Starting phenix.real_space_refine on Fri May 30 04:51:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fne_29310/05_2025/8fne_29310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fne_29310/05_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_29310/05_2025/8fne_29310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fne_29310/05_2025/8fne_29310.map" model { file = "/net/cci-nas-00/data/ceres_data/8fne_29310/05_2025/8fne_29310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fne_29310/05_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-5687/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: 41.97, per 1000 atoms: 1.25 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: 8.67 Conformation dependent library (CDL) restraints added in 2.6 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: 2.94 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: 12.32 Time building geometry restraints manager: 10.29 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: 6.480 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: 0.530 Extract box with map and model: 1.330 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 93.480 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.880 ------------------------------------------------------------------------------- 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 : 2.573 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: 0.7992 time to fit residues: 906.8310 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 : 2.688 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143785 restraints weight = 123747.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148731 restraints weight = 60844.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152127 restraints weight = 37521.351| |-----------------------------------------------------------------------------| 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 : 2.797 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: 0.8797 (p0) cc_final: 0.8537 (p0) REVERT: A 52 GLU cc_start: 0.9088 (tp30) cc_final: 0.8788 (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: 0.8467 (t) REVERT: A 158 ILE cc_start: 0.9223 (mt) cc_final: 0.8897 (mt) REVERT: A 185 VAL cc_start: 0.9311 (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: 0.9100 (tpt90) cc_final: 0.8767 (tpt90) REVERT: A 345 MET cc_start: 0.8543 (pmm) cc_final: 0.8314 (pmm) REVERT: A 397 ASN cc_start: 0.8716 (t0) cc_final: 0.8415 (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: 0.8542 (t80) REVERT: A 464 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8079 (mp10) REVERT: A 500 GLU cc_start: 0.9262 (tp30) cc_final: 0.8899 (tp30) REVERT: B 32 THR cc_start: 0.6957 (t) cc_final: 0.6706 (m) REVERT: B 101 MET cc_start: 0.7905 (mtm) cc_final: 0.7330 (mtm) REVERT: B 219 PHE cc_start: 0.8148 (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: 0.9278 (m-40) cc_final: 0.8603 (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: 0.7874 (mtm) cc_final: 0.7318 (mtm) REVERT: C 144 ASP cc_start: 0.9082 (m-30) cc_final: 0.8791 (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: 0.8259 (m110) REVERT: C 380 MET cc_start: 0.8710 (mmm) cc_final: 0.8277 (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: 0.8520 (t) REVERT: D 185 VAL cc_start: 0.9241 (m) cc_final: 0.8924 (p) REVERT: D 249 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7585 (pp30) REVERT: D 253 PHE cc_start: 0.7146 (m-80) cc_final: 0.6898 (m-80) REVERT: D 333 ARG cc_start: 0.9053 (tpt90) cc_final: 0.8701 (tpt90) REVERT: D 397 ASN cc_start: 0.8679 (t0) cc_final: 0.8335 (t0) REVERT: D 452 GLN cc_start: 0.8210 (tp40) cc_final: 0.7918 (tp40) REVERT: D 464 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8159 (mp10) REVERT: D 500 GLU cc_start: 0.9247 (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: 0.7144 time to fit residues: 676.6778 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 : 2.671 ------------------------------------------------------------------------------- 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: 0.6980 chunk 153 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 262 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 262 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 = 0.3941 r_free = 0.3941 target = 0.150572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127650 restraints weight = 132862.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132424 restraints weight = 62941.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135725 restraints weight = 37734.864| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17176 Z= 0.216 Angle : 0.646 5.490 23268 Z= 0.362 Chirality : 0.043 0.376 2584 Planarity : 0.005 0.065 3088 Dihedral : 5.220 24.344 2316 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.44 % Allowed : 14.75 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2124 helix: 0.47 (0.18), residues: 742 sheet: -0.15 (0.23), residues: 460 loop : 0.32 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 331 HIS 0.008 0.002 HIS B 153 PHE 0.025 0.002 PHE A 533 TYR 0.032 0.002 TYR A 271 ARG 0.007 0.001 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 790) hydrogen bonds : angle 5.75369 ( 2316) covalent geometry : bond 0.00444 (17176) covalent geometry : angle 0.64630 (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 667 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 605 time to evaluate : 2.723 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: A 33 ASP cc_start: 0.9033 (p0) cc_final: 0.8632 (p0) REVERT: A 52 GLU cc_start: 0.9228 (tp30) cc_final: 0.8795 (tp30) REVERT: A 56 GLN cc_start: 0.8659 (mm-40) cc_final: 