Starting phenix.real_space_refine on Tue Jul 29 10:40:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zn2_11309/07_2025/6zn2_11309.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zn2_11309/07_2025/6zn2_11309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zn2_11309/07_2025/6zn2_11309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zn2_11309/07_2025/6zn2_11309.map" model { file = "/net/cci-nas-00/data/ceres_data/6zn2_11309/07_2025/6zn2_11309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zn2_11309/07_2025/6zn2_11309.cif" } resolution = 4.3 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= 0.001 sd= 0.006 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 Fe 4 7.16 5 S 36 5.16 5 C 7192 2.51 5 N 1932 2.21 5 O 2156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11320 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 130 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, F, H, C, E, G Time building chain proxies: 5.64, per 1000 atoms: 0.50 Number of scatterers: 11320 At special positions: 0 Unit cell: (106.05, 87.15, 121.8, 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) Fe 4 26.01 S 36 16.00 O 2156 8.00 N 1932 7.00 C 7192 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: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 58.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.531A pdb=" N ASP A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.546A pdb=" N ARG A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 244 removed outlier: 3.608A pdb=" N ILE A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.698A pdb=" N LEU A 252 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.585A pdb=" N LYS A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.831A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.723A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.852A pdb=" N LEU A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 3.500A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 47 through 57 removed outlier: 4.174A pdb=" N ALA B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 removed outlier: 3.531A pdb=" N ASP C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 212 removed outlier: 3.546A pdb=" N ARG C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.608A pdb=" N ILE C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 removed outlier: 3.698A pdb=" N LEU C 252 " --> pdb=" O CYS C 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.586A pdb=" N LYS C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 removed outlier: 3.831A pdb=" N PHE C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 391 through 394 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.724A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 436 through 451 removed outlier: 3.852A pdb=" N LEU C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 496 removed outlier: 3.581A pdb=" N ARG C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLY C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 485 " --> pdb=" O GLY C 481 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU C 486 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 492 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 496 " --> pdb=" O ALA C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 47 through 57 removed outlier: 4.174A pdb=" N ALA D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 180 removed outlier: 3.531A pdb=" N ASP E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.545A pdb=" N ARG E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 244 removed outlier: 3.608A pdb=" N ILE E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 262 removed outlier: 3.699A pdb=" N LEU E 252 " --> pdb=" O CYS E 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 283 removed outlier: 3.585A pdb=" N LYS E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 305 removed outlier: 3.832A pdb=" N PHE E 299 " --> pdb=" O SER E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 341 through 355 Processing helix chain 'E' and resid 359 through 374 Processing helix chain 'E' and resid 391 through 394 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.722A pdb=" N LEU E 403 " --> pdb=" O LEU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'E' and resid 436 through 451 removed outlier: 3.852A pdb=" N LEU E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 496 removed outlier: 3.582A pdb=" N ARG E 477 " --> pdb=" O GLN E 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY E 481 " --> pdb=" O ARG E 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 485 " --> pdb=" O GLY E 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 486 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA E 490 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS E 491 " --> pdb=" O ASP E 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 492 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 496 " --> pdb=" O ALA E 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 47 through 57 removed outlier: 4.174A pdb=" N ALA F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.530A pdb=" N ASP G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 212 removed outlier: 3.546A pdb=" N ARG G 200 " --> pdb=" O ASP G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 244 removed outlier: 3.608A pdb=" N ILE G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 262 removed outlier: 3.698A pdb=" N LEU G 252 " --> pdb=" O CYS G 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU G 253 " --> pdb=" O GLY G 249 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 283 removed outlier: 3.585A pdb=" N LYS G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 305 removed outlier: 3.831A pdb=" N PHE G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 335 Processing helix chain 'G' and resid 341 through 355 Processing helix chain 'G' and resid 359 through 374 Processing helix chain 'G' and resid 391 through 394 Processing helix chain 'G' and resid 395 through 403 removed outlier: 3.724A pdb=" N LEU G 403 " --> pdb=" O LEU G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 418 Processing helix chain 'G' and resid 436 through 451 removed outlier: 3.852A pdb=" N LEU G 444 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 496 removed outlier: 3.500A pdb=" N VAL G 475 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG G 477 " --> pdb=" O GLN G 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER G 478 " --> pdb=" O ALA G 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY G 481 " --> pdb=" O ARG G 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 486 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA G 490 " --> pdb=" O LEU G 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS G 491 " --> pdb=" O ASP G 487 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 492 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 496 " --> pdb=" O ALA G 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 47 through 57 removed outlier: 4.174A pdb=" N ALA H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.156A pdb=" N GLN A 286 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS A 310 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ARG A 288 " --> pdb=" O CYS A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 387 removed outlier: 6.219A pdb=" N LEU A 378 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS A 458 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 286 through 289 removed outlier: 6.157A pdb=" N GLN C 286 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS C 310 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ARG C 288 " --> pdb=" O CYS