Starting phenix.real_space_refine on Thu Sep 26 07:50:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ikc_60655/09_2024/9ikc_60655.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ikc_60655/09_2024/9ikc_60655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ikc_60655/09_2024/9ikc_60655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ikc_60655/09_2024/9ikc_60655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ikc_60655/09_2024/9ikc_60655.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ikc_60655/09_2024/9ikc_60655.cif" } resolution = 1.9 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= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 7878 2.51 5 N 2091 2.21 5 O 2508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12555 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4135 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 26, 'TRANS': 502} Chain: "B" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4135 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 26, 'TRANS': 502} Chain: "C" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4135 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 26, 'TRANS': 502} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Time building chain proxies: 8.84, per 1000 atoms: 0.70 Number of scatterers: 12555 At special positions: 0 Unit cell: (98.15, 98.8, 102.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2508 8.00 N 2091 7.00 C 7878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.7 seconds 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 33 sheets defined 20.4% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.544A pdb=" N SER A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 276 through 292 removed outlier: 3.795A pdb=" N ASP A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 455 through 464 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.548A pdb=" N SER B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 276 through 292 removed outlier: 3.748A pdb=" N ASP B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 455 through 465 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 512 through 517 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 183 through 186 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 276 through 292 removed outlier: 3.739A pdb=" N ASP C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 455 through 464 Processing helix chain 'C' and resid 491 through 495 Processing helix chain 'C' and resid 512 through 517 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 39 removed outlier: 3.914A pdb=" N ILE A 212 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN A 65 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 214 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N MET A 63 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE A 66 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 39 removed outlier: 3.914A pdb=" N ILE A 212 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN A 65 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 214 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N MET A 63 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 43 removed outlier: 6.863A pdb=" N ARG A 93 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 108 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 95 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A 106 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 97 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 236 removed outlier: 4.693A pdb=" N MET A 521 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE A 236 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG A 519 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 251 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 528 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS A 249 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.986A pdb=" N CYS A 249 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 528 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 251 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.451A pdb=" N ALA A 500 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 442 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 502 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET A 440 " --> pdb=" O ARG A 502 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 504 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE A 444 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AB1, first strand: chain 'A' and resid 317 through 320 removed outlier: 6.531A pdb=" N ASP A 324 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A 365 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE A 326 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG A 328 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR A 369 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP A 330 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A 362 " --> pdb=" O HIS A 383 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS A 383 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 364 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 381 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 366 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AB3, first strand: chain 'B' and resid 31 through 39 removed outlier: 3.908A pdb=" N ILE B 212 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASN B 65 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 214 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET B 63 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B 66 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 39 removed outlier: 3.908A pdb=" N ILE B 212 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASN B 65 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 214 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET B 63 " --> pdb=" O TYR B 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.842A pdb=" N ARG B 93 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER B 108 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 95 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU B 106 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 97 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB7, first strand: chain 'B' and resid 136 through 138 Processing sheet with id=AB8, first strand: chain 'B' and resid 224 through 233 removed outlier: 3.871A pdb=" N SER B 251 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 528 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS B 249 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 471 through 474 removed outlier: 6.974A pdb=" N CYS B 249 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 528 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 251 " --> pdb=" O ASN B 526 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.467A pdb=" N ALA B 500 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 442 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG B 502 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET B 440 " --> pdb=" O ARG B 502 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR B 504 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE B 444 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL B 448 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 293 through 296 Processing sheet with id=AC3, first strand: chain 'B' and resid 317 through 320 removed outlier: 6.535A pdb=" N ASP B 324 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE B 365 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE B 326 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLY B 367 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG B 328 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR B 369 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP B 330 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B 362 " --> pdb=" O HIS B 383 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS B 383 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 364 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 381 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 366 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AC5, first strand: chain 'C' and resid 31 through 39 removed outlier: 3.914A pdb=" N ILE C 212 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN C 65 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR C 214 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N MET C 63 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 66 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 31 through 39 removed outlier: 3.914A pdb=" N ILE C 212 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN C 65 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR C 214 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N MET C 63 " --> pdb=" O TYR C 214 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 41 through 43 removed outlier: 6.822A pdb=" N ARG C 93 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER C 108 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 95 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU C 106 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL C 97 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC9, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AD1, first strand: chain 'C' and resid 224 through 236 removed outlier: 4.615A pdb=" N MET C 521 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE C 236 " --> pdb=" O ARG C 519 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG C 519 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER C 251 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 528 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS C 249 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 471 through 474 removed outlier: 6.969A pdb=" N CYS C 249 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 528 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER C 251 " --> pdb=" O ASN C 526 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 240 through 243 removed outlier: 6.460A pdb=" N ALA C 500 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 442 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG C 502 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET C 440 " --> pdb=" O ARG C 502 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR C 504 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE C 444 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL C 448 " --> pdb=" O PHE C 444 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 293 through 296 Processing sheet with id=AD5, first strand: chain 'C' and resid 317 through 320 removed outlier: 6.581A pdb=" N ASP C 324 " --> pdb=" O SER C 363 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE C 365 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE C 326 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY C 367 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 328 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR C 369 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP C 330 " --> pdb=" O TYR C 369 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE C 362 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS C 383 " --> pdb=" O PHE C 362 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 364 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA C 381 " --> pdb=" O ALA C 364 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR C 366 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 346 through 347 518 hydrogen bonds defined for protein. 1308 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: 4.57 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4068 1.34 - 1.46: 2837 1.46 - 1.58: 5635 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 12669 Sorted by residual: bond pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CG ARG C 350 " pdb=" CD ARG C 350 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.76e-01 bond pdb=" CG ARG B 350 " pdb=" CD ARG B 350 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.40e-01 bond pdb=" CB GLU B 305 " pdb=" CG GLU B 305 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 3.98e-01 bond pdb=" CB ASN B 491 " pdb=" CG ASN B 491 " ideal model delta sigma weight residual 1.516 1.531 -0.015 2.50e-02 1.60e+03 3.80e-01 ... (remaining 12664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 16993 1.56 - 3.13: 198 3.13 - 4.69: 33 4.69 - 6.26: 4 6.26 - 7.82: 1 Bond angle restraints: 17229 Sorted by residual: angle pdb=" CB MET B 32 " pdb=" CG MET B 32 " pdb=" SD MET B 32 " ideal model delta sigma weight residual 112.70 120.52 -7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " pdb=" NE ARG A 350 " ideal model delta