0.7957 (mm110) REVERT: A 69 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7524 (t0) REVERT: A 72 GLN cc_start: 0.8819 (mp10) cc_final: 0.8121 (mp10) REVERT: A 95 VAL cc_start: 0.9092 (t) cc_final: 0.8692 (p) REVERT: A 185 VAL cc_start: 0.9151 (m) cc_final: 0.8706 (p) REVERT: A 189 ASP cc_start: 0.8162 (m-30) cc_final: 0.7949 (m-30) REVERT: A 253 PHE cc_start: 0.7493 (m-80) cc_final: 0.7270 (m-80) REVERT: A 266 PHE cc_start: 0.9309 (p90) cc_final: 0.8710 (p90) REVERT: A 333 ARG cc_start: 0.9147 (tpt90) cc_final: 0.8769 (tpt90) REVERT: A 345 MET cc_start: 0.8564 (pmm) cc_final: 0.8287 (pmm) REVERT: A 397 ASN cc_start: 0.9016 (t0) cc_final: 0.8642 (t0) REVERT: A 402 ASN cc_start: 0.8539 (m-40) cc_final: 0.8223 (m-40) REVERT: A 426 ASN cc_start: 0.8662 (m-40) cc_final: 0.8287 (m-40) REVERT: A 447 TYR cc_start: 0.8585 (t80) cc_final: 0.7918 (t80) REVERT: A 452 GLN cc_start: 0.8106 (tp40) cc_final: 0.7765 (tp-100) REVERT: A 500 GLU cc_start: 0.9384 (tp30) cc_final: 0.8957 (tp30) REVERT: A 504 ARG cc_start: 0.9667 (ttm-80) cc_final: 0.9390 (ttm-80) REVERT: A 529 TRP cc_start: 0.8961 (m100) cc_final: 0.8554 (m100) REVERT: A 535 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8664 (tm-30) REVERT: B 56 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: B 174 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8169 (mm-30) REVERT: B 205 MET cc_start: 0.7654 (mtm) cc_final: 0.6773 (tpt) REVERT: B 379 ASN cc_start: 0.8741 (m-40) cc_final: 0.8482 (m-40) REVERT: B 380 MET cc_start: 0.8862 (mmm) cc_final: 0.8479 (mmm) REVERT: C 56 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: C 69 ASP cc_start: 0.7150 (t0) cc_final: 0.6768 (t0) REVERT: C 72 GLN cc_start: 0.7711 (mp10) cc_final: 0.7473 (mp10) REVERT: C 103 ASN cc_start: 0.7787 (t0) cc_final: 0.7572 (t0) REVERT: C 144 ASP cc_start: 0.9275 (m-30) cc_final: 0.8921 (m-30) REVERT: C 174 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8464 (mm-30) REVERT: C 205 MET cc_start: 0.7836 (mtm) cc_final: 0.6897 (tpt) REVERT: C 224 MET cc_start: 0.8132 (mmm) cc_final: 0.7914 (tmm) REVERT: C 379 ASN cc_start: 0.8816 (m-40) cc_final: 0.8165 (m-40) REVERT: C 380 MET cc_start: 0.8923 (mmm) cc_final: 0.8534 (mmm) REVERT: C 452 GLN cc_start: 0.8034 (tp40) cc_final: 0.7713 (tp40) REVERT: C 507 LYS cc_start: 0.9655 (mttt) cc_final: 0.9423 (mtmm) REVERT: D 33 ASP cc_start: 0.8978 (p0) cc_final: 0.8738 (p0) REVERT: D 56 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8382 (mm110) REVERT: D 72 GLN cc_start: 0.8810 (mp10) cc_final: 0.8389 (mp10) REVERT: D 95 VAL cc_start: 0.9096 (t) cc_final: 0.8721 (p) REVERT: D 159 ASN cc_start: 0.8789 (t0) cc_final: 0.8245 (t0) REVERT: D 253 PHE cc_start: 0.7655 (m-80) cc_final: 0.7399 (m-80) REVERT: D 266 PHE cc_start: 0.9262 (p90) cc_final: 0.8766 (p90) REVERT: D 317 PHE cc_start: 0.9373 (t80) cc_final: 0.9086 (t80) REVERT: D 345 MET cc_start: 0.8532 (pmm) cc_final: 0.8280 (pmm) REVERT: D 397 ASN cc_start: 0.9015 (t0) cc_final: 0.8616 (t0) REVERT: D 447 TYR cc_start: 0.8462 (t80) cc_final: 0.7787 (t80) REVERT: D 452 GLN cc_start: 0.8160 (tp40) cc_final: 0.7745 (tp-100) REVERT: D 500 GLU cc_start: 0.9396 (tp30) cc_final: 0.8983 (tp30) REVERT: D 504 ARG cc_start: 0.9678 (ttm110) cc_final: 0.9207 (ttm-80) REVERT: D 520 TYR cc_start: 0.8308 (m-80) cc_final: 0.7973 (m-80) REVERT: D 529 TRP cc_start: 0.8963 (m100) cc_final: 0.8631 (m100) outliers start: 62 outliers final: 50 residues processed: 633 average time/residue: 0.7000 time to fit residues: 645.0816 Evaluate side-chains 597 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 543 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP 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 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 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 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 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 56 GLN 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 C residue 546 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 457 LEU 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: 3.9990 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 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 92 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 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 = 0.3845 r_free = 0.3845 target = 0.145128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123823 restraints weight = 141273.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128282 restraints weight = 67021.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131354 restraints weight = 40298.455| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 17176 Z= 0.310 Angle : 0.717 6.320 23268 Z= 0.408 Chirality : 0.045 0.383 2584 Planarity : 0.006 0.075 3088 Dihedral : 5.692 22.894 2316 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Rotamer: Outliers : 5.10 % Allowed : 16.46 % Favored : 78.44 % 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: -0.92 (0.17), residues: 2124 helix: -0.36 (0.18), residues: 742 sheet: -0.92 (0.22), residues: 452 loop : -0.45 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 331 HIS 0.012 0.002 HIS A 153 PHE 0.022 0.003 PHE A 134 TYR 0.021 0.003 TYR B 489 ARG 0.007 0.001 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 790) hydrogen bonds : angle 6.16947 ( 2316) covalent geometry : bond 0.00632 (17176) covalent geometry : angle 0.71727 (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 623 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 531 time to evaluate : 2.472 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: A 69 