C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 385 through 387 removed outlier: 6.220A pdb=" N LEU C 378 " --> pdb=" O SER C 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS C 458 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 286 through 289 removed outlier: 6.156A pdb=" N GLN E 286 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS E 310 " --> pdb=" O GLN E 286 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ARG E 288 " --> pdb=" O CYS E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 385 through 387 removed outlier: 6.220A pdb=" N LEU E 378 " --> pdb=" O SER E 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS E 458 " --> pdb=" O ASP E 467 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 286 through 289 removed outlier: 6.156A pdb=" N GLN G 286 " --> pdb=" O PHE G 308 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS G 310 " --> pdb=" O GLN G 286 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ARG G 288 " --> pdb=" O CYS G 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 385 through 387 removed outlier: 6.220A pdb=" N LEU G 378 " --> pdb=" O SER G 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS G 458 " --> pdb=" O ASP G 467 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1494 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: 3.54 Time building geometry restraints manager: 3.31 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: 3772 1.34 - 1.46: 2157 1.46 - 1.58: 5615 1.58 - 1.69: 4 1.69 - 1.81: 44 Bond restraints: 11592 Sorted by residual: bond pdb=" CB ASN A 268 " pdb=" CG ASN A 268 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.46e+00 bond pdb=" C3 LDP G 501 " pdb=" O1 LDP G 501 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" CB ASN C 268 " pdb=" CG ASN C 268 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.42e+00 bond pdb=" CB ASN G 268 " pdb=" CG ASN G 268 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.39e+00 bond pdb=" CB ASN E 268 " pdb=" CG ASN E 268 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.38e+00 ... (remaining 11587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 15411 2.87 - 5.74: 245 5.74 - 8.62: 34 8.62 - 11.49: 14 11.49 - 14.36: 8 Bond angle restraints: 15712 Sorted by residual: angle pdb=" CA GLU C 227 " pdb=" CB GLU C 227 " pdb=" CG GLU C 227 " ideal model delta sigma weight residual 114.10 126.90 -12.80 2.00e+00 2.50e-01 4.10e+01 angle pdb=" CA GLU A 227 " pdb=" CB GLU A 227 " pdb=" CG GLU A 227 " ideal model delta sigma weight residual 114.10 126.87 -12.77 2.00e+00 2.50e-01 4.08e+01 angle pdb=" CA GLU G 227 " pdb=" CB GLU G 227 " pdb=" CG GLU G 227 " ideal model delta sigma weight residual 114.10 126.86 -12.76 2.00e+00 2.50e-01 4.07e+01 angle pdb=" CA GLU E 227 " pdb=" CB GLU E 227 " pdb=" CG GLU E 227 " ideal model delta sigma weight residual 114.10 126.85 -12.75 2.00e+00 2.50e-01 4.06e+01 angle pdb=" CA GLU C 480 " pdb=" CB GLU C 480 " pdb=" CG GLU C 480 " ideal model delta sigma weight residual 114.10 125.06 -10.96 2.00e+00 2.50e-01 3.01e+01 ... (remaining 15707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 5973 14.66 - 29.33: 650 29.33 - 43.99: 229 43.99 - 58.65: 80 58.65 - 73.31: 8 Dihedral angle restraints: 6940 sinusoidal: 2788 harmonic: 4152 Sorted by residual: dihedral pdb=" CA GLU D 48 " pdb=" C GLU D 48 " pdb=" N ARG D 49 " pdb=" CA ARG D 49 " ideal model delta harmonic sigma weight residual -180.00 -150.76 -29.24 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLU F 48 " pdb=" C GLU F 48 " pdb=" N ARG F 49 " pdb=" CA ARG F 49 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLU B 48 " pdb=" C GLU B 48 " pdb=" N ARG B 49 " pdb=" CA ARG B 49 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 6937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1113 0.038 - 0.076: 426 0.076 - 0.114: 119 0.114 - 0.152: 22 0.152 - 0.190: 4 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CB VAL C 275 " pdb=" CA VAL C 275 " pdb=" CG1 VAL C 275 " pdb=" CG2 VAL C 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CB VAL A 275 " pdb=" CA VAL A 275 " pdb=" CG1 VAL A 275 " pdb=" CG2 VAL A 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CB VAL E 275 " pdb=" CA VAL E 275 " pdb=" CG1 VAL E 275 " pdb=" CG2 VAL E 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 1681 not shown) Planarity restraints: 2068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 477 " 0.166 9.50e-02 1.11e+02 7.48e-02 3.71e+00 pdb=" NE ARG A 477 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 477 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 477 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 477 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 477 " -0.165 9.50e-02 1.11e+02 7.44e-02 3.69e+00 pdb=" NE ARG G 477 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 477 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 477 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 477 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 477 " 0.166 9.50e-02 1.11e+02 7.47e-02 3.69e+00 pdb=" NE ARG E 477 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 477 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 477 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 477 " 0.009 2.00e-02 2.50e+03 ... (remaining 2065 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 307 2.58 - 3.16: 10413 3.16 - 3.74: 19762 3.74 - 4.32: 26200 4.32 - 4.90: 39927 Nonbonded interactions: 96609 Sorted by model distance: nonbonded pdb=" N GLU E 480 " pdb=" OE1 GLU E 480 " model vdw 2.001 3.120 nonbonded pdb=" N GLU C 480 " pdb=" OE1 GLU C 480 " model vdw 2.001 3.120 nonbonded pdb=" N GLU A 480 " pdb=" OE1 GLU A 480 " model vdw 2.001 3.120 nonbonded pdb=" N GLU G 480 " pdb=" OE1 GLU G 480 " model vdw 2.002 3.120 nonbonded pdb=" N GLU A 227 " pdb=" OE1 GLU A 227 " model vdw 2.025 3.120 ... (remaining 96604 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: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.420 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.004 0.067 11592 Z= 0.182 Angle : 0.929 14.360 15712 Z= 0.492 Chirality : 0.043 0.190 1684 Planarity : 0.005 0.075 2068 Dihedral : 15.059 73.314 4252 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.35 % Allowed : 3.01 % Favored : 90.64 % 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: -1.42 (0.22), residues: 1396 helix: -0.86 (0.20), residues: 632 sheet: -1.08 (0.43), residues: 160 loop : -0.78 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 371 HIS 0.006 0.001 HIS E 491 PHE 0.024 0.001 PHE C 344 TYR 0.009 0.001 TYR C 243 ARG 0.010 0.001 ARG G 477 Details of bonding type rmsd hydrogen bonds : bond 0.32640 ( 510) hydrogen bonds : angle 9.39496 ( 1494) covalent geometry : bond 0.00402 (11592) covalent geometry : angle 0.92922 (15712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 569 time to evaluate : 1.311 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: A 169 LYS cc_start: 0.8656 (mppt) cc_final: 0.8178 (mtpt) REVERT: A 172 GLU cc_start: 0.9163 (pm20) cc_final: 0.8688 (pm20) REVERT: A 186 ASP cc_start: 0.7957 (t0) cc_final: 0.7629 (t0) REVERT: A 208 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9058 (mm-30) REVERT: A 212 GLN cc_start: 0.9353 (pt0) cc_final: 0.9133 (tp40) REVERT: A 242 LEU cc_start: 0.9414 (tp) cc_final: 0.9120 (pp) REVERT: A 341 ASP cc_start: 0.8499 (t0) cc_final: 0.7841 (p0) REVERT: A 379 CYS cc_start: 0.9387 (p) cc_final: 0.9084 (p) REVERT: A 393 LEU cc_start: 0.9209 (mp) cc_final: 0.8580 (mp) REVERT: A 413 ASP cc_start: 0.9513 (t0) cc_final: 0.9236 (t0) REVERT: C 182 LYS cc_start: 0.8687 (pttm) cc_final: 0.8467 (ptpp) REVERT: C 186 ASP cc_start: 0.7997 (t0) cc_final: 0.7650 (t0) REVERT: