REVERT: C 379 ASN cc_start: 0.8704 (m-40) cc_final: 0.8456 (m-40) REVERT: C 380 MET cc_start: 0.9072 (mmm) cc_final: 0.8401 (mmm) REVERT: C 452 GLN cc_start: 0.8839 (tp40) cc_final: 0.8287 (tp40) REVERT: D 38 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7657 (ttt-90) REVERT: D 62 ASP cc_start: 0.8830 (t0) cc_final: 0.8412 (t0) REVERT: D 72 GLN cc_start: 0.8322 (mp10) cc_final: 0.7837 (mp10) REVERT: D 144 ASP cc_start: 0.8418 (m-30) cc_final: 0.8147 (m-30) REVERT: D 157 VAL cc_start: 0.9037 (m) cc_final: 0.8836 (t) REVERT: D 185 VAL cc_start: 0.9160 (m) cc_final: 0.8830 (p) REVERT: D 188 CYS cc_start: 0.9362 (m) cc_final: 0.9134 (m) REVERT: D 253 PHE cc_start: 0.7810 (m-80) cc_final: 0.7588 (m-80) REVERT: D 266 PHE cc_start: 0.9088 (p90) cc_final: 0.8739 (p90) REVERT: D 442 PRO cc_start: 0.9282 (Cg_exo) cc_final: 0.8984 (Cg_endo) REVERT: D 447 TYR cc_start: 0.8580 (t80) cc_final: 0.7884 (t80) REVERT: D 452 GLN cc_start: 0.7976 (tp40) cc_final: 0.7683 (tp-100) REVERT: D 500 GLU cc_start: 0.9491 (tp30) cc_final: 0.9065 (tp30) REVERT: D 504 ARG cc_start: 0.9687 (ttm110) cc_final: 0.9211 (ttm-80) REVERT: E 602 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7878 (p90) outliers start: 57 outliers final: 49 residues processed: 589 average time/residue: 0.7075 time to fit residues: 608.8690 Evaluate side-chains 586 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 536 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 57 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN D 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124500 restraints weight = 134632.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129097 restraints weight = 65555.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.132279 restraints weight = 40114.387| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.8366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17176 Z= 0.179 Angle : 0.584 6.379 23268 Z= 0.319 Chirality : 0.042 0.383 2584 Planarity : 0.005 0.097 3088 Dihedral : 4.581 18.751 2316 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.38 % Allowed : 21.62 % Favored : 75.00 % 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: -0.00 (0.18), residues: 2124 helix: 0.81 (0.19), residues: 744 sheet: -0.84 (0.23), residues: 458 loop : -0.04 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 331 HIS 0.006 0.001 HIS B 498 PHE 0.018 0.002 PHE D 533 TYR 0.027 0.002 TYR A 513 ARG 0.015 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 790) hydrogen bonds : angle 5.14902 ( 2316) covalent geometry : bond 0.00374 (17176) covalent geometry : angle 0.58356 (23268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 548 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8668 (t0) cc_final: 0.8233 (t0) REVERT: A 72 GLN cc_start: 0.8588 (mp10) cc_final: 0.8270 (mp10) REVERT: A 95 VAL cc_start: 0.9162 (t) cc_final: 0.8805 (p) REVERT: A 144 ASP cc_start: 0.8103 (m-30) cc_final: 0.7861 (m-30) REVERT: A 185 VAL cc_start: 0.9138 (m) cc_final: 0.8874 (p) REVERT: A 266 PHE cc_start: 0.9091 (p90) cc_final: 0.8828 (p90) REVERT: A 397 ASN cc_start: 0.9132 (t0) cc_final: 0.8885 (t0) REVERT: A 402 ASN cc_start: 0.8464 (m-40) cc_final: 0.8261 (m-40) REVERT: A 442 PRO cc_start: 0.9264 (Cg_exo) cc_final: 0.8997 (Cg_endo) REVERT: A 447 TYR cc_start: 0.8783 (t80) cc_final: 0.7826 (t80) REVERT: A 500 GLU cc_start: 0.9445 (tp30) cc_final: 0.9112 (tp30) REVERT: B 103 ASN cc_start: 0.8378 (t0) cc_final: 0.8072 (t0) REVERT: B 174 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8366 (mm-30) REVERT: B 205 MET cc_start: 0.8299 (mtm) cc_final: 0.7848 (tpt) REVERT: B 379 ASN cc_start: 0.8861 (m-40) cc_final: 0.8604 (m-40) REVERT: B 380 MET