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8230 (t0) REVERT: A 72 GLN cc_start: 0.9015 (mp10) cc_final: 0.8572 (mp10) REVERT: A 95 VAL cc_start: 0.9227 (t) cc_final: 0.8811 (p) REVERT: A 266 PHE cc_start: 0.9341 (p90) cc_final: 0.8796 (p90) REVERT: A 373 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7251 (t80) REVERT: A 397 ASN cc_start: 0.9079 (t0) cc_final: 0.8804 (t0) REVERT: A 426 ASN cc_start: 0.8883 (m-40) cc_final: 0.8539 (m-40) REVERT: A 447 TYR cc_start: 0.8795 (t80) cc_final: 0.7849 (t80) REVERT: A 500 GLU cc_start: 0.9457 (tp30) cc_final: 0.9091 (tp30) REVERT: A 504 ARG cc_start: 0.9680 (ttm-80) cc_final: 0.9469 (ttm-80) REVERT: A 535 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8654 (tm-30) REVERT: B 56 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8675 (mp10) REVERT: B 174 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8584 (mt-10) REVERT: B 179 GLN cc_start: 0.9566 (mt0) cc_final: 0.9114 (mt0) REVERT: B 205 MET cc_start: 0.7964 (mtm) cc_final: 0.7228 (tpt) REVERT: B 379 ASN cc_start: 0.8932 (m-40) cc_final: 0.8695 (m-40) REVERT: B 380 MET cc_start: 0.8935 (mmm) cc_final: 0.7910 (mmm) REVERT: B 400 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8967 (tp) REVERT: B 453 LEU cc_start: 0.8525 (mp) cc_final: 0.8081 (mp) REVERT: B 502 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8183 (mtt180) REVERT: B 523 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7988 (mtp-110) REVERT: C 56 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8662 (mp10) REVERT: C 69 ASP cc_start: 0.7321 (t0) cc_final: 0.6948 (t0) REVERT: C 72 GLN cc_start: 0.7922 (mp10) cc_final: 0.7659 (mp10) REVERT: C 103 ASN cc_start: 0.8386 (t0) cc_final: 0.8008 (t0) REVERT: C 144 ASP cc_start: 0.9282 (m-30) cc_final: 0.8918 (m-30) REVERT: C 205 MET cc_start: 0.8139 (mtm) cc_final: 0.7380 (tpt) REVERT: C 258 ASP cc_start: 0.8010 (p0) cc_final: 0.7750 (p0) REVERT: C 379 ASN cc_start: 0.8953 (m-40) cc_final: 0.8740 (m-40) REVERT: C 380 MET cc_start: 0.9075 (mmm) cc_final: 0.8108 (mmm) REVERT: C 529 TRP cc_start: 0.8896 (m100) cc_final: 0.8628 (m100) REVERT: D 56 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8518 (mm110) REVERT: D 72 GLN cc_start: 0.8904 (mp10) cc_final: 0.8576 (mp10) REVERT: D 95 VAL cc_start: 0.9210 (t) cc_final: 0.8777 (p) REVERT: D 103 ASN cc_start: 0.8283 (t0) cc_final: 0.7969 (t0) REVERT: D 185 VAL cc_start: 0.9204 (m) cc_final: 0.8914 (p) REVERT: D 266 PHE cc_start: 0.9298 (p90) cc_final: 0.8837 (p90) REVERT: D 317 PHE cc_start: 0.9443 (t80) cc_final: 0.9139 (t80) REVERT: D 345 MET cc_start: 0.8499 (pmm) cc_final: 0.8212 (pmm) REVERT: D 397 ASN cc_start: 0.9093 (t0) cc_final: 0.8824 (t0) REVERT: D 426 ASN cc_start: 0.9442 (m-40) cc_final: 0.9199 (m110) REVERT: D 500 GLU cc_start: 0.9478 (tp30) cc_final: 0.9146 (tp30) outliers start: 92 outliers final: 76 residues processed: 579 average time/residue: 0.6980 time to fit residues: 589.5585 Evaluate side-chains 584 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 502 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 80 LEU 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 187 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 373 PHE 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 510 ASP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 99 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 175 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 308 LYS 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 528 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 105 GLN 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 175 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 255 GLU 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 400 ILE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 88 ILE 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 354 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 380 MET Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 522 THR 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 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: 0.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** 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 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 = 0.3899 r_free = 0.3899 target = 0.150024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126534 restraints weight = 131928.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131023 restraints weight = 65385.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134127 restraints weight = 40729.689| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17176 Z= 0.135 Angle : 0.563 8.455 23268 Z= 0.304 Chirality : 0.042 0.387 2584 Planarity : 0.005 0.069 3088 Dihedral : 4.990 21.378 2316 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.16 % Allowed : 19.73 % Favored : 77.11 % 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: -0.22 (0.18), residues: 2124 helix: 0.50 (0.18), residues: 742 sheet: -0.84 (0.23), residues: 454 loop : -0.13 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 331 HIS 0.004 0.001 HIS B 498 PHE 0.016 0.001 PHE A 373 TYR 0.025 0.001 TYR C 489 ARG 0.009 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 790) hydrogen bonds : angle 5.36315 ( 2316) covalent geometry : bond 0.00291 (17176) covalent geometry : angle 0.56288 (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 634 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 577 time to evaluate : 2.818 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: A 38 ARG cc_start: 0.8017 (ttt-90) cc_final: 0.7806 (ttt-90) REVERT: A 72 GLN cc_start: 0.8940 (mp10) cc_final: 0.8433 (mp10) REVERT: A 95 VAL cc_start: 0.9169 (t) cc_final: 0.8790 (p) REVERT: A 144 ASP cc_start: 0.8123 (m-30) cc_final: 0.7898 (m-30) REVERT: A 266 PHE cc_start: 0.9156 (p90) cc_final: 0.8737 (p90) REVERT: A 397 ASN cc_start: 0.9072 (t0) cc_final: 0.8808 (t0) REVERT: A 426 ASN cc_start: 0.8833 (m-40) cc_final: 0.8544 (m-40) REVERT: A 447 TYR cc_start: 0.8669 (t80) cc_final: 0.7791 (t80) REVERT: A 500 GLU cc_start: 0.9450 (tp30) cc_final: 0.9084 (tp30) REVERT: B 205 MET cc_start: 0.8053 (mtm) cc_final: 0.7333 (tpt) REVERT: B 324 ARG cc_start: 0.8676 (ptp90) cc_final: 0.8220 (mtm-85) REVERT: B 346 ARG cc_start: 0.9303 (mtm-85) cc_final: 0.8190 (ptm160) REVERT: B 379 ASN cc_start: 0.8808 (m-40) cc_final: 0.8561 (m-40) REVERT: B 380 MET cc_start: 0.8853 (mmm) cc_final: 0.8125 (mmm) REVERT: B 502 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8119 (mtt180) REVERT: C 46 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8686 (t80) REVERT: C 69 ASP cc_start: 0.7081 (t0) cc_final: 0.6755 (t0) REVERT: C 72 GLN cc_start: 0.7836 (mp10) cc_final: 0.7595 (mp10) REVERT: C 103 ASN cc_start: 0.8353 (t0) cc_final: 0.7960 (t0) REVERT: C 144 ASP cc_start: 0.9204 (m-30) cc_final: 0.8752 (m-30) REVERT: C 205 MET cc_start: 0.8151 (mtm) cc_final: 0.7310 (tpt) REVERT: C 224 MET cc_start: 0.8471 (mmm) cc_final: 0.8142 (tmm) REVERT: C 379 ASN cc_start: 0.8819 (m-40) cc_final: 0.8582 (m-40) REVERT: C 380 MET cc_start: 0.8939 (mmm) cc_final: 0.8174 (mmm) REVERT: C 452 GLN cc_start: 0.8694 (tp40) cc_final: 0.8177 (tp40) REVERT: D 69 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.6919 (t0) REVERT: D 72 GLN cc_start: 0.8781 (mp10) cc_final: 0.8254 (mp10) REVERT: D 188 CYS cc_start: 0.9368 (m) cc_final: 0.9092 (m) REVERT: D 266 PHE cc_start: 0.9128 (p90) cc_final: 0.8703 (p90) REVERT: D 345 MET cc_start: 0.8477 (pmm) cc_final: 0.8179 (pmm) REVERT: D 397 ASN cc_start: 0.9095 (t0) cc_final: 0.8819 (t0) REVERT: D 452 GLN cc_start: 0.8097 (tp40) cc_final: 0.7575 (tp-100) REVERT: D 500 GLU cc_start: 0.9453 (tp30) cc_final: 0.9042 (tp30) REVERT: D 504 ARG cc_start: 0.9701 (ttm110) cc_final: 0.9232 (ttm-80) outliers start: 57 outliers final: 47 residues processed: 604 average time/residue: 0.7050 time to fit residues: 613.1353 Evaluate side-chains 573 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 524 time to evaluate : 2.571 ------------------------------------------------------------------------------- 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 187 LEU 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 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 179 GLN 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 468 ASP Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 PHE 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 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 175 LEU 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 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 69 ASP 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 522 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 183 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126174 restraints weight = 132767.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130686 restraints weight = 65604.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133832 restraints weight = 40785.340| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.8120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17176 Z= 0.156 Angle : 0.562 4.667 23268 Z= 0.306 Chirality : 0.042 0.385 2584 Planarity : 0.005 0.077 3088 Dihedral : 4.823 20.673 2316 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.66 % Allowed : 21.18 % Favored : 75.17 % 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: -0.24 (0.18), residues: 2124 helix: 0.63 (0.18), residues: 744 sheet: -0.98 (0.22), residues: 470 loop : -0.18 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 331 HIS 0.006 0.001 HIS D 498 PHE 0.015 0.001 PHE A 373 TYR 0.029 0.002 TYR C 489 ARG 0.011 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 790) hydrogen bonds : angle 5.29545 ( 2316) covalent geometry : bond 0.00335 (17176) covalent geometry : angle 0.56222 (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 612 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 546 time to evaluate : 2.686 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 38 ARG cc_start: 0.8052 (ttt-90) cc_final: 0.7681 (ttt-90) REVERT: A 72 GLN cc_start: 0.8918 (mp10) cc_final: 0.8585 (mp10) REVERT: A 95 VAL cc_start: 0.9181 (t) cc_final: 0.8819 (p) REVERT: A 144 ASP cc_start: 0.8154 (m-30) cc_final: 0.7913 (m-30) REVERT: A 266 PHE cc_start: 0.9135 (p90) cc_final: 0.8781 (p90) REVERT: A 397 ASN cc_start: 0.9103 (t0) cc_final: 0.8864 (t0) REVERT: A 426 ASN cc_start: 0.8928 (m-40) cc_final: 0.8593 (m-40) REVERT: A 447 TYR cc_start: 0.8649 (t80) cc_final: 0.7681 (t80) REVERT: A 500 GLU cc_start: 0.9448 (tp30) cc_final: 0.9098 (tp30) REVERT: A 535 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: B 205 MET cc_start: 0.8099 (mtm) cc_final: 0.7356 (tpt) REVERT: B 324 ARG cc_start: 0.8660 (ptp90) cc_final: 0.8358 (mtm-85) REVERT: B 379 ASN cc_start: 0.8785 (m-40) cc_final: 0.8540 (m-40) REVERT: B 380 MET cc_start: 0.8888 (mmm) cc_final: 0.8157 (mmm) REVERT: B 529 TRP cc_start: 0.8842 (m100) cc_final: 0.8122 (m100) REVERT: C 46 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8720 (t80) REVERT: C 69 ASP cc_start: 0.7189 (t0) cc_final: 0.6948 (t0) REVERT: C 72 GLN cc_start: 0.7819 (mp10) cc_final: 0.7605 (mp10) REVERT: C 144 ASP cc_start: 0.9224 (m-30) cc_final: 0.8757 (m-30) REVERT: C 205 MET cc_start: 0.8281 (mtm) cc_final: 0.7430 (tpt) REVERT: C 321 ASN cc_start: 0.9027 (m-40) cc_final: 0.8385 (t0) REVERT: C 379 ASN cc_start: 0.8806 (m-40) cc_final: 0.8583 (m-40) REVERT: C 380 MET cc_start: 0.8968 (mmm) cc_final: 0.8228 (mmm) REVERT: C 452 GLN cc_start: 0.8768 (tp40) cc_final: 0.8189 (tp40) REVERT: C 453 LEU cc_start: 0.9057 (mp) cc_final: 0.8508 (mp) REVERT: C 502 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8143 (mtt180) REVERT: D 69 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.6566 (t0) REVERT: D 72 GLN cc_start: 0.8748 (mp10) cc_final: 0.8105 (mp10) REVERT: D 144 ASP cc_start: 0.8284 (m-30) cc_final: 0.7998 (m-30) REVERT: D 266 PHE cc_start: 0.9086 (p90) cc_final: 0.8808 (p90) REVERT: D 345 MET cc_start: 0.8470 (pmm) cc_final: 0.8179 (pmm) REVERT: D 397 ASN cc_start: 0.9132 (t0) cc_final: 0.8875 (t0) REVERT: D 452 GLN cc_start: 0.8019 (tp40) cc_final: 0.7433 (tp-100) REVERT: D 500 GLU cc_start: 0.9480 (tp30) cc_final: 0.9062 (tp30) REVERT: D 504 ARG cc_start: 0.9714 (ttm110) cc_final: 0.9256 (ttm-80) outliers start: 66 outliers final: 54 residues processed: 581 average time/residue: 0.7435 time to fit residues: 626.5470 Evaluate side-chains 577 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 520 time to evaluate : 2.838 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 354 LEU 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 457 LEU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 LEU 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 179 GLN 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 348 ILE 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 470 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 56 GLN 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 171 LEU Chi-restraints excluded: chain C residue 175 LEU 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 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain D residue 69 ASP 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 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: 3.9990 chunk 162 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124376 restraints weight = 138455.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128870 restraints weight = 67092.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131965 restraints weight = 40796.705| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.8661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17176 Z= 0.222 Angle : 0.613 5.434 23268 Z= 0.341 Chirality : 0.042 0.380 2584 Planarity : 0.005 0.074 3088 Dihedral : 5.047 20.604 2316 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.71 % Allowed : 21.18 % 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: -0.70 (0.18), residues: 2124 helix: 0.26 (0.18), residues: 754 sheet: -1.21 (0.22), residues: 466 loop : -0.50 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 331 HIS 0.007 0.002 HIS C 60 PHE 0.015 0.002 PHE A 373 TYR 0.026 0.002 TYR B 489 ARG 0.011 0.001 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 790) hydrogen bonds : angle 5.54947 ( 2316) covalent geometry : bond 0.00460 (17176) covalent geometry : angle 0.61322 (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 623 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 538 time to evaluate : 2.855 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: A 62 ASP cc_start: 0.8956 (t0) cc_final: 0.8398 (t0) REVERT: A 72 GLN cc_start: 0.9010 (mp10) cc_final: 0.8707 (mp10) REVERT: A 95 VAL cc_start: 0.9233 (t) cc_final: 0.8862 (p) REVERT: A 111 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8657 (tppt) REVERT: A 144 ASP cc_start: 0.8237 (m-30) cc_final: 0.8000 (m-30) REVERT: A 266 PHE cc_start: 0.9105 (p90) cc_final: 0.8812 (p90) REVERT: A 307 LEU cc_start: 0.9444 (tp) cc_final: 0.9184 (tt) REVERT: A 397 ASN cc_start: 0.9178 (t0) cc_final: 0.8948 (t0) REVERT: A 426 ASN cc_start: 0.8989 (m-40) cc_final: 0.8655 (m-40) REVERT: A 447 TYR cc_start: 0.8647 (t80) cc_final: 0.7555 (t80) REVERT: A 500 GLU cc_start: 0.9469 (tp30) cc_final: 0.9132 (tp30) REVERT: A 535 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: B 205 MET cc_start: 0.8126 (mtm) cc_final: 0.7439 (tpt) REVERT: B 324 ARG cc_start: 0.8643 (ptp90) cc_final: 0.8302 (mtm-85) REVERT: B 379 ASN cc_start: 0.8938 (m-40) cc_final: 0.8714 (m-40) REVERT: B 380 MET cc_start: 0.8958 (mmm) cc_final: 0.8235 (mmm) REVERT: B 502 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8215 (mtt180) REVERT: C 69 ASP cc_start: 0.7316 (t0) cc_final: 0.7090 (t0) REVERT: C 72 GLN cc_start: 0.7850 (mp10) cc_final: 0.7628 (mp10) REVERT: C 144 ASP cc_start: 0.9254 (m-30) cc_final: 0.8799 (m-30) REVERT: C 165 ILE cc_start: 0.9141 (mt) cc_final: 0.8550 (mp) REVERT: C 205 MET cc_start: 0.8264 (mtm) cc_final: 0.7583 (tpt) REVERT: C 224 MET cc_start: 0.8582 (mmm) cc_final: 0.8226 (tmm) REVERT: C 379 ASN cc_start: 0.8928 (m-40) cc_final: 0.8697 (m-40) REVERT: C 380 MET cc_start: 0.9025 (mmm) cc_final: 0.8304 (mmm) REVERT: C 502 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8222 (mtt180) REVERT: D 69 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.6971 (t0) REVERT: D 72 GLN cc_start: 0.8859 (mp10) cc_final: 0.8277 (mp10) REVERT: D 144 ASP cc_start: 0.8369 (m-30) cc_final: 0.8057 (m-30) REVERT: D 185 VAL cc_start: 0.9102 (m) cc_final: 0.8797 (p) REVERT: D 266 PHE cc_start: 0.9096 (p90) cc_final: 0.8840 (p90) REVERT: D 345 MET cc_start: 0.8533 (pmm) cc_final: 0.8243 (pmm) REVERT: D 397 ASN cc_start: 0.9152 (t0) cc_final: 0.8904 (t0) REVERT: D 426 ASN cc_start: 0.9362 (m-40) cc_final: 0.9084 (m110) REVERT: D 447 TYR cc_start: 0.8522 (t80) cc_final: 0.7601 (t80) REVERT: D 500 GLU cc_start: 0.9486 (tp30) cc_final: 