C 212 GLN cc_start: 0.9385 (pt0) cc_final: 0.9178 (tp40) REVERT: C 242 LEU cc_start: 0.9357 (tp) cc_final: 0.9100 (pp) REVERT: C 243 TYR cc_start: 0.9285 (m-10) cc_final: 0.9077 (m-10) REVERT: C 269 ILE cc_start: 0.8196 (tt) cc_final: 0.7979 (tt) REVERT: C 338 MET cc_start: 0.9048 (mmp) cc_final: 0.8792 (mmp) REVERT: C 341 ASP cc_start: 0.8435 (t0) cc_final: 0.7990 (p0) REVERT: C 393 LEU cc_start: 0.9148 (mp) cc_final: 0.8546 (mp) REVERT: C 463 THR cc_start: 0.8345 (t) cc_final: 0.8060 (t) REVERT: E 182 LYS cc_start: 0.8540 (pttm) cc_final: 0.8299 (ptpp) REVERT: E 186 ASP cc_start: 0.7914 (t0) cc_final: 0.7574 (t0) REVERT: E 212 GLN cc_start: 0.9379 (pt0) cc_final: 0.9173 (tp40) REVERT: E 242 LEU cc_start: 0.9378 (tp) cc_final: 0.9091 (pp) REVERT: E 338 MET cc_start: 0.8688 (mmp) cc_final: 0.8296 (mmp) REVERT: E 341 ASP cc_start: 0.8472 (t0) cc_final: 0.7992 (p0) REVERT: E 349 GLN cc_start: 0.9236 (tt0) cc_final: 0.8929 (tt0) REVERT: E 393 LEU cc_start: 0.9132 (mp) cc_final: 0.8610 (mp) REVERT: E 463 THR cc_start: 0.8166 (t) cc_final: 0.7911 (t) REVERT: G 186 ASP cc_start: 0.7918 (t0) cc_final: 0.7616 (t0) REVERT: G 212 GLN cc_start: 0.9366 (pt0) cc_final: 0.9154 (tp40) REVERT: G 242 LEU cc_start: 0.9361 (tp) cc_final: 0.9111 (pp) REVERT: G 341 ASP cc_start: 0.8458 (t0) cc_final: 0.8061 (p0) REVERT: G 393 LEU cc_start: 0.9184 (mp) cc_final: 0.8563 (mp) outliers start: 76 outliers final: 33 residues processed: 609 average time/residue: 0.2851 time to fit residues: 230.5763 Evaluate side-chains 458 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 425 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN C 491 HIS ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN ** E 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 GLN G 491 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.120043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091328 restraints weight = 25711.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094839 restraints weight = 17189.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097432 restraints weight = 12574.352| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11592 Z= 0.295 Angle : 0.864 11.000 15712 Z= 0.451 Chirality : 0.049 0.175 1684 Planarity : 0.006 0.059 2068 Dihedral : 5.332 24.854 1568 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.67 % Allowed : 5.69 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.22), residues: 1396 helix: -1.52 (0.16), residues: 780 sheet: -1.01 (0.51), residues: 128 loop : -0.67 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP C 371 HIS 0.014 0.003 HIS A 251 PHE 0.023 0.002 PHE E 412 TYR 0.021 0.003 TYR C 264 ARG 0.012 0.001 ARG H 49 Details of bonding type rmsd hydrogen bonds : bond 0.06744 ( 510) hydrogen bonds : angle 6.58172 ( 1494) covalent geometry : bond 0.00600 (11592) covalent geometry : angle 0.86366 (15712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 500 time to evaluate : 1.305 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: A 172 GLU cc_start: 0.8588 (pm20) cc_final: 0.8172 (pm20) REVERT: A 175 LYS cc_start: 0.8063 (pptt) cc_final: 0.7812 (tttt) REVERT: A 184 ASP cc_start: 0.8278 (m-30) cc_final: 0.8076 (m-30) REVERT: A 186 ASP cc_start: 0.8162 (t0) cc_final: 0.7842 (t0) REVERT: A 208 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 236 TYR cc_start: 0.8502 (t80) cc_final: 0.8177 (t80) REVERT: A 239 LEU cc_start: 0.8324 (pp) cc_final: 0.7830 (pp) REVERT: A 251 HIS cc_start: 0.6532 (m170) cc_final: 0.6316 (m-70) REVERT: A 308 PHE cc_start: 0.8597 (t80) cc_final: 0.8187 (t80) REVERT: A 331 GLU cc_start: 0.8532 (pt0) cc_final: 0.8119 (pt0) REVERT: A 338 MET cc_start: 0.7629 (mmp) cc_final: 0.7012 (mmp) REVERT: A 341 ASP cc_start: 0.8682 (t0) cc_final: 0.7878 (p0) REVERT: A 347 PHE cc_start: 0.8961 (t80) cc_final: 0.8713 (t80) REVERT: A 369 LEU cc_start: 0.8980 (mm) cc_final: 0.8592 (mm) REVERT: A 379 CYS cc_start: 0.7042 (p) cc_final: 0.6341 (p) REVERT: A 392 LEU cc_start: 0.9392 (mt) cc_final: 0.8989 (mt) REVERT: A 393 LEU cc_start: 0.8854 (mp) cc_final: 0.8466 (mp) REVERT: A 413 ASP cc_start: 0.9367 (t0) cc_final: 0.9030 (t0) REVERT: C 175 LYS cc_start: 0.8141 (pptt) cc_final: 0.7717 (tttt) REVERT: C 186 ASP cc_start: 0.8095 (t0) cc_final: 0.7844 (t0) REVERT: C 239 LEU cc_start: 0.8404 (pp) cc_final: 0.7879 (pp) REVERT: C 246 HIS cc_start: 0.8646 (m-70) cc_final: 0.7696 (m170) REVERT: C 251 HIS cc_start: 0.6966 (m-70) cc_final: 0.6666 (m-70) REVERT: C 308 PHE cc_start: 0.8675 (t80) cc_final: 0.8250 (t80) REVERT: C 338 MET cc_start: 0.7587 (mmp) cc_final: 0.7145 (mmp) REVERT: C 339 LEU cc_start: 0.9191 (pp) cc_final: 0.8793 (pp) REVERT: C 341 ASP cc_start: 0.8887 (t0) cc_final: 0.7843 (p0) REVERT: C 347 PHE cc_start: 0.8887 (t80) cc_final: 0.8478 (t80) REVERT: C 351 ILE cc_start: 0.9087 (mp) cc_final: 0.8860 (mp) REVERT: C 360 ASP cc_start: 0.9197 (m-30) cc_final: 0.8725 (p0) REVERT: C 361 GLU cc_start: 0.9337 (tp30) cc_final: 0.8935 (tp30) REVERT: C 369 LEU cc_start: 0.8892 (mm) cc_final: 0.8479 (mm) REVERT: C 393 LEU cc_start: 0.8990 (mp) cc_final: 0.8559 (mp) REVERT: C 453 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7858 (ttm110) REVERT: C 485 GLU cc_start: 0.9080 (mp0) cc_final: 0.8814 (mp0) REVERT: E 175 LYS cc_start: 0.8100 (pptt) cc_final: 0.7708 (tttt) REVERT: E 186 ASP cc_start: 0.8044 (t0) cc_final: 0.7784 (t0) REVERT: E 211 PHE cc_start: 0.8549 (t80) cc_final: 0.8208 (t80) REVERT: E 239 LEU cc_start: 0.8294 (pp) cc_final: 0.7734 (pp) REVERT: E 246 HIS cc_start: 0.8642 (m-70) cc_final: 0.7678 (m170) REVERT: E 255 PHE cc_start: 0.9194 (t80) cc_final: 0.8863 (t80) REVERT: E 273 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7760 (mm-30) REVERT: E 276 SER cc_start: 0.9104 (m) cc_final: 0.8839 (p) REVERT: E 308 PHE cc_start: 0.8621 (t80) cc_final: 0.8209 (t80) REVERT: E 339 LEU cc_start: 0.9196 (pp) cc_final: 0.8779 (pp) REVERT: E 341 ASP cc_start: 0.8888 (t0) cc_final: 0.7990 (p0) REVERT: E 347 PHE cc_start: 0.8951 (t80) cc_final: 0.8624 (t80) REVERT: E 361 GLU cc_start: 0.9393 (tp30) cc_final: 0.8888 (tm-30) REVERT: E 362 GLU cc_start: 0.8991 (mp0) cc_final: 0.8597 (mp0) REVERT: E 369 LEU cc_start: 0.8989 (mm) cc_final: 0.8531 (mm) REVERT: E 393 LEU cc_start: 0.8967 (mp) cc_final: 0.8544 (mp) REVERT: E 415 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8275 (mp0) REVERT: E 485 GLU cc_start: 0.8957 (mp0) cc_final: 0.8708 (mp0) REVERT: E 487 ASP cc_start: 0.8729 (m-30) cc_final: 0.8523 (m-30) REVERT: G 172 GLU cc_start: 0.8732 (pm20) cc_final: 0.8256 (pm20) REVERT: G 175 LYS cc_start: 0.8095 (pptt) cc_final: 0.7732 (tttt) REVERT: G 184 ASP cc_start: 0.8228 (m-30) cc_final: 0.8018 (m-30) REVERT: G 186 ASP cc_start: 0.8101 (t0) cc_final: 0.7812 (t0) REVERT: G 219 ILE cc_start: 0.8803 (mt) cc_final: 0.8500 (mm) REVERT: G 239 LEU cc_start: 0.8271 (pp) cc_final: 0.7749 (pp) REVERT: G 240 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8465 (mtpp) REVERT: G 242 LEU cc_start: 0.8875 (tp) cc_final: 0.8659 (pp) REVERT: G 246 HIS cc_start: 0.8643 (m-70) cc_final: 0.7718 (m170) REVERT: G 251 HIS cc_start: 0.6845 (m-70) cc_final: 0.6640 (m-70) REVERT: G 273 GLU cc_start: 0.7997 (tp30) cc_final: 0.7406 (tp30) REVERT: G 308 PHE cc_start: 0.8671 (t80) cc_final: 0.8416 (t80) REVERT: G 310 CYS cc_start: 0.8545 (p) cc_final: 0.8093 (p) REVERT: G 331 GLU cc_start: 0.8517 (pt0) cc_final: 0.8057 (mp0) REVERT: G 339 LEU cc_start: 0.9141 (pp) cc_final: 0.8809 (pp) REVERT: G 341 ASP cc_start: 0.8854 (t0) cc_final: 0.8306 (p0) REVERT: G 347 PHE cc_start: 0.8817 (t80) cc_final: 0.8338 (t80) REVERT: G 360 ASP cc_start: 0.9259 (m-30) cc_final: 0.8872 (p0) REVERT: G 369 LEU cc_start: 0.8958 (mm) cc_final: 0.8553 (mm) REVERT: G 393 LEU cc_start: 0.8947 (mp) cc_final: 0.8560 (mp) REVERT: G 460 ASP cc_start: 0.9115 (t0) cc_final: 0.8908 (t0) REVERT: G 479 LEU cc_start: 0.8251 (mt) cc_final: 0.7984 (mt) outliers start: 8 outliers final: 3 residues processed: 501 average time/residue: 0.2613 time to fit residues: 177.4319 Evaluate side-chains 406 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 403 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 133 optimal weight: 0.0070 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 ASN G 178 HIS ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 382 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.122304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092672 restraints weight = 25769.