cc_start: 0.9065 (mmm) cc_final: 0.8407 (mmm) REVERT: B 452 GLN cc_start: 0.8762 (tp40) cc_final: 0.8171 (tp40) REVERT: C 69 ASP cc_start: 0.7142 (t0) cc_final: 0.6812 (t0) REVERT: C 144 ASP cc_start: 0.9239 (m-30) cc_final: 0.8790 (m-30) REVERT: C 205 MET cc_start: 0.8271 (mtm) cc_final: 0.7443 (tpt) REVERT: C 313 GLU cc_start: 0.9284 (mp0) cc_final: 0.8835 (mp0) REVERT: C 379 ASN cc_start: 0.8826 (m-40) cc_final: 0.8573 (m-40) REVERT: C 380 MET cc_start: 0.9105 (mmm) cc_final: 0.8442 (mmm) REVERT: C 502 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8169 (mtt180) REVERT: D 38 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7805 (ttt180) REVERT: D 62 ASP cc_start: 0.8827 (t0) cc_final: 0.8369 (t0) REVERT: D 144 ASP cc_start: 0.8410 (m-30) cc_final: 0.8099 (m-30) REVERT: D 157 VAL cc_start: 0.9101 (m) cc_final: 0.8867 (t) REVERT: D 185 VAL cc_start: 0.9114 (m) cc_final: 0.8775 (p) REVERT: D 188 CYS cc_start: 0.9426 (m) cc_final: 0.9126 (m) REVERT: D 266 PHE cc_start: 0.9045 (p90) cc_final: 0.8791 (p90) REVERT: D 324 ARG cc_start: 0.9063 (mtt90) cc_final: 0.8727 (mtt90) REVERT: D 426 ASN cc_start: 0.9181 (m-40) cc_final: 0.8752 (m110) REVERT: D 442 PRO cc_start: 0.9275 (Cg_exo) cc_final: 0.8993 (Cg_endo) REVERT: D 447 TYR cc_start: 0.8608 (t80) cc_final: 0.7821 (t80) REVERT: D 500 GLU cc_start: 0.9498 (tp30) cc_final: 0.9092 (tp30) REVERT: D 504 ARG cc_start: 0.9687 (ttm110) cc_final: 0.9215 (ttm-80) outliers start: 61 outliers final: 55 residues processed: 576 average time/residue: 0.7050 time to fit residues: 589.3109 Evaluate side-chains 586 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 531 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain F residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 70 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 516 ASN ** D 249 GLN ** 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 = 0.3929 r_free = 0.3929 target = 0.153555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130138 restraints weight = 131543.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134825 restraints weight = 64334.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138037 restraints weight = 39552.890| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.8526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17176 Z= 0.116 Angle : 0.569 9.180 23268 Z= 0.300 Chirality : 0.042 0.392 2584 Planarity : 0.005 0.074 3088 Dihedral : 4.359 19.511 2316 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.22 % Allowed : 22.28 % Favored : 74.50 % 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: 0.25 (0.18), residues: 2124 helix: 1.05 (0.18), residues: 758 sheet: -0.71 (0.23), residues: 454 loop : 0.05 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 331 HIS 0.003 0.001 HIS A 438 PHE 0.015 0.001 PHE A 373 TYR 0.021 0.001 TYR B 489 ARG 0.011 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 790) hydrogen bonds : angle 4.83075 ( 2316) covalent geometry : bond 0.00263 (17176) covalent geometry : angle 0.56867 (23268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 555 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8386 (t0) cc_final: 0.8123 (t0) REVERT: A 72 GLN cc_start: 0.8490 (mp10) cc_final: 0.8128 (mp10) REVERT: A 95 VAL cc_start: 0.9148 (t) cc_final: 0.8807 (p) REVERT: A 144 ASP cc_start: 0.8050 (m-30) cc_final: 0.7794 (m-30) REVERT: A 266 PHE cc_start: 0.9003 (p90) cc_final: 0.8715 (p90) REVERT: A 397 ASN cc_start: 0.9117 (t0) cc_final: 0.8890 (t0) REVERT: A 402 ASN cc_start: 0.8446 (m-40) cc_final: 0.8244 (m-40) REVERT: A 442 PRO cc_start: 0.9233 (Cg_exo) cc_final: 0.8968 (Cg_endo) REVERT: A 447 TYR cc_start: 0.8770 (t80) cc_final: 0.7726 (t80) REVERT: A 492 GLN cc_start: 0.8544 (mm110) cc_final: 0.8134 (mm-40) REVERT: A 500 GLU cc_start: 0.9422 (tp30) cc_final: 0.9079 (tp30) REVERT: A 529 TRP cc_start: 0.9046 (m100) cc_final: 0.8801 (m100) REVERT: B 127 GLU cc_start: 0.8783 (pp20) cc_final: 0.8378 (pp20) REVERT: B 174 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8366 (mm-30) REVERT: B 205 MET cc_start: 0.8325 (mtm) cc_final: 0.7863 (tpt) REVERT: B 379 ASN cc_start: 0.8750 (m-40) cc_final: 0.8504 (m-40) REVERT: B 380 MET cc_start: 0.9049 (mmm) cc_final: 0.8435 (mmm) REVERT: B 452 GLN cc_start: 0.8761 (tp40) cc_final: 0.8168 (tp40) REVERT: B 523 ARG cc_start: 0.8440 (mtp180) cc_final: 0.8136 (mtp-110) REVERT: C 69 ASP cc_start: 0.6928 (t0) cc_final: 0.6697 (t0) REVERT: C 144 ASP cc_start: 0.9205 (m-30) cc_final: 0.8765 (m-30) REVERT: C 205 MET cc_start: 0.8261 (mtm) cc_final: 0.7447 (tpt) REVERT: C 302 ARG cc_start: 0.7686 (ptp-110) cc_final: 0.7175 (ptp-170) REVERT: C 313 GLU cc_start: 0.9241 (mp0) cc_final: 0.8766 (mp0) REVERT: C 379 ASN cc_start: 0.8740 (m-40) cc_final: 0.8487 (m-40) REVERT: C 380 MET cc_start: 0.9096 (mmm) cc_final: 0.8179 (mmm) REVERT: D 144 ASP cc_start: 0.8413 (m-30) cc_final: 0.8110 (m-30) REVERT: D 157 VAL cc_start: 0.9062 (m) cc_final: 0.8812 (t) REVERT: D 185 VAL cc_start: 0.9149 (m) cc_final: 0.8837 (p) REVERT: D 266 PHE cc_start: 0.8967 (p90) cc_final: 0.8748 (p90) REVERT: D 426 ASN cc_start: 0.9314 (m-40) cc_final: 0.8932 (m110) REVERT: D 442 PRO cc_start: 0.9229 (Cg_exo) cc_final: 0.8971 (Cg_endo) REVERT: D 447 TYR cc_start: 0.8591 (t80) cc_final: 0.7758 (t80) REVERT: D 500 GLU cc_start: 0.9503 (tp30) cc_final: 0.9083 (tp30) REVERT: D 504 ARG cc_start: 0.9686 (ttm110) cc_final: 0.9215 (ttm-80) REVERT: E 602 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7906 (p90) outliers start: 58 outliers final: 52 residues processed: 581 average time/residue: 0.7005 time to fit residues: 588.3240 Evaluate side-chains 586 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 533 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain F residue 602 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 134 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.149620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126948 restraints weight = 134540.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131630 restraints weight = 65749.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134884 restraints weight = 40164.732| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.8765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17176 Z= 0.155 Angle : 0.585 7.665 23268 Z= 0.315 Chirality : 0.042 0.387 2584 Planarity : 0.005 0.107 3088 Dihedral : 4.444 18.757 2316 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.33 % Allowed : 22.39 % Favored : 74.28 % 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: 0.12 (0.18), residues: 2124 helix: 0.99 (0.19), residues: 744 sheet: -0.72 (0.23), residues: 470 loop : -0.08 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 331 HIS 0.006 0.001 HIS C 60 PHE 0.013 0.001 PHE D 533 TYR 0.018 0.001 TYR B 489 ARG 0.018 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 790) hydrogen bonds : angle 4.98278 ( 2316) covalent geometry : bond 0.00333 (17176) covalent geometry : angle 0.58502 (23268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 522 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8505 (t0) cc_final: 0.8251 (t0) REVERT: A 72 GLN cc_start: 0.8555 (mp10) cc_final: 0.8215 (mp10) REVERT: A 95 VAL cc_start: 0.9201 (t) cc_final: 0.8845 (p) REVERT: A 111 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8628 (tppt) REVERT: A 144 ASP cc_start: 0.8077 (m-30) cc_final: 