sigma weight residual 112.00 117.62 -5.62 2.20e+00 2.07e-01 6.52e+00 angle pdb=" C ASP B 262 " pdb=" N ALA B 263 " pdb=" CA ALA B 263 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.61e+00 angle pdb=" C ASP A 262 " pdb=" N ALA A 263 " pdb=" CA ALA A 263 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" C SER A 480 " pdb=" N THR A 481 " pdb=" CA THR A 481 " ideal model delta sigma weight residual 121.54 125.98 -4.44 1.91e+00 2.74e-01 5.41e+00 ... (remaining 17224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6912 17.98 - 35.96: 526 35.96 - 53.94: 144 53.94 - 71.92: 51 71.92 - 89.89: 20 Dihedral angle restraints: 7653 sinusoidal: 2973 harmonic: 4680 Sorted by residual: dihedral pdb=" CG ARG B 377 " pdb=" CD ARG B 377 " pdb=" NE ARG B 377 " pdb=" CZ ARG B 377 " ideal model delta sinusoidal sigma weight residual -90.00 -39.94 -50.06 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA ASP A 162 " pdb=" CB ASP A 162 " pdb=" CG ASP A 162 " pdb=" OD1 ASP A 162 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CB GLU C 131 " pdb=" CG GLU C 131 " pdb=" CD GLU C 131 " pdb=" OE1 GLU C 131 " ideal model delta sinusoidal sigma weight residual 0.00 -89.89 89.89 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1065 0.026 - 0.053: 528 0.053 - 0.079: 182 0.079 - 0.105: 138 0.105 - 0.131: 88 Chirality restraints: 2001 Sorted by residual: chirality pdb=" CA VAL A 189 " pdb=" N VAL A 189 " pdb=" C VAL A 189 " pdb=" CB VAL A 189 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE B 320 " pdb=" N ILE B 320 " pdb=" C ILE B 320 " pdb=" CB ILE B 320 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL C 189 " pdb=" N VAL C 189 " pdb=" C VAL C 189 " pdb=" CB VAL C 189 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1998 not shown) Planarity restraints: 2223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 332 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO B 333 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO C 333 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 350 " 0.131 9.50e-02 1.11e+02 5.91e-02 2.73e+00 pdb=" NE ARG A 350 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 350 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 350 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 350 " 0.000 2.00e-02 2.50e+03 ... (remaining 2220 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1469 2.76 - 3.29: 11990 3.29 - 3.83: 22434 3.83 - 4.36: 26887 4.36 - 4.90: 44579 Nonbonded interactions: 107359 Sorted by model distance: nonbonded pdb=" OH TYR C 356 " pdb=" OD1 ASP C 389 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 356 " pdb=" OD1 ASP A 389 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 356 " pdb=" OD1 ASP B 389 " model vdw 2.231 3.040 nonbonded pdb=" O MET C 123 " pdb=" OG SER C 126 " model vdw 2.244 3.040 nonbonded pdb=" O MET B 123 " pdb=" OG SER B 126 " model vdw 2.253 3.040 ... (remaining 107354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.970 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.002 0.035 12669 Z= 0.130 Angle : 0.474 7.820 17229 Z= 0.253 Chirality : 0.045 0.131 2001 Planarity : 0.004 0.059 2223 Dihedral : 15.818 89.894 4617 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.50 % Allowed : 13.48 % Favored : 86.02 % 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: 0.18 (0.20), residues: 1581 helix: -0.18 (0.31), residues: 273 sheet: 1.02 (0.23), residues: 450 loop : -0.20 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 397 HIS 0.002 0.001 HIS A 341 PHE 0.011 0.001 PHE B 326 TYR 0.011 0.001 TYR A 516 ARG 0.013 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 1.362 Fit side-chains REVERT: A 192 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: A 217 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7419 (tttm) REVERT: B 192 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6643 (pm20) REVERT: B 433 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7937 (mptp) REVERT: C 217 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7350 (tttm) REVERT: C 222 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7450 (mmm160) REVERT: C 232 ARG cc_start: 0.8787 (tpt170) cc_final: 0.8426 (tpt170) REVERT: C 351 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7393 (mmtm) outliers start: 7 outliers final: 2 residues processed: 231 average time/residue: 1.7273 time to fit residues: 423.6546 Evaluate side-chains 230 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 225 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 192 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12669 Z= 0.161 Angle : 0.525 10.535 17229 Z= 0.283 Chirality : 0.047 0.150 2001 Planarity : 0.004 0.039 2223 Dihedral : 5.036 39.170 1743 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.79 % Allowed : 11.33 % Favored : 87.89 % 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 (0.20), residues: 1581 helix: -0.12 (0.30), residues: 276 sheet: 0.95 (0.24), residues: 441 loop : -0.24 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.002 0.001 HIS A 341 PHE 0.011 0.001 PHE B 483 TYR 0.015 0.001 TYR A 516 ARG 0.007 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 227 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 217 LYS cc_start: 0.7631 (tttp) cc_final: 0.7330 (tttm) REVERT: B 120 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: B 509 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: C 217 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7376 (tttm) REVERT: C 232 ARG cc_start: 0.8778 (tpt170) cc_final: 0.8430 (tpt170) REVERT: C 351 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7417 (mmtm) outliers start: 11 outliers final: 4 residues processed: 233 average time/residue: 1.7021 time to fit residues: 421.6741 Evaluate side-chains 223 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 217 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 509 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12669 Z= 0.372 Angle : 0.691 12.281 17229 Z= 0.375 Chirality : 0.052 0.157 2001 Planarity : 0.005 0.045 2223 Dihedral : 5.244 33.793 1733 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.22 % Allowed : 11.04 % Favored : 87.74 % 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: -0.11 (0.20), residues: 1581 helix: -0.51 (0.29), residues: 270 sheet: 0.89 (0.23), residues: 435 loop : -0.37 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 