0.9074 (tp30) REVERT: D 504 ARG cc_start: 0.9699 (ttm110) cc_final: 0.9216 (ttm-80) REVERT: D 535 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8055 (tm-30) outliers start: 85 outliers final: 70 residues processed: 577 average time/residue: 0.7219 time to fit residues: 601.0196 Evaluate side-chains 577 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 504 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 96 THR 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 211 GLU Chi-restraints excluded: chain A residue 236 ILE 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 457 LEU 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 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 175 LEU Chi-restraints excluded: chain B residue 179 GLN 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 468 ASP Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 546 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 85 ARG Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 105 GLN 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 175 LEU 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 314 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 457 LEU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 157 VAL 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 535 GLU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E 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: 1.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 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 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 = 0.3894 r_free = 0.3894 target = 0.152293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129179 restraints weight = 135616.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133644 restraints weight = 67334.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.136737 restraints weight = 41849.318| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.8909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17176 Z= 0.145 Angle : 0.568 6.241 23268 Z= 0.307 Chirality : 0.042 0.385 2584 Planarity : 0.005 0.090 3088 Dihedral : 4.756 20.179 2316 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.71 % Allowed : 22.89 % Favored : 73.39 % 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: -0.41 (0.18), residues: 2124 helix: 0.62 (0.18), residues: 758 sheet: -1.20 (0.21), residues: 490 loop : -0.31 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.005 0.001 HIS B 498 PHE 0.016 0.001 PHE D 323 TYR 0.020 0.001 TYR C 489 ARG 0.014 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 790) hydrogen bonds : angle 5.19107 ( 2316) covalent geometry : bond 0.00311 (17176) covalent geometry : angle 0.56778 (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 596 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 529 time to evaluate : 2.615 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 22 LEU cc_start: 0.8632 (mt) cc_final: 0.8393 (mt) REVERT: A 38 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7656 (ttt180) REVERT: A 72 GLN cc_start: 0.9007 (mp10) cc_final: 0.8706 (mp10) REVERT: A 95 VAL cc_start: 0.9306 (t) cc_final: 0.8995 (p) REVERT: A 108 LEU cc_start: 0.6397 (tp) cc_final: 0.6146 (tp) REVERT: A 111 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8634 (tppt) REVERT: A 144 ASP cc_start: 0.8194 (m-30) cc_final: 0.7964 (m-30) REVERT: A 266 PHE cc_start: 0.9045 (p90) cc_final: 0.8771 (p90) REVERT: A 307 LEU cc_start: 0.9427 (tp) cc_final: 0.9182 (tt) REVERT: A 397 ASN cc_start: 0.9142 (t0) cc_final: 0.8937 (t0) REVERT: A 426 ASN cc_start: 0.8952 (m-40) cc_final: 0.8611 (m-40) REVERT: A 447 TYR cc_start: 0.8688 (t80) cc_final: 0.7637 (t80) REVERT: A 500 GLU cc_start: 0.9501 (tp30) cc_final: 0.9143 (tp30) REVERT: B 205 MET cc_start: 0.8174 (mtm) cc_final: 0.7523 (tpt) REVERT: B 313 GLU cc_start: 0.9209 (mp0) cc_final: 0.8739 (mm-30) REVERT: B 324 ARG cc_start: 0.8638 (ptp90) cc_final: 0.8291 (mtm-85) REVERT: B 379 ASN cc_start: 0.8906 (m-40) cc_final: 0.8683 (m-40) REVERT: B 380 MET cc_start: 0.9023 (mmm) cc_final: 0.8337 (mmm) REVERT: B 502 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8197 (mtt180) REVERT: B 523 ARG cc_start: 0.8324 (mtp-110) cc_final: 0.7720 (mtp-110) REVERT: C 144 ASP cc_start: 0.9221 (m-30) cc_final: 0.8755 (m-30) REVERT: C 205 MET cc_start: 0.8337 (mtm) cc_final: 0.7575 (tpt) REVERT: C 224 MET cc_start: 0.8557 (mmm) cc_final: 0.8205 (tmm) REVERT: C 379 ASN cc_start: 0.8855 (m-40) cc_final: 0.8616 (m-40) REVERT: C 380 MET cc_start: 0.9035 (mmm) cc_final: 0.8303 (mmm) REVERT: C 502 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8200 (mtt180) REVERT: D 69 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.6532 (t0) REVERT: D 72 GLN cc_start: 0.8753 (mp10) cc_final: 0.8220 (mp10) REVERT: D 144 ASP cc_start: 0.8315 (m-30) cc_final: 0.7998 (m-30) REVERT: D 185 VAL cc_start: 0.9142 (m) cc_final: 0.8814 (p) REVERT: D 345 MET cc_start: 0.8524 (pmm) cc_final: 0.8255 (pmm) REVERT: D 397 ASN cc_start: 0.9139 (t0) cc_final: 0.8912 (t0) REVERT: D 426 ASN cc_start: 0.9467 (m-40) cc_final: 0.9181 (m110) REVERT: D 447 TYR cc_start: 0.8589 (t80) cc_final: 0.7744 (t80) REVERT: D 500 GLU cc_start: 0.9503 (tp30) cc_final: 0.9079 (tp30) REVERT: D 504 ARG cc_start: 0.9711 (ttm110) cc_final: 0.9220 (ttm-80) REVERT: D 535 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8581 (tm-30) outliers start: 67 outliers final: 58 residues processed: 562 average time/residue: 0.7210 time to fit residues: 586.1403 Evaluate side-chains 573 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 513 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 LYS 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 457 LEU Chi-restraints excluded: chain A residue 465 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 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 GLN 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 451 ILE Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 486 MET 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 175 LEU 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 307 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 69 ASP 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 249 GLN Chi-restraints excluded: chain D residue 316 LEU 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 550 MET Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain F 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: 2.