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.096544 restraints weight = 16997.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099407 restraints weight = 12291.292| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11592 Z= 0.206 Angle : 0.752 7.958 15712 Z= 0.391 Chirality : 0.046 0.165 1684 Planarity : 0.005 0.042 2068 Dihedral : 5.303 27.526 1568 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.42 % Allowed : 4.93 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1396 helix: -1.25 (0.17), residues: 776 sheet: -0.98 (0.48), residues: 136 loop : -0.94 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP G 371 HIS 0.012 0.002 HIS C 401 PHE 0.029 0.002 PHE A 372 TYR 0.019 0.002 TYR A 213 ARG 0.007 0.001 ARG C 297 Details of bonding type rmsd hydrogen bonds : bond 0.05525 ( 510) hydrogen bonds : angle 6.14451 ( 1494) covalent geometry : bond 0.00432 (11592) covalent geometry : angle 0.75187 (15712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 471 time to evaluate : 1.163 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: A 175 LYS cc_start: 0.8150 (pptt) cc_final: 0.7829 (tttt) REVERT: A 184 ASP cc_start: 0.8447 (m-30) cc_final: 0.8160 (m-30) REVERT: A 186 ASP cc_start: 0.8236 (t0) cc_final: 0.7898 (t0) REVERT: A 239 LEU cc_start: 0.8591 (pp) cc_final: 0.7624 (pp) REVERT: A 267 ASP cc_start: 0.8983 (p0) cc_final: 0.8040 (p0) REVERT: A 308 PHE cc_start: 0.8618 (t80) cc_final: 0.8025 (t80) REVERT: A 338 MET cc_start: 0.7786 (mmp) cc_final: 0.7428 (mmp) REVERT: A 341 ASP cc_start: 0.8634 (t0) cc_final: 0.8069 (p0) REVERT: A 347 PHE cc_start: 0.8964 (t80) cc_final: 0.8634 (t80) REVERT: A 349 GLN cc_start: 0.8881 (tt0) cc_final: 0.8463 (tt0) REVERT: A 361 GLU cc_start: 0.9418 (tp30) cc_final: 0.9089 (tm-30) REVERT: A 362 GLU cc_start: 0.9086 (mp0) cc_final: 0.8805 (mp0) REVERT: A 369 LEU cc_start: 0.9061 (mm) cc_final: 0.8689 (mm) REVERT: A 393 LEU cc_start: 0.8827 (mp) cc_final: 0.8448 (mp) REVERT: A 413 ASP cc_start: 0.9355 (t0) cc_final: 0.8989 (t0) REVERT: A 456 SER cc_start: 0.8370 (t) cc_final: 0.8167 (t) REVERT: C 174 ASP cc_start: 0.7946 (t70) cc_final: 0.7710 (t0) REVERT: C 175 LYS cc_start: 0.8040 (pptt) cc_final: 0.7622 (tttt) REVERT: C 184 ASP cc_start: 0.8287 (m-30) cc_final: 0.8057 (m-30) REVERT: C 186 ASP cc_start: 0.8157 (t0) cc_final: 0.7843 (t0) REVERT: C 239 LEU cc_start: 0.8650 (pp) cc_final: 0.7597 (pp) REVERT: C 246 HIS cc_start: 0.8589 (m-70) cc_final: 0.7591 (m170) REVERT: C 251 HIS cc_start: 0.7221 (m-70) cc_final: 0.6657 (m-70) REVERT: C 255 PHE cc_start: 0.9047 (t80) cc_final: 0.8816 (t80) REVERT: C 267 ASP cc_start: 0.9046 (p0) cc_final: 0.8430 (p0) REVERT: C 297 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8490 (tpp-160) REVERT: C 308 PHE cc_start: 0.8579 (t80) cc_final: 0.8163 (t80) REVERT: C 313 TYR cc_start: 0.8498 (p90) cc_final: 0.8260 (p90) REVERT: C 341 ASP cc_start: 0.8834 (t0) cc_final: 0.7909 (p0) REVERT: C 347 PHE cc_start: 0.8752 (t80) cc_final: 0.8442 (t80) REVERT: C 351 ILE cc_start: 0.9063 (mp) cc_final: 0.8859 (mp) REVERT: C 360 ASP cc_start: 0.9010 (m-30) cc_final: 0.8680 (p0) REVERT: C 361 GLU cc_start: 0.9285 (tp30) cc_final: 0.8750 (tm-30) REVERT: C 369 LEU cc_start: 0.8993 (mm) cc_final: 0.8520 (mm) REVERT: C 393 LEU cc_start: 0.8862 (mp) cc_final: 0.8450 (mp) REVERT: E 175 LYS cc_start: 0.8064 (pptt) cc_final: 0.7663 (tttt) REVERT: E 184 ASP cc_start: 0.8278 (m-30) cc_final: 0.8041 (m-30) REVERT: E 186 ASP cc_start: 0.8074 (t0) cc_final: 0.7761 (t0) REVERT: E 239 LEU cc_start: 0.8584 (pp) cc_final: 0.7568 (pp) REVERT: E 246 HIS cc_start: 0.8554 (m-70) cc_final: 0.7557 (m170) REVERT: E 267 ASP cc_start: 0.9010 (p0) cc_final: 0.8398 (p0) REVERT: E 276 SER cc_start: 0.9115 (m) cc_final: 0.8818 (p) REVERT: E 308 PHE cc_start: 0.8565 (t80) cc_final: 0.8083 (t80) REVERT: E 313 TYR cc_start: 0.8543 (p90) cc_final: 0.8333 (p90) REVERT: E 341 ASP cc_start: 0.8812 (t0) cc_final: 0.7897 (p0) REVERT: E 347 PHE cc_start: 0.8921 (t80) cc_final: 0.8537 (t80) REVERT: E 349 GLN cc_start: 0.9057 (tt0) cc_final: 0.8467 (tt0) REVERT: E 361 GLU cc_start: 0.9298 (tp30) cc_final: 0.8973 (tm-30) REVERT: E 362 GLU cc_start: 0.9116 (mp0) cc_final: 0.8793 (mp0) REVERT: E 364 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9109 (mt-10) REVERT: E 369 LEU cc_start: 0.9052 (mm) cc_final: 0.8534 (mm) REVERT: E 393 LEU cc_start: 0.8842 (mp) cc_final: 0.8393 (mp) REVERT: E 450 ARG cc_start: 0.8941 (mtt90) cc_final: 0.8700 (ttm110) REVERT: E 456 SER cc_start: 0.8449 (t) cc_final: 0.8240 (t) REVERT: E 487 ASP cc_start: 0.8755 (m-30) cc_final: 0.8527 (m-30) REVERT: G 166 PHE cc_start: 0.9191 (p90) cc_final: 0.8975 (p90) REVERT: G 175 LYS cc_start: 0.8118 (pptt) cc_final: 0.7744 (tttt) REVERT: G 184 ASP cc_start: 0.8369 (m-30) cc_final: 0.8092 (m-30) REVERT: G 186 ASP cc_start: 0.8172 (t0) cc_final: 0.7830 (t0) REVERT: G 239 LEU cc_start: 0.8265 (pp) cc_final: 0.7554 (pp) REVERT: G 246 HIS cc_start: 0.8564 (m-70) cc_final: 0.7597 (m170) REVERT: G 251 HIS cc_start: 0.7089 (m-70) cc_final: 0.6784 (m-70) REVERT: G 267 ASP cc_start: 0.8995 (p0) cc_final: 0.8346 (p0) REVERT: G 268 ASN cc_start: 0.8822 (p0) cc_final: 0.8143 (p0) REVERT: G 308 PHE cc_start: 0.8603 (t80) cc_final: 0.8201 (t80) REVERT: G 310 CYS cc_start: 0.8621 (p) cc_final: 0.8388 (p) REVERT: G 338 MET cc_start: 0.7706 (mmp) cc_final: 0.7286 (mmp) REVERT: G 341 ASP cc_start: 0.8808 (t0) cc_final: 0.7957 (p0) REVERT: G 347 PHE cc_start: 0.8938 (t80) cc_final: 0.8375 (t80) REVERT: G 350 ASP cc_start: 0.8321 (m-30) cc_final: 0.8104 (m-30) REVERT: G 361 GLU cc_start: 0.9245 (tp30) cc_final: 0.8823 (tm-30) REVERT: G 362 GLU cc_start: 0.9101 (mp0) cc_final: 0.8825 (mp0) REVERT: G 364 GLU cc_start: 0.9393 (mt-10) cc_final: 0.9116 (mt-10) REVERT: G 369 LEU cc_start: 0.8999 (mm) cc_final: 0.8593 (mm) REVERT: G 393 LEU cc_start: 0.8788 (mp) cc_final: 0.8443 (mp) REVERT: G 450 ARG cc_start: 0.8989 (mtt90) cc_final: 0.8709 (ttm110) REVERT: G 456 SER cc_start: 0.8347 (t) cc_final: 0.8110 (t) REVERT: H 48 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7791 (tp30) outliers start: 5 outliers final: 1 residues processed: 473 average time/residue: 0.3135 time to fit residues: 206.1668 Evaluate side-chains 421 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 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 = 0.3879 r_free = 0.3879 target = 0.118880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090208 restraints weight = 26010.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.094023 restraints weight = 16900.