105 HIS 0.005 0.002 HIS C 341 PHE 0.021 0.003 PHE A 419 TYR 0.020 0.003 TYR C 516 ARG 0.008 0.001 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 230 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 217 LYS cc_start: 0.7758 (tttp) cc_final: 0.7401 (tttm) REVERT: A 227 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: A 245 ASP cc_start: 0.8567 (m-30) cc_final: 0.8322 (m-30) REVERT: B 120 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: B 227 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: B 509 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: C 130 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7876 (ttp-170) REVERT: C 192 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: C 217 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7386 (tttm) REVERT: C 232 ARG cc_start: 0.8839 (tpt170) cc_final: 0.8485 (tpt170) REVERT: C 351 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7444 (mmtm) outliers start: 17 outliers final: 7 residues processed: 239 average time/residue: 1.6947 time to fit residues: 430.7330 Evaluate side-chains 233 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 220 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 334 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12669 Z= 0.232 Angle : 0.592 13.033 17229 Z= 0.319 Chirality : 0.049 0.156 2001 Planarity : 0.004 0.034 2223 Dihedral : 5.028 30.043 1733 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 10.82 % Favored : 87.60 % 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: -0.08 (0.20), residues: 1581 helix: -0.34 (0.29), residues: 270 sheet: 0.73 (0.23), residues: 441 loop : -0.30 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 105 HIS 0.003 0.001 HIS B 341 PHE 0.013 0.002 PHE B 483 TYR 0.016 0.002 TYR A 516 ARG 0.007 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6867 (pm20) REVERT: A 217 LYS cc_start: 0.7723 (tttp) cc_final: 0.7412 (tttm) REVERT: A 227 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: B 120 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: B 192 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: B 227 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: B 509 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: C 58 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7240 (pptt) REVERT: C 192 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: C 217 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7382 (tttm) REVERT: C 227 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: C 232 ARG cc_start: 0.8814 (tpt170) cc_final: 0.8463 (tpt170) REVERT: C 351 LYS cc_start: 0.7781 (mmmt) cc_final: 0.7438 (mmtm) outliers start: 22 outliers final: 7 residues processed: 236 average time/residue: 1.8423 time to fit residues: 460.7825 Evaluate side-chains 230 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.0370 chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12669 Z= 0.276 Angle : 0.626 13.042 17229 Z= 0.338 Chirality : 0.050 0.159 2001 Planarity : 0.005 0.037 2223 Dihedral : 5.131 31.066 1733 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.36 % Allowed : 11.33 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1581 helix: -0.45 (0.29), residues: 270 sheet: 0.71 (0.23), residues: 441 loop : -0.33 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 105 HIS 0.004 0.001 HIS C 341 PHE 0.016 0.002 PHE A 419 TYR 0.018 0.002 TYR C 516 ARG 0.009 0.001 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6873 (pm20) REVERT: A 217 LYS cc_start: 0.7735 (tttp) cc_final: 0.7379 (tttm) REVERT: A 227 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: A 245 ASP cc_start: 0.8555 (m-30) cc_final: 0.8309 (m-30) REVERT: B 120 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: B 192 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: B 509 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: C 58 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7232 (pptt) REVERT: C 192 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: C 217 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7368 (tttm) REVERT: C 227 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: C 232 ARG cc_start: 0.8825 (tpt170) cc_final: 0.8476 (tpt170) REVERT: C 502 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8076 (ttm110) outliers start: 19 outliers final: 7 residues processed: 229 average time/residue: 1.7612 time to fit residues: 428.0772 Evaluate side-chains 231 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 502 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12669 Z= 0.189 Angle : 0.560 13.502 17229 Z= 0.299 Chirality : 0.048 0.154 2001 Planarity : 0.004 0.036 2223 Dihedral : 4.872 27.654 1733 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.36 % Allowed : 11.25 % Favored : 87.38 % 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: -0.04 (0.20), residues: 1581 helix: -0.21 (0.30), residues: 270 sheet: 0.72 (0.24), residues: 441 loop : -0.29 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.001 PHE B 483 TYR 0.015 0.001 TYR A 516 ARG 0.008 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: A 217 LYS cc_start: 0.7707 (tttp) cc_final: 0.7421 (tttm) REVERT: A 245 ASP cc_start: 0.8556 (m-30) cc_final: 0.8304 (m-30) REVERT: B 120 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: B 192 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6978 (pm20) REVERT: B 509 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: C 58 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7211 (pptt) REVERT: C 217 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7341 (tttm) REVERT: C 227 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: C 232 ARG cc_start: 0.8792 (tpt170) cc_final: 0.8441 (tpt170) outliers start: 19 outliers final: 7 residues processed: 231 average time/residue: 1.7733 time to fit residues: 434.5959 Evaluate side-chains 228 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 215 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12669 Z= 0.200 Angle : 0.572 13.355 17229 Z= 0.305 Chirality : 0.048 0.155 2001 Planarity : 0.004 0.039 2223 Dihedral : 4.889 27.790 1733 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.22 % Allowed : 11.61 % Favored : 87.17 % 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: -0.03 (0.20), residues: 1581 helix: -0.19 (0.30), residues: 270 sheet: 0.71 (0.24), residues: 441 loop : -0.27 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 105 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.002 PHE B 483 TYR 0.015 0.001 TYR B 516 ARG 0.010 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: A 217 LYS cc_start: 0.7716 (tttp) cc_final: 0.7432 (tttm) REVERT: A 245 ASP cc_start: 0.8556 (m-30) cc_final: 0.8303 (m-30) REVERT: B 120 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: B 192 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6981 (pm20) REVERT: B 509 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: C 58 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7205 (pptt) REVERT: C 192 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: C 217 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7364 (tttm) REVERT: C 227 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: C 232 ARG cc_start: 0.8799 (tpt170) cc_final: 0.8447 (tpt170) outliers start: 17 outliers final: 7 residues processed: 226 average time/residue: 1.7816 time to fit residues: 427.4288 Evaluate side-chains 227 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12669 Z= 0.211 Angle : 0.585 13.265 17229 Z= 0.312 Chirality : 0.048 0.155 2001 Planarity : 0.004 0.047 2223 Dihedral : 4.927 28.322 1733 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.08 % Allowed : 11.54 % Favored : 87.38 % 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: -0.04 (0.20), residues: 1581 helix: -0.21 (0.30), residues: 270 sheet: 0.69 (0.24), residues: 441 loop : -0.27 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 105 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.002 PHE B 483 TYR 0.015 0.002 TYR B 516 ARG 0.014 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: A 217 LYS cc_start: 0.7723 (tttp) cc_final: 0.7438 (tttm) REVERT: A 245 ASP cc_start: 0.8551 (m-30) cc_final: 0.8310 (m-30) REVERT: B 120 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: B 192 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: B 509 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: C 58 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7205 (pptt) REVERT: C 192 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: C 217 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7373 (tttm) REVERT: C 227 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: C 232 ARG cc_start: 0.8804 (tpt170) cc_final: 0.8453 (tpt170) outliers start: 15 outliers final: 7 residues processed: 228 average time/residue: 1.8199 time to fit residues: 440.5944 Evaluate side-chains 231 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 217 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 0.0670 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12669 Z= 0.174 Angle : 0.556 13.489 17229 Z= 0.293 Chirality : 0.047 0.152 2001 Planarity : 0.004 0.053 2223 Dihedral : 4.751 25.414 1733 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.15 % Allowed : 11.68 % Favored : 87.17 % 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: -0.03 (0.20), residues: 1581 helix: -0.17 (0.30), residues: 276 sheet: 0.71 (0.24), residues: 441 loop : -0.28 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.003 0.001 HIS A 341 PHE 0.012 0.001 PHE B 483 TYR 0.014 0.001 TYR B 516 ARG 0.014 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: A 217 LYS cc_start: 0.7715 (tttp) cc_final: 0.7441 (tttm) REVERT: A 227 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: A 245 ASP cc_start: 0.8559 (m-30) cc_final: 0.8311 (m-30) REVERT: B 120 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: B 192 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: B 509 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: C 192 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6978 (pm20) REVERT: C 217 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7345 (tttm) REVERT: C 227 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: C 232 ARG cc_start: 0.8778 (tpt170) cc_final: 0.8430 (tpt170) outliers start: 16 outliers final: 7 residues processed: 226 average time/residue: 1.7746 time to fit residues: 425.2042 Evaluate side-chains 227 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12669 Z= 0.326 Angle : 0.681 12.883 17229 Z= 0.365 Chirality : 0.051 0.159 2001 Planarity : 0.005 0.053 2223 Dihedral : 5.228 32.954 1733 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.00 % Allowed : 11.97 % Favored : 87.03 % 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: -0.12 (0.20), residues: 1581 helix: -0.42 (0.29), residues: 270 sheet: 0.71 (0.23), residues: 441 loop : -0.31 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 105 HIS 0.004 0.001 HIS C 341 PHE 0.019 0.002 PHE A 419 TYR 0.018 0.002 TYR C 516 ARG 0.015 0.001 ARG A 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: A 217 LYS cc_start: 0.7744 (tttp) cc_final: 0.7442 (tttm) REVERT: A 245 ASP cc_start: 0.8555 (m-30) cc_final: 0.8321 (m-30) REVERT: B 120 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: B 192 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: B 509 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: C 192 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: C 217 LYS cc_start: 0.7755 (ttmt) cc_final: 0.7349 (tttm) REVERT: C 227 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: C 232 ARG cc_start: 0.8829 (tpt170) cc_final: 0.8478 (tpt170) outliers start: 14 outliers final: 6 residues processed: 228 average time/residue: 1.8106 time to fit residues: 438.1850 Evaluate side-chains 233 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 221 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116762 restraints weight = 9092.874| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.16 r_work: 0.3209 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12669 Z= 0.368 Angle : 0.716 12.872 17229 Z= 0.384 Chirality : 0.052 0.161 2001 Planarity : 0.005 0.059 2223 Dihedral : 5.327 32.628 1733 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.08 % Allowed : 12.04 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1581 helix: -0.64 (0.28), residues: 270 sheet: 0.71 (0.23), residues: 441 loop : -0.36 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 105 HIS 0.004 0.001 HIS A 152 PHE 0.020 0.003 PHE A 419 TYR 0.020 0.003 TYR C 516 ARG 0.016 0.001 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6929.27 seconds wall clock time: 120 minutes 55.84 seconds (7255.84 seconds total)