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.0270 chunk 46 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 117 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.0242 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 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 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 = 0.3911 r_free = 0.3911 target = 0.150450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127462 restraints weight = 134018.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132084 restraints weight = 65726.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135314 restraints weight = 40341.239| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.9054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17176 Z= 0.121 Angle : 0.569 9.326 23268 Z= 0.302 Chirality : 0.042 0.392 2584 Planarity : 0.005 0.074 3088 Dihedral : 4.532 19.797 2316 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.38 % Allowed : 23.50 % Favored : 73.12 % 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: 0.91 (0.18), residues: 756 sheet: -1.09 (0.22), residues: 490 loop : -0.16 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 331 HIS 0.005 0.001 HIS D 438 PHE 0.018 0.001 PHE D 394 TYR 0.017 0.001 TYR B 489 ARG 0.011 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 790) hydrogen bonds : angle 4.96910 ( 2316) covalent geometry : bond 0.00271 (17176) covalent geometry : angle 0.56928 (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 586 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 525 time to evaluate : 2.448 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: A 72 GLN cc_start: 0.8983 (mp10) cc_final: 0.8647 (mp10) REVERT: A 95 VAL cc_start: 0.9322 (t) cc_final: 0.9073 (p) REVERT: A 111 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8612 (tppt) REVERT: A 144 ASP cc_start: 0.8137 (m-30) cc_final: 0.7886 (m-30) REVERT: A 266 PHE cc_start: 0.8948 (p90) cc_final: 0.8748 (p90) REVERT: A 331 TRP cc_start: 0.8324 (p-90) cc_final: 0.7743 (p-90) REVERT: A 401 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8893 (mm-30) REVERT: A 426 ASN cc_start: 0.8960 (m-40) cc_final: 0.8627 (m-40) REVERT: A 447 TYR cc_start: 0.8665 (t80) cc_final: 0.7619 (t80) REVERT: A 500 GLU cc_start: 0.9452 (tp30) cc_final: 0.9099 (tp30) REVERT: B 174 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8576 (mt-10) REVERT: B 205 MET cc_start: 0.8244 (mtm) cc_final: 0.7550 (tpt) REVERT: B 313 GLU cc_start: 0.9233 (mp0) cc_final: 0.8655 (mm-30) REVERT: B 324 ARG cc_start: 0.8652 (ptp90) cc_final: 0.8381 (mtm-85) REVERT: B 379 ASN cc_start: 0.8818 (m-40) cc_final: 0.8582 (m-40) REVERT: B 380 MET cc_start: 0.9024 (mmm) cc_final: 0.8346 (mmm) REVERT: B 498 HIS cc_start: 0.8341 (t-90) cc_final: 0.8009 (t-90) REVERT: B 502 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8204 (mtt180) REVERT: C 28 ARG cc_start: 0.8746 (ptp-170) cc_final: 0.8310 (mtm110) REVERT: C 144 ASP cc_start: 0.9196 (m-30) cc_final: 0.8748 (m-30) REVERT: C 205 MET cc_start: 0.8382 (mtm) cc_final: 0.7627 (tpt) REVERT: C 224 MET cc_start: 0.8476 (mmm) cc_final: 0.8071 (tmm) REVERT: C 302 ARG cc_start: 0.6937 (mtt90) cc_final: 0.6221 (mtt90) REVERT: C 379 ASN cc_start: 0.8791 (m-40) cc_final: 0.8524 (m-40) REVERT: C 452 GLN cc_start: 0.8800 (tp40) cc_final: 0.8020 (tp40) REVERT: C 502 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8195 (mtt180) REVERT: D 72 GLN cc_start: 0.8707 (mp10) cc_final: 0.8199 (mp10) REVERT: D 144 ASP cc_start: 0.8283 (m-30) cc_final: 0.7965 (m-30) REVERT: D 185 VAL cc_start: 0.9127 (m) cc_final: 0.8815 (p) REVERT: D 345 MET cc_start: 0.8524 (pmm) cc_final: 0.8266 (pmm) REVERT: D 426 ASN cc_start: 0.9467 (m-40) cc_final: 0.9217 (m110) REVERT: D 447 TYR cc_start: 0.8596 (t80) cc_final: 0.7736 (t80) REVERT: D 452 GLN cc_start: 0.8431 (tp40) cc_final: 0.7812 (tp-100) REVERT: D 500 GLU cc_start: 0.9471 (tp30) cc_final: 0.9152 (tp30) REVERT: D 504 ARG cc_start: 0.9692 (ttm110) cc_final: 0.9477 (ttm-80) outliers start: 61 outliers final: 54 residues processed: 552 average time/residue: 0.7202 time to fit residues: 564.9812 Evaluate side-chains 559 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 505 time to evaluate : 2.770 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 LYS 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 457 LEU 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 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 GLN 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 451 ILE Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 56 GLN 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 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 307 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 249 GLN Chi-restraints excluded: chain D residue 316 LEU 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 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: 1.9990 chunk 54 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.149742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127881 restraints weight = 138549.