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.096829 restraints weight = 12126.732| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11592 Z= 0.241 Angle : 0.760 7.652 15712 Z= 0.401 Chirality : 0.047 0.198 1684 Planarity : 0.006 0.046 2068 Dihedral : 5.498 31.315 1568 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.42 % Allowed : 4.77 % Favored : 94.82 % 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: -1.94 (0.21), residues: 1396 helix: -1.23 (0.17), residues: 788 sheet: -0.69 (0.55), residues: 96 loop : -1.20 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 371 HIS 0.012 0.002 HIS G 401 PHE 0.021 0.002 PHE A 372 TYR 0.021 0.002 TYR C 236 ARG 0.010 0.001 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 510) hydrogen bonds : angle 6.21239 ( 1494) covalent geometry : bond 0.00495 (11592) covalent geometry : angle 0.76008 (15712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 472 time to evaluate : 1.272 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: A 175 LYS cc_start: 0.8265 (pptt) cc_final: 0.8025 (tttt) REVERT: A 184 ASP cc_start: 0.8377 (m-30) cc_final: 0.8108 (m-30) REVERT: A 186 ASP cc_start: 0.8121 (t0) cc_final: 0.7829 (t0) REVERT: A 221 ARG cc_start: 0.8274 (mmt90) cc_final: 0.8069 (mmm-85) REVERT: A 239 LEU cc_start: 0.8592 (pp) cc_final: 0.7678 (pp) REVERT: A 255 PHE cc_start: 0.9247 (t80) cc_final: 0.9020 (t80) REVERT: A 297 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7888 (mmt90) REVERT: A 308 PHE cc_start: 0.8681 (t80) cc_final: 0.7935 (t80) REVERT: A 313 TYR cc_start: 0.8616 (p90) cc_final: 0.8349 (p90) REVERT: A 331 GLU cc_start: 0.8545 (pt0) cc_final: 0.8091 (pt0) REVERT: A 338 MET cc_start: 0.8031 (mmp) cc_final: 0.7607 (mmp) REVERT: A 341 ASP cc_start: 0.8700 (t0) cc_final: 0.8112 (p0) REVERT: A 347 PHE cc_start: 0.9040 (t80) cc_final: 0.8687 (t80) REVERT: A 349 GLN cc_start: 0.8869 (tt0) cc_final: 0.8301 (tt0) REVERT: A 350 ASP cc_start: 0.8430 (m-30) cc_final: 0.8229 (m-30) REVERT: A 361 GLU cc_start: 0.9426 (tp30) cc_final: 0.9182 (pm20) REVERT: A 363 ILE cc_start: 0.9509 (mm) cc_final: 0.9289 (mm) REVERT: A 369 LEU cc_start: 0.9057 (mm) cc_final: 0.8697 (mm) REVERT: A 393 LEU cc_start: 0.8984 (mp) cc_final: 0.8685 (mp) REVERT: A 413 ASP cc_start: 0.9430 (t0) cc_final: 0.9082 (t0) REVERT: C 175 LYS cc_start: 0.8179 (pptt) cc_final: 0.7890 (tttt) REVERT: C 219 ILE cc_start: 0.8865 (mt) cc_final: 0.8509 (mm) REVERT: C 239 LEU cc_start: 0.8695 (pp) cc_final: 0.7749 (pp) REVERT: C 242 LEU cc_start: 0.8584 (pp) cc_final: 0.8183 (pp) REVERT: C 246 HIS cc_start: 0.8470 (m-70) cc_final: 0.7555 (m170) REVERT: C 251 HIS cc_start: 0.7212 (m-70) cc_final: 0.6949 (m-70) REVERT: C 255 PHE cc_start: 0.9124 (t80) cc_final: 0.8865 (t80) REVERT: C 273 GLU cc_start: 0.8005 (tp30) cc_final: 0.7667 (tp30) REVERT: C 308 PHE cc_start: 0.8628 (t80) cc_final: 0.8101 (t80) REVERT: C 313 TYR cc_start: 0.8667 (p90) cc_final: 0.8336 (p90) REVERT: C 338 MET cc_start: 0.8090 (mmp) cc_final: 0.7263 (mmt) REVERT: C 339 LEU cc_start: 0.9178 (pp) cc_final: 0.8727 (pp) REVERT: C 341 ASP cc_start: 0.8880 (t0) cc_final: 0.7929 (p0) REVERT: C 347 PHE cc_start: 0.8981 (t80) cc_final: 0.8448 (t80) REVERT: C 360 ASP cc_start: 0.9088 (m-30) cc_final: 0.8702 (p0) REVERT: C 361 GLU cc_start: 0.9362 (tp30) cc_final: 0.8813 (tm-30) REVERT: C 362 GLU cc_start: 0.9099 (mp0) cc_final: 0.8732 (mp0) REVERT: C 369 LEU cc_start: 0.9042 (mm) cc_final: 0.8649 (mm) REVERT: C 393 LEU cc_start: 0.9000 (mp) cc_final: 0.8573 (mp) REVERT: C 447 TYR cc_start: 0.8977 (t80) cc_final: 0.8614 (t80) REVERT: C 455 PHE cc_start: 0.8150 (p90) cc_final: 0.7895 (p90) REVERT: E 175 LYS cc_start: 0.8232 (pptt) cc_final: 0.7974 (tttt) REVERT: E 239 LEU cc_start: 0.8601 (pp) cc_final: 0.7770 (pp) REVERT: E 242 LEU cc_start: 0.8467 (pp) cc_final: 0.8122 (pp) REVERT: E 246 HIS cc_start: 0.8609 (m-70) cc_final: 0.7709 (m170) REVERT: E 251 HIS cc_start: 0.7084 (m-70) cc_final: 0.6726 (m90) REVERT: E 255 PHE cc_start: 0.9213 (t80) cc_final: 0.9012 (t80) REVERT: E 308 PHE cc_start: 0.8708 (t80) cc_final: 0.8130 (t80) REVERT: E 313 TYR cc_start: 0.8712 (p90) cc_final: 0.8386 (p90) REVERT: E 338 MET cc_start: 0.7790 (mmp) cc_final: 0.7143 (mmt) REVERT: E 341 ASP cc_start: 0.8877 (t0) cc_final: 0.7982 (p0) REVERT: E 347 PHE cc_start: 0.9067 (t80) cc_final: 0.8642 (t80) REVERT: E 349 GLN cc_start: 0.9002 (tt0) cc_final: 0.8503 (tt0) REVERT: E 361 GLU cc_start: 0.9318 (tp30) cc_final: 0.8966 (tm-30) REVERT: E 362 GLU cc_start: 0.9168 (mp0) cc_final: 0.8777 (mp0) REVERT: E 364 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9090 (mt-10) REVERT: E 369 LEU cc_start: 0.9083 (mm) cc_final: 0.8650 (mm) REVERT: E 393 LEU cc_start: 0.8838 (mp) cc_final: 0.8411 (mp) REVERT: E 447 TYR cc_start: 0.8921 (t80) cc_final: 0.8336 (t80) REVERT: E 450 ARG cc_start: 0.8993 (mtt90) cc_final: 0.8640 (ttm110) REVERT: E 460 ASP cc_start: 0.9153 (t0) cc_final: 0.8953 (t0) REVERT: G 166 PHE cc_start: 0.9283 (p90) cc_final: 0.9005 (p90) REVERT: G 175 LYS cc_start: 0.8220 (pptt) cc_final: 0.7944 (tttt) REVERT: G 184 ASP cc_start: 0.8460 (m-30) cc_final: 0.8202 (m-30) REVERT: G 239 LEU cc_start: 0.8591 (pp) cc_final: 0.7627 (pp) REVERT: G 251 HIS cc_start: 0.7051 (m-70) cc_final: 0.6753 (m-70) REVERT: G 255 PHE cc_start: 0.9208 (t80) cc_final: 0.8974 (t80) REVERT: G 308 PHE cc_start: 0.8616 (t80) cc_final: 0.8090 (t80) REVERT: G 313 TYR cc_start: 0.8616 (p90) cc_final: 0.8368 (p90) REVERT: G 338 MET cc_start: 0.8022 (mmp) cc_final: 0.7611 (mmp) REVERT: G 341 ASP cc_start: 0.8887 (t0) cc_final: 0.7971 (p0) REVERT: G 347 PHE cc_start: 0.8995 (t80) cc_final: 0.8439 (t80) REVERT: G 350 ASP cc_start: 0.8452 (m-30) cc_final: 0.8192 (m-30) REVERT: G 360 ASP cc_start: 0.9021 (m-30) cc_final: 0.8807 (p0) REVERT: G 361 GLU cc_start: 0.9301 (tp30) cc_final: 0.8960 (tm-30) REVERT: G 362 GLU cc_start: 0.9104 (mp0) cc_final: 0.8767 (mp0) REVERT: G 363 ILE cc_start: 0.9534 (mm) cc_final: 0.9320 (mm) REVERT: G 369 LEU cc_start: 0.9024 (mm) cc_final: 0.8645 (mm) REVERT: G 393 LEU cc_start: 0.8836 (mp) cc_final: 0.8424 (mp) REVERT: G 450 ARG cc_start: 0.8993 (mtt90) cc_final: 0.8687 (ttm110) outliers start: 5 outliers final: 3 residues processed: 473 average time/residue: 0.2893 time to fit residues: 190.4220 Evaluate side-chains 408 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 405 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 57 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 10 optimal weight: 0.0970 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN E 178 HIS ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS G 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.122420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.093325 restraints weight = 25404.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.097298 restraints weight = 16507.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.100289 restraints weight = 11819.134| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 11592 Z= 0.154 Angle : 0.731 8.897 15712 Z= 0.368 Chirality : 0.046 0.240 1684 Planarity : 0.005 0.065 2068 Dihedral : 5.379 31.964 1568 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.25 % Allowed : 3.34 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.22), residues: 1396 helix: -0.87 (0.18), residues: 784 sheet: -0.67 (0.55), residues: 96 loop : -1.19 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 371 HIS 0.013 0.002 HIS E 401 PHE 0.017 0.002 PHE A 344 TYR 0.021 0.002 TYR C 236 ARG 0.010 0.001 ARG H 49 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 510) hydrogen bonds : angle 5.93069 ( 1494) covalent geometry : bond 0.00350 (11592) covalent geometry : angle 0.73091 (15712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 465 time to evaluate : 1.358 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: A 175 LYS cc_start: 0.8162 (pptt) cc_final: 0.7925 (tttt) REVERT: A 184 ASP cc_start: 0.8349 (m-30) cc_final: 0.8107 (m-30) REVERT: A 186 ASP cc_start: 0.8192 (t0) cc_final: 0.7871 (t0) REVERT: A 221 ARG cc_start: 0.8271 (mmt90) cc_final: 0.8071 (mmm-85) REVERT: A 239 LEU cc_start: 0.8542 (pp) cc_final: 0.7637 (pp) REVERT: A 255 PHE cc_start: 0.9159 (t80) cc_final: 0.8938 (t80) REVERT: A 297 ARG cc_start: 0.8169 (mmt90) cc_final: 0.7884 (mmt90) REVERT: A 308 PHE cc_start: 0.8660 (t80) cc_final: 0.8099 (t80) REVERT: A 328 CYS cc_start: 0.8446 (p) cc_final: 0.7845 (p) REVERT: A 338 MET cc_start: 0.8152 (mmp) cc_final: 0.7348 (mmp) REVERT: A 341 ASP cc_start: 0.8589 (t0) cc_final: 0.7929 (p0) REVERT: A 347 PHE cc_start: 0.8999 (t80) cc_final: 0.8622 (t80) REVERT: A 349 GLN cc_start: 0.8522 (tt0) cc_final: 0.8195 (tt0) REVERT: A 350 ASP cc_start: 0.8407 (m-30) cc_final: 0.8042 (m-30) REVERT: A 361 GLU cc_start: 0.9385 (tp30) cc_final: 0.9081 (pm20) REVERT: A 362 GLU cc_start: 0.9166 (mp0) cc_final: 0.8384 (mp0) REVERT: A 363 ILE cc_start: 0.9467 (mm) cc_final: 0.9262 (mm) REVERT: A 369 LEU cc_start: 0.8987 (mm) cc_final: 0.8555 (mm) REVERT: A 393 LEU cc_start: 0.8757 (mp) cc_final: 0.8468 (mp) REVERT: A 413 ASP cc_start: 0.9403 (t0) cc_final: 0.8983 (t0) REVERT: A 445 ARG cc_start: 0.8597 (mmt180) cc_final: 0.8049 (mmt180) REVERT: A 480 GLU cc_start: 0.8467 (tt0) cc_final: 0.7862 (tp30) REVERT: A 485 GLU cc_start: 0.9087 (mp0) cc_final: 0.8824 (mp0) REVERT: C 166 PHE cc_start: 0.9118 (p90) cc_final: 0.8881 (p90) REVERT: C 175 LYS cc_start: 0.7971 (pptt) cc_final: 0.7718 (tttt) REVERT: C 184 ASP cc_start: 0.8352 (m-30) cc_final: 0.8127 (m-30) REVERT: C 214 ARG cc_start: 0.8634 (mmp80) cc_final: 0.8417 (mmp80) REVERT: C 239 LEU cc_start: 0.8648 (pp) cc_final: 0.7877 (pp) REVERT: C 242 LEU cc_start: 0.8494 (pp) cc_final: 0.8265 (pp) REVERT: C 246 HIS cc_start: 0.8490 (m-70) cc_final: 0.7671 (m170) REVERT: C 251 HIS cc_start: 0.7086 (m-70) cc_final: 0.6849 (m-70) REVERT: C 300 LEU cc_start: 0.7883 (pp) cc_final: 0.7177 (pp) REVERT: C 308 PHE cc_start: 0.8603 (t80) cc_final: 0.8148 (t80) REVERT: C 313 TYR cc_start: 0.8586 (p90) cc_final: 0.8332 (p90) REVERT: C 338 MET cc_start: 0.8091 (mmp) cc_final: 0.7537 (mmt) REVERT: C 341 ASP cc_start: 0.8808 (t0) cc_final: 0.8126 (p0) REVERT: C 347 PHE cc_start: 0.8760 (t80) cc_final: 0.8448 (t80) REVERT: C 361 GLU cc_start: 0.9319 (tp30) cc_final: 0.8643 (tm-30) REVERT: C 362 GLU cc_start: 0.9117 (mp0) cc_final: 0.8506 (mp0) REVERT: C 363 ILE cc_start: 0.9437 (mp) cc_final: 0.9024 (mp) REVERT: C 369 LEU cc_start: 0.8931 (mm) cc_final: 0.8457 (mm) REVERT: C 393 LEU cc_start: 0.8790 (mp) cc_final: 0.8440 (mp) REVERT: C 413 ASP cc_start: 0.9240 (t70) cc_final: 0.8992 (t0) REVERT: C 447 TYR cc_start: 0.8923 (t80) cc_final: 0.8624 (t80) REVERT: C 455 PHE cc_start: 0.8137 (p90) cc_final: 0.7855 (p90) REVERT: C 480 GLU cc_start: 0.8511 (tt0) cc_final: 0.8095 (tp30) REVERT: C 485 GLU cc_start: 0.9151 (mp0) cc_final: 0.8844 (mp0) REVERT: E 175 LYS cc_start: 0.7995 (pptt) cc_final: 0.7782 (tttt) REVERT: E 213 TYR cc_start: 0.8570 (t80) cc_final: 0.8057 (t80) REVERT: E 239 LEU cc_start: 0.8555 (pp) cc_final: 0.7860 (pp) REVERT: E 251 HIS cc_start: 0.7181 (m-70) cc_final: 0.6957 (m-70) REVERT: E 299 PHE cc_start: 0.8776 (t80) cc_final: 0.8478 (t80) REVERT: E 308 PHE cc_start: 0.8635 (t80) cc_final: 0.8105 (t80) REVERT: E 313 TYR cc_start: 0.8644 (p90) cc_final: 0.8314 (p90) REVERT: E 338 MET cc_start: 0.7867 (mmp) cc_final: 0.7640 (mmp) REVERT: E 341 ASP cc_start: 0.8856 (t0) cc_final: 0.8037 (p0) REVERT: E 347 PHE cc_start: 0.8975 (t80) cc_final: 0.8620 (t80) REVERT: E 349 GLN cc_start: 0.8803 (tt0) cc_final: 0.8289 (tt0) REVERT: E 361 GLU cc_start: 0.9265 (tp30) cc_final: 0.8916 (tm-30) REVERT: E 362 GLU cc_start: 0.9108 (mp0) cc_final: 0.8691 (mp0) REVERT: E 364 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9148 (mt-10) REVERT: E 369 LEU cc_start: 0.9029 (mm) cc_final: 0.8519 (mm) REVERT: E 393 LEU cc_start: 0.8674 (mp) cc_final: 0.8353 (mp) REVERT: E 447 TYR cc_start: 0.8837 (t80) cc_final: 0.8356 (t80) REVERT: E 450 ARG cc_start: 0.8944 (mtt90) cc_final: 0.8551 (ttm110) REVERT: E 480 GLU cc_start: 0.8504 (tt0) cc_final: 0.8181 (tp30) REVERT: E 485 GLU cc_start: 0.9086 (mp0) cc_final: 0.8732 (mp0) REVERT: G 166 PHE cc_start: 0.9233 (p90) cc_final: 0.9005 (p90) REVERT: G 175 LYS cc_start: 0.8070 (pptt) cc_final: 0.7780 (tttt) REVERT: G 184 ASP cc_start: 0.8334 (m-30) cc_final: 0.8092 (m-30) REVERT: G 186 ASP cc_start: 0.7989 (t0) cc_final: 0.7718 (t0) REVERT: G 239 LEU cc_start: 0.8542 (pp) cc_final: 0.7733 (pp) REVERT: G 240 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8581 (mtpp) REVERT: G 246 HIS cc_start: 0.8615 (m-70) cc_final: 0.7892 (m170) REVERT: G 297 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.8239 (tpp-160) REVERT: G 299 PHE cc_start: 0.8797 (t80) cc_final: 0.8578 (t80) REVERT: G 308 PHE cc_start: 0.8560 (t80) cc_final: 0.8210 (t80) REVERT: G 338 MET cc_start: 0.7993 (mmp) cc_final: 0.7334 (mmt) REVERT: G 341 ASP cc_start: 0.8838 (t0) cc_final: 0.8163 (p0) REVERT: G 347 PHE cc_start: 0.8948 (t80) cc_final: 0.8378 (t80) REVERT: G 361 GLU cc_start: 0.9222 (tp30) cc_final: 0.8770 (tm-30) REVERT: G 364 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9020 (mt-10) REVERT: G 369 LEU cc_start: 0.8937 (mm) cc_final: 0.8513 (mm) REVERT: G 393 LEU cc_start: 0.8666 (mp) cc_final: 0.8441 (mp) REVERT: G 450 ARG cc_start: 0.8937 (mtt90) cc_final: 0.8612 (ttm110) REVERT: G 480 GLU cc_start: 0.8519 (tt0) cc_final: 0.7876 (tp30) REVERT: G 485 GLU cc_start: 0.9093 (mp0) cc_final: 0.8835 (mp0) outliers start: 3 outliers final: 2 residues processed: 467 average time/residue: 0.2541 time to fit residues: 164.3853 Evaluate side-chains 405 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 403 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN A 428 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 GLN ** G 428 GLN ** 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 = 0.3946 r_free = 0.3946 target = 0.123954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.094316 restraints weight = 25546.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.098286 restraints weight = 16856.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101332 restraints weight = 12203.163| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11592 Z= 0.143 Angle : 0.743 10.128 15712 Z= 0.370 Chirality : 0.046 0.221 1684 Planarity : 0.006 0.143 2068 Dihedral : 5.291 31.200 1568 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % 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: -1.48 (0.22), residues: 1396 helix: -0.88 (0.18), residues: 784 sheet: -0.63 (0.55), residues: 96 loop : -0.93 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP E 371 HIS 0.012 0.002 HIS G 401 PHE 0.016 0.002 PHE A 376 TYR 0.013 0.002 TYR C 236 ARG 0.020 0.001 ARG C 297 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 510) hydrogen bonds : angle 5.85074 ( 1494) covalent geometry : bond 0.00320 (11592) covalent geometry : angle 0.74327 (15712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 1.242 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: A 175 LYS cc_start: 0.7888 (pptt) cc_final: 0.7623 (tttt) REVERT: A 184 ASP cc_start: 0.8406 (m-30) cc_final: 0.8151 (m-30) REVERT: A 186 ASP cc_start: 0.8188 (t0) cc_final: 0.7873 (t0) REVERT: A 236 TYR cc_start: 0.8919 (t80) cc_final: 0.8636 (t80) REVERT: A 239 LEU cc_start: 0.8559 (pp) cc_final: 0.7675 (pp) REVERT: A 240 LYS cc_start: 0.9143 (tttt) cc_final: 0.8842 (tttt) REVERT: A 297 ARG cc_start: 0.8202 (mmt90) cc_final: 0.7977 (mmt90) REVERT: A 308 PHE cc_start: 0.8673 (t80) cc_final: 0.8167 (t80) REVERT: A 338 MET cc_start: 0.8187 (mmp) cc_final: 0.7245 (mmt) REVERT: A 341 ASP cc_start: 0.8650 (t0) cc_final: 0.7982 (p0) REVERT: A 347 PHE