0.7833 (m-30) REVERT: A 185 VAL cc_start: 0.9162 (m) cc_final: 0.8851 (p) REVERT: A 397 ASN cc_start: 0.9155 (t0) cc_final: 0.8932 (t0) REVERT: A 402 ASN cc_start: 0.8459 (m-40) cc_final: 0.8253 (m-40) REVERT: A 442 PRO cc_start: 0.9258 (Cg_exo) cc_final: 0.8984 (Cg_endo) REVERT: A 447 TYR cc_start: 0.8734 (t80) cc_final: 0.7853 (t80) REVERT: A 452 GLN cc_start: 0.8275 (tp40) cc_final: 0.7906 (tp-100) REVERT: A 500 GLU cc_start: 0.9456 (tp30) cc_final: 0.9117 (tp30) REVERT: B 174 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8370 (mm-30) REVERT: B 205 MET cc_start: 0.8328 (mtm) cc_final: 0.7856 (tpt) REVERT: B 379 ASN cc_start: 0.8796 (m-40) cc_final: 0.8555 (m-40) REVERT: B 380 MET cc_start: 0.9057 (mmm) cc_final: 0.8424 (mmm) REVERT: B 452 GLN cc_start: 0.8796 (tp40) cc_final: 0.7994 (tp40) REVERT: C 144 ASP cc_start: 0.9199 (m-30) cc_final: 0.8752 (m-30) REVERT: C 205 MET cc_start: 0.8267 (mtm) cc_final: 0.7493 (tpt) REVERT: C 302 ARG cc_start: 0.7756 (ptp-110) cc_final: 0.7231 (ptp-110) REVERT: C 379 ASN cc_start: 0.8742 (m-40) cc_final: 0.8510 (m-40) REVERT: C 380 MET cc_start: 0.9013 (mmm) cc_final: 0.8284 (mmm) REVERT: C 502 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8197 (mtt180) REVERT: D 144 ASP cc_start: 0.8442 (m-30) cc_final: 0.8130 (m-30) REVERT: D 157 VAL cc_start: 0.9066 (m) cc_final: 0.8835 (t) REVERT: D 185 VAL cc_start: 0.9103 (m) cc_final: 0.8824 (p) REVERT: D 324 ARG cc_start: 0.9057 (mtt90) cc_final: 0.8753 (mtt90) REVERT: D 401 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8801 (mm-30) REVERT: D 426 ASN cc_start: 0.9327 (m-40) cc_final: 0.8943 (m110) REVERT: D 442 PRO cc_start: 0.9261 (Cg_exo) cc_final: 0.8998 (Cg_endo) REVERT: D 447 TYR cc_start: 0.8559 (t80) cc_final: 0.7627 (t80) REVERT: D 452 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7661 (tp-100) REVERT: D 500 GLU cc_start: 0.9464 (tp30) cc_final: 0.9085 (tp30) REVERT: D 504 ARG cc_start: 0.9673 (ttm110) cc_final: 0.9215 (ttm-80) REVERT: D 535 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8134 (tm-30) outliers start: 60 outliers final: 54 residues processed: 550 average time/residue: 0.7236 time to fit residues: 579.4691 Evaluate side-chains 569 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 514 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain F residue 602 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 163 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.159314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133874 restraints weight = 127894.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138500 restraints weight = 66109.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141544 restraints weight = 42373.883| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.8873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17176 Z= 0.116 Angle : 0.584 10.091 23268 Z= 0.307 Chirality : 0.042 0.395 2584 Planarity : 0.005 0.097 3088 Dihedral : 4.284 19.343 2316 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.61 % Allowed : 23.28 % Favored : 74.11 % 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: 0.32 (0.18), residues: 2124 helix: 1.20 (0.19), residues: 758 sheet: -0.63 (0.23), residues: 472 loop : -0.01 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 331 HIS 0.004 0.001 HIS B 498 PHE 0.022 0.001 PHE D 323 TYR 0.018 0.001 TYR B 489 ARG 0.016 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 790) hydrogen bonds : angle 4.74037 ( 2316) covalent geometry : bond 0.00266 (17176) covalent geometry : angle 0.58445 (23268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14231.65 seconds wall clock time: 245 minutes 32.38 seconds (14732.38 seconds total)