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132440 restraints weight = 67120.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135610 restraints weight = 40659.504| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.9250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17176 Z= 0.138 Angle : 0.587 7.785 23268 Z= 0.316 Chirality : 0.042 0.388 2584 Planarity : 0.005 0.111 3088 Dihedral : 4.506 19.658 2316 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.99 % Allowed : 24.28 % Favored : 72.73 % 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: -0.13 (0.18), residues: 2124 helix: 0.93 (0.18), residues: 756 sheet: -1.06 (0.21), residues: 490 loop : -0.21 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 331 HIS 0.005 0.001 HIS B 498 PHE 0.022 0.001 PHE D 394 TYR 0.014 0.001 TYR B 489 ARG 0.017 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 790) hydrogen bonds : angle 5.00041 ( 2316) covalent geometry : bond 0.00303 (17176) covalent geometry : angle 0.58677 (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 562 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 508 time to evaluate : 2.715 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: A 72 GLN cc_start: 0.8991 (mp10) cc_final: 0.8655 (mp10) REVERT: A 95 VAL cc_start: 0.9334 (t) cc_final: 0.9089 (p) REVERT: A 111 LYS cc_start: 0.8978 (ttpt) cc_final: 0.8626 (tppt) REVERT: A 144 ASP cc_start: 0.8141 (m-30) cc_final: 0.7902 (m-30) REVERT: A 331 TRP cc_start: 0.8466 (p-90) cc_final: 0.7948 (p-90) REVERT: A 426 ASN cc_start: 0.8994 (m-40) cc_final: 0.8654 (m-40) REVERT: A 447 TYR cc_start: 0.8713 (t80) cc_final: 0.7668 (t80) REVERT: A 452 GLN cc_start: 0.8320 (tp40) cc_final: 0.7838 (tp-100) REVERT: A 500 GLU cc_start: 0.9382 (tp30) cc_final: 0.9049 (tp30) REVERT: B 174 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8570 (mt-10) REVERT: B 205 MET cc_start: 0.8222 (mtm) cc_final: 0.7493 (tpt) REVERT: B 313 GLU cc_start: 0.9235 (mp0) cc_final: 0.8713 (mm-30) REVERT: B 324 ARG cc_start: 0.8666 (ptp90) cc_final: 0.8380 (mtm-85) REVERT: B 379 ASN cc_start: 0.8781 (m-40) cc_final: 0.8542 (m-40) REVERT: B 380 MET cc_start: 0.9003 (mmm) cc_final: 0.8352 (mmm) REVERT: B 502 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8154 (mtt180) REVERT: C 28 ARG cc_start: 0.8728 (ptp-170) cc_final: 0.8287 (mtm110) REVERT: C 144 ASP cc_start: 0.9172 (m-30) cc_final: 0.8716 (m-30) REVERT: C 205 MET cc_start: 0.8389 (mtm) cc_final: 0.7583 (tpt) REVERT: C 224 MET cc_start: 0.8635 (mmm) cc_final: 0.8193 (tmm) REVERT: C 302 ARG cc_start: 0.7050 (mtt90) cc_final: 0.6336 (mtt90) REVERT: C 379 ASN cc_start: 0.8760 (m-40) cc_final: 0.8477 (m-40) REVERT: C 452 GLN cc_start: 0.8811 (tp40) cc_final: 0.8091 (tp40) REVERT: D 31 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6762 (mmm160) REVERT: D 72 GLN cc_start: 0.8575 (mp10) cc_final: 0.8145 (mp10) REVERT: D 144 ASP cc_start: 0.8251 (m-30) cc_final: 0.7922 (m-30) REVERT: D 185 VAL cc_start: 0.9143 (m) cc_final: 0.8824 (p) REVERT: D 345 MET cc_start: 0.8555 (pmm) cc_final: 0.8297 (pmm) REVERT: D 426 ASN cc_start: 0.9411 (m-40) cc_final: 0.9158 (m110) REVERT: D 447 TYR cc_start: 0.8646 (t80) cc_final: 0.7882 (t80) REVERT: D 500 GLU cc_start: 0.9427 (tp30) cc_final: 0.9058 (tp30) outliers start: 54 outliers final: 52 residues processed: 532 average time/residue: 0.7378 time to fit residues: 560.4358 Evaluate side-chains 555 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 503 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 LYS 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 457 LEU 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 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 GLN 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 468 ASP Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 56 GLN 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 239 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 550 MET 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 249 GLN Chi-restraints excluded: chain D residue 316 LEU 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 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: 5.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128265 restraints weight = 136924.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132902 restraints weight = 65993.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136126 restraints weight = 39834.861| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.9366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17176 Z= 0.117 Angle : 0.579 7.835 23268 Z= 0.308 Chirality : 0.042 0.395 2584 Planarity : 0.005 0.097 3088 Dihedral : 4.352 19.443 2316 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.72 % Allowed : 24.61 % Favored : 72.67 % 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: 0.05 (0.18), residues: 2124 helix: 1.13 (0.19), residues: 756 sheet: -0.96 (0.22), residues: 490 loop : -0.18 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 331 HIS 0.004 0.001 HIS B 498 PHE 0.017 0.001 PHE D 394 TYR 0.013 0.001 TYR D 513 ARG 0.016 0.001 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 790) hydrogen bonds : angle 4.84853 ( 2316) covalent geometry : bond 0.00268 (17176) covalent geometry : angle 0.57905 (23268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13338.04 seconds wall clock time: 229 minutes 59.02 seconds (13799.02 seconds total)