cc_start: 0.8942 (t80) cc_final: 0.8616 (t80) REVERT: A 349 GLN cc_start: 0.8715 (tt0) cc_final: 0.7934 (tt0) REVERT: A 350 ASP cc_start: 0.8309 (m-30) cc_final: 0.8107 (m-30) REVERT: A 362 GLU cc_start: 0.9128 (mp0) cc_final: 0.7946 (mp0) REVERT: A 369 LEU cc_start: 0.8963 (mm) cc_final: 0.8620 (mm) REVERT: A 393 LEU cc_start: 0.8733 (mp) cc_final: 0.8452 (mp) REVERT: A 413 ASP cc_start: 0.9329 (t0) cc_final: 0.8916 (t0) REVERT: A 445 ARG cc_start: 0.8549 (tpp80) cc_final: 0.7956 (mmm160) REVERT: A 480 GLU cc_start: 0.8478 (tt0) cc_final: 0.8173 (tp30) REVERT: A 485 GLU cc_start: 0.9121 (mp0) cc_final: 0.8796 (mp0) REVERT: C 175 LYS cc_start: 0.7963 (pptt) cc_final: 0.7694 (mttm) REVERT: C 214 ARG cc_start: 0.8663 (mmp80) cc_final: 0.8446 (mmp80) REVERT: C 239 LEU cc_start: 0.8719 (pp) cc_final: 0.8006 (pp) REVERT: C 242 LEU cc_start: 0.8573 (pp) cc_final: 0.8292 (pp) REVERT: C 246 HIS cc_start: 0.8460 (m-70) cc_final: 0.7670 (m170) REVERT: C 251 HIS cc_start: 0.7080 (m-70) cc_final: 0.6874 (m-70) REVERT: C 280 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8306 (ttpt) REVERT: C 308 PHE cc_start: 0.8578 (t80) cc_final: 0.8127 (t80) REVERT: C 313 TYR cc_start: 0.8519 (p90) cc_final: 0.8290 (p90) REVERT: C 327 ASP cc_start: 0.6865 (p0) cc_final: 0.6664 (p0) REVERT: C 338 MET cc_start: 0.8080 (mmp) cc_final: 0.7338 (mmt) REVERT: C 341 ASP cc_start: 0.8765 (t0) cc_final: 0.7998 (p0) REVERT: C 347 PHE cc_start: 0.8835 (t80) cc_final: 0.8389 (t80) REVERT: C 361 GLU cc_start: 0.9326 (tp30) cc_final: 0.8687 (tm-30) REVERT: C 362 GLU cc_start: 0.9030 (mp0) cc_final: 0.8528 (mp0) REVERT: C 369 LEU cc_start: 0.8857 (mm) cc_final: 0.8477 (mm) REVERT: C 455 PHE cc_start: 0.8082 (p90) cc_final: 0.7830 (p90) REVERT: C 480 GLU cc_start: 0.8488 (tt0) cc_final: 0.8125 (tp30) REVERT: C 485 GLU cc_start: 0.9099 (mp0) cc_final: 0.8773 (mp0) REVERT: E 175 LYS cc_start: 0.7967 (pptt) cc_final: 0.7715 (tttt) REVERT: E 239 LEU cc_start: 0.8561 (pp) cc_final: 0.7868 (pp) REVERT: E 246 HIS cc_start: 0.8715 (m-70) cc_final: 0.8413 (m-70) REVERT: E 308 PHE cc_start: 0.8531 (t80) cc_final: 0.8057 (t80) REVERT: E 338 MET cc_start: 0.7856 (mmp) cc_final: 0.7572 (mmp) REVERT: E 341 ASP cc_start: 0.8809 (t0) cc_final: 0.8010 (p0) REVERT: E 347 PHE cc_start: 0.8939 (t80) cc_final: 0.8592 (t80) REVERT: E 349 GLN cc_start: 0.8719 (tt0) cc_final: 0.8312 (tt0) REVERT: E 361 GLU cc_start: 0.9202 (tp30) cc_final: 0.8980 (tm-30) REVERT: E 362 GLU cc_start: 0.9065 (mp0) cc_final: 0.8576 (mp0) REVERT: E 364 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9133 (mt-10) REVERT: E 369 LEU cc_start: 0.9032 (mm) cc_final: 0.8538 (mm) REVERT: E 385 VAL cc_start: 0.8848 (p) cc_final: 0.8633 (p) REVERT: E 393 LEU cc_start: 0.8523 (mp) cc_final: 0.8284 (mp) REVERT: E 450 ARG cc_start: 0.8859 (mtt90) cc_final: 0.8543 (ttm110) REVERT: E 455 PHE cc_start: 0.8046 (p90) cc_final: 0.7811 (p90) REVERT: E 480 GLU cc_start: 0.8479 (tt0) cc_final: 0.8130 (tp30) REVERT: E 485 GLU cc_start: 0.9083 (mp0) cc_final: 0.8784 (mp0) REVERT: G 175 LYS cc_start: 0.8066 (pptt) cc_final: 0.7788 (tttt) REVERT: G 213 TYR cc_start: 0.8492 (t80) cc_final: 0.8106 (t80) REVERT: G 239 LEU cc_start: 0.8533 (pp) cc_final: 0.7801 (pp) REVERT: G 240 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8591 (mtpp) REVERT: G 246 HIS cc_start: 0.8553 (m-70) cc_final: 0.7867 (m170) REVERT: G 251 HIS cc_start: 0.7100 (m-70) cc_final: 0.6725 (m-70) REVERT: G 255 PHE cc_start: 0.9168 (t80) cc_final: 0.8877 (t80) REVERT: G 308 PHE cc_start: 0.8515 (t80) cc_final: 0.8176 (t80) REVERT: G 313 TYR cc_start: 0.8481 (p90) cc_final: 0.8271 (p90) REVERT: G 338 MET cc_start: 0.7929 (mmp) cc_final: 0.7150 (mmt) REVERT: G 341 ASP cc_start: 0.8781 (t0) cc_final: 0.8037 (p0) REVERT: G 347 PHE cc_start: 0.8718 (t80) cc_final: 0.8328 (t80) REVERT: G 361 GLU cc_start: 0.9326 (tp30) cc_final: 0.8694 (tm-30) REVERT: G 362 GLU cc_start: 0.9106 (mp0) cc_final: 0.8372 (mp0) REVERT: G 363 ILE cc_start: 0.9456 (mm) cc_final: 0.9234 (mm) REVERT: G 369 LEU cc_start: 0.8895 (mm) cc_final: 0.8554 (mm) REVERT: G 393 LEU cc_start: 0.8548 (mp) cc_final: 0.8341 (mp) REVERT: G 450 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8570 (ttm110) REVERT: G 480 GLU cc_start: 0.8511 (tt0) cc_final: 0.7854 (tp30) REVERT: G 485 GLU cc_start: 0.9018 (mp0) cc_final: 0.8776 (mp0) outliers start: 1 outliers final: 0 residues processed: 461 average time/residue: 0.2482 time to fit residues: 157.5689 Evaluate side-chains 415 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS A 382 ASN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 428 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 = 0.3875 r_free = 0.3875 target = 0.118843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.090573 restraints weight = 26616.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.094457 restraints weight = 17164.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.097310 restraints weight = 12227.865| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11592 Z= 0.226 Angle : 0.783 8.124 15712 Z= 0.406 Chirality : 0.048 0.209 1684 Planarity : 0.006 0.096 2068 Dihedral : 5.464 31.299 1568 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: -1.80 (0.21), residues: 1396 helix: -1.10 (0.17), residues: 792 sheet: -0.96 (0.53), residues: 96 loop : -1.10 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP A 371 HIS 0.013 0.002 HIS A 251 PHE 0.024 0.002 PHE C 376 TYR 0.017 0.002 TYR C 236 ARG 0.009 0.001 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 510) hydrogen bonds : angle 6.11843 ( 1494) covalent geometry : bond 0.00474 (11592) covalent geometry : angle 0.78305 (15712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.156 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: A 175 LYS cc_start: 0.8069 (pptt) cc_final: 0.7807 (tttt) REVERT: A 184 ASP cc_start: 0.8490 (m-30) cc_final: 0.8247 (m-30) REVERT: A 239 LEU cc_start: 0.8583 (pp) cc_final: 0.7716 (pp) REVERT: A 240 LYS cc_start: 0.9127 (tttt) cc_final: 0.8763 (tttt) REVERT: A 297 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7845 (mmt90) REVERT: A 308 PHE cc_start: 0.8765 (t80) cc_final: 0.8108 (t80) REVERT: A 347 PHE cc_start: 0.8973 (t80) cc_final: 0.8666 (t80) REVERT: A 349 GLN cc_start: 0.8749 (tt0) cc_final: 0.8212 (tt0) REVERT: A 363 ILE cc_start: 0.9528 (mm) cc_final: 0.9235 (mm) REVERT: A 369 LEU cc_start: 0.9040 (mm) cc_final: 0.8662 (mm) REVERT: A 393 LEU cc_start: 0.8900 (mp) cc_final: 0.8681 (mp) REVERT: A 413 ASP cc_start: 0.9417 (t0) cc_final: 0.9033 (t0) REVERT: A 445 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8341 (ttm-80) REVERT: A 480 GLU cc_start: 0.8566 (tt0) cc_final: 0.8269 (tp30) REVERT: C 166 PHE cc_start: 0.9214 (p90) cc_final: 0.8859 (p90) REVERT: C 175 LYS cc_start: 0.7933 (pptt) cc_final: 0.7677 (tttt) REVERT: C 239 LEU cc_start: 0.8767 (pp) cc_final: 0.8229 (pp) REVERT: C 242 LEU cc_start: 0.8507 (pp) cc_final: 0.8263 (pp) REVERT: C 246 HIS cc_start: 0.8479 (m-70) cc_final: 0.7847 (m170) REVERT: C 255 PHE cc_start: 0.9056 (t80) cc_final: 0.8789 (t80) REVERT: C 308 PHE cc_start: 0.8664 (t80) cc_final: 0.8097 (t80) REVERT: C 313 TYR cc_start: 0.8591 (p90) cc_final: 0.8330 (p90) REVERT: C 338 MET cc_start: 0.8202 (mmp) cc_final: 0.7693 (mmp) REVERT: C 341 ASP cc_start: 0.8854 (t0) cc_final: 0.7988 (p0) REVERT: C 347 PHE cc_start: 0.8927 (t80) cc_final: 0.8414 (t80) REVERT: C 361 GLU cc_start: 0.9342 (tp30) cc_final: 0.8821 (tm-30) REVERT: C 369 LEU cc_start: 0.8963 (mm) cc_final: 0.8568 (mm) REVERT: C 455 PHE cc_start: 0.8146 (p90) cc_final: 0.7887 (p90) REVERT: C 466 ILE cc_start: 0.8907 (mm) cc_final: 0.8598 (mm) REVERT: C 480 GLU cc_start: 0.8596 (tt0) cc_final: 0.8171 (tp30) REVERT: E 175 LYS cc_start: 0.7980 (pptt) cc_final: 0.7711 (tttt) REVERT: E 221 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7925 (mmt90) REVERT: E 239 LEU cc_start: 0.8567 (pp) cc_final: 0.8005 (pp) REVERT: E 251 HIS cc_start: 0.7288 (m-70) cc_final: 0.6942 (m-70) REVERT: E 267 ASP cc_start: 0.8927 (p0) cc_final: 0.8568 (p0) REVERT: E 308 PHE cc_start: 0.8627 (t80) cc_final: 0.7979 (t80) REVERT: E 338 MET cc_start: 0.7971 (mmp) cc_final: 0.7645 (mmp) REVERT: E 347 PHE cc_start: 0.9000 (t80) cc_final: 0.8633 (t80) REVERT: E 361 GLU cc_start: 0.9127 (tp30) cc_final: 0.8824 (tm-30) REVERT: E 362 GLU cc_start: 0.9060 (mp0) cc_final: 0.8807 (mp0) REVERT: E 364 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9080 (mt-10) REVERT: E 369 LEU cc_start: 0.9022 (mm) cc_final: 0.8672 (mm) REVERT: E 393 LEU cc_start: 0.8621 (mp) cc_final: 0.8409 (mp) REVERT: E 443 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8173 (mtpt) REVERT: E 480 GLU cc_start: 0.8607 (tt0) cc_final: 0.8162 (tp30) REVERT: G 166 PHE cc_start: 0.9299 (p90) cc_final: 0.9018 (p90) REVERT: G 175 LYS cc_start: 0.8027 (pptt) cc_final: 0.7657 (tttt) REVERT: G 213 TYR cc_start: 0.8588 (t80) cc_final: 0.8168 (t80) REVERT: G 219 ILE cc_start: 0.8896 (mt) cc_final: 0.8531 (mt) REVERT: G 239 LEU cc_start: 0.8613 (pp) cc_final: 0.7989 (pp) REVERT: G 251 HIS cc_start: 0.7057 (m-70) cc_final: 0.6707 (m-70) REVERT: G 255 PHE cc_start: 0.9075 (t80) cc_final: 0.8799 (t80) REVERT: G 266 GLU cc_start: 0.7622 (pm20) cc_final: 0.7384 (pm20) REVERT: G 273 GLU cc_start: 0.8092 (tp30) cc_final: 0.7742 (tp30) REVERT: G 297 ARG cc_start: 0.8789 (tpp-160) cc_final: 0.8446 (tpp-160) REVERT: G 308 PHE cc_start: 0.8612 (t80) cc_final: 0.8122 (t80) REVERT: G 313 TYR cc_start: 0.8531 (p90) cc_final: 0.8310 (p90) REVERT: G 338 MET cc_start: 0.7999 (mmp) cc_final: 0.7027 (mmt) REVERT: G 341 ASP cc_start: 0.8862 (t0) cc_final: 0.7976 (p0) REVERT: G 346 GLN cc_start: 0.8779 (tp40) cc_final: 0.8535 (tp-100) REVERT: G 347 PHE cc_start: 0.8955 (t80) cc_final: 0.8407 (t80) REVERT: G 350 ASP cc_start: 0.8442 (m-30) cc_final: 0.8176 (m-30) REVERT: G 362 GLU cc_start: 0.9038 (mp0) cc_final: 0.8783 (mp0) REVERT: G 369 LEU cc_start: 0.8985 (mm) cc_final: 0.8591 (mm) REVERT: G 427 TYR cc_start: 0.8109 (m-80) cc_final: 0.7539 (m-80) REVERT: G 450 ARG cc_start: 0.8836 (mtt90) cc_final: 0.8552 (ttm110) REVERT: G 456 SER cc_start: 0.8299 (t) cc_final: 0.8099 (t) REVERT: G 480 GLU cc_start: 0.8578 (tt0) cc_final: 0.8229 (tp30) REVERT: G 487 ASP cc_start: 0.8751 (m-30) cc_final: 0.8539 (m-30) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.2496 time to fit residues: 155.1742 Evaluate side-chains 389 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** G 428 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 = 0.3872 r_free = 0.3872 target = 0.118782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.090679 restraints weight = 25793.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.094465 restraints weight = 16655.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.097329 restraints weight = 11918.379| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 11592 Z= 0.195 Angle : 0.774 10.031 15712 Z= 0.397 Chirality : 0.047 0.192 1684 Planarity : 0.006 0.065 2068 Dihedral : 5.522 31.682 1568 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.08 % Allowed : 2.01 % Favored : 97.91 % 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: -1.81 (0.21), residues: 1396 helix: -1.01 (0.17), residues: 792 sheet: -1.36 (0.50), residues: 96 loop : -1.20 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP E 371 HIS 0.017 0.003 HIS E 401 PHE 0.030 0.002 PHE G 376 TYR 0.014 0.002 TYR C 213 ARG 0.008 0.001 ARG G 297 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 510) hydrogen bonds : angle 6.01477 ( 1494) covalent geometry : bond 0.00421 (11592) covalent geometry : angle 0.77377 (15712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 1.220 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: A 171 SER cc_start: 0.8810 (m) cc_final: 0.8502 (p) REVERT: A 172 GLU cc_start: 0.8561 (mp0) cc_final: 0.8303 (mp0) REVERT: A 175 LYS cc_start: 0.8016 (pptt) cc_final: 0.7741 (tttt) REVERT: A 239 LEU cc_start: 0.8573 (pp) cc_final: 0.7725 (pp) REVERT: A 240 LYS cc_start: 0.9111 (tttt) cc_final: 0.8737 (tttt) REVERT: A 297 ARG cc_start: 0.8190 (mmt90) cc_final: 0.7936 (mmt90) REVERT: A 308 PHE cc_start: 0.8757 (t80) cc_final: 0.8077 (t80) REVERT: A 347 PHE cc_start: 0.9006 (t80) cc_final: 0.8673 (t80) REVERT: A 349 GLN cc_start: 0.8762 (tt0) cc_final: 0.8184 (tt0) REVERT: A 363 ILE cc_start: 0.9503 (mm) cc_final: 0.9258 (mm) REVERT: A 369 LEU cc_start: 0.9039 (mm) cc_final: 0.8637 (mm) REVERT: A 393 LEU cc_start: 0.8718 (mp) cc_final: 0.8464 (mp) REVERT: A 413 ASP cc_start: 0.9398 (t0) cc_final: 0.9015 (t0) REVERT: A 480 GLU cc_start: 0.8540 (tt0) cc_final: 0.8038 (tp30) REVERT: A 485 GLU cc_start: 0.9069 (mp0) cc_final: 0.8812 (mp0) REVERT: A 487 ASP cc_start: 0.8760 (m-30) cc_final: 0.8539 (m-30) REVERT: C 166 PHE cc_start: 0.9227 (p90) cc_final: 0.8943 (p90) REVERT: C 175 LYS cc_start: 0.7943 (pptt) cc_final: 0.7671 (tttt) REVERT: C 184 ASP cc_start: 0.8282 (m-30) cc_final: 0.8039 (m-30) REVERT: C 239 LEU cc_start: 0.8792 (pp) cc_final: 0.8286 (pp) REVERT: C 280 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8307 (ttpt) REVERT: C 308 PHE cc_start: 0.8631 (t80) cc_final: 0.8063 (t80) REVERT: C 313 TYR cc_start: 0.8573 (p90) cc_final: 0.8307 (p90) REVERT: C 338 MET cc_start: 0.8087 (mmp) cc_final: 0.7829 (mmp) REVERT: C 347 PHE cc_start: 0.8903 (t80) cc_final: 0.8615 (t80) REVERT: C 361 GLU cc_start: 0.9328 (tp30) cc_final: 0.8669 (tm-30) REVERT: C 362 GLU cc_start: 0.8935 (mp0) cc_final: 0.8598 (mp0) REVERT: C 369 LEU cc_start: 0.8973 (mm) cc_final: 0.8537 (mm) REVERT: C 455 PHE cc_start: 0.8133 (p90) cc_final: 0.7888 (p90) REVERT: C 480 GLU cc_start: 0.8529 (tt0) cc_final: 0.8153 (tp30) REVERT: E 166 PHE cc_start: 0.9203 (p90) cc_final: 0.8982 (p90) REVERT: E 175 LYS cc_start: 0.7969 (pptt) cc_final: 0.7686 (tttt) REVERT: E 221 ARG cc_start: 0.8162 (mmt90) cc_final: 0.7898 (mmt90) REVERT: E 239 LEU cc_start: 0.8630 (pp) cc_final: 0.8148 (pp) REVERT: E 251 HIS cc_start: 0.7314 (m-70) cc_final: 0.6876 (m-70) REVERT: E 267 ASP cc_start: 0.8889 (p0) cc_final: 0.8659 (p0) REVERT: E 308 PHE cc_start: 0.8624 (t80) cc_final: 0.8039 (t80) REVERT: E 338 MET cc_start: 0.7894 (mmp) cc_final: 0.7024 (mmt) REVERT: E 341 ASP cc_start: 0.8878 (t0) cc_final: 0.8136 (p0) REVERT: E 347 PHE cc_start: 0.8966 (t80) cc_final: 0.8626 (t80) REVERT: E 361 GLU cc_start: 0.9166 (tp30) cc_final: 0.8869 (tm-30) REVERT: E 362 GLU cc_start: 0.9059 (mp0) cc_final: 0.8554 (mp0) REVERT: E 364 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9200 (mt-10) REVERT: E 369 LEU cc_start: 0.9018 (mm) cc_final: 0.8661 (mm) REVERT: E 427 TYR cc_start: 0.8210 (m-80) cc_final: 0.7605 (m-80) REVERT: E 443 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8161 (mtpt) REVERT: E 455 PHE cc_start: 0.8025 (p90) cc_final: 0.7796 (p90) REVERT: E 480 GLU cc_start: 0.8598 (tt0) cc_final: 0.8247 (tp30) REVERT: E 483 GLN cc_start: 0.8884 (pm20) cc_final: 0.8448 (pm20) REVERT: G 166 PHE cc_start: 0.9263 (p90) cc_final: 0.8931 (p90) REVERT: G 171 SER cc_start: 0.8932 (m) cc_final: 0.8635 (p) REVERT: G 172 GLU cc_start: 0.8621 (mp0) cc_final: 0.8341 (mp0) REVERT: G 175 LYS cc_start: 0.8032 (pptt) cc_final: 0.7690 (tttt) REVERT: G 184 ASP cc_start: 0.8351 (m-30) cc_final: 0.8119 (m-30) REVERT: G 213 TYR cc_start: 0.8558 (t80) cc_final: 0.8217 (t80) REVERT: G 239 LEU cc_start: 0.8601 (pp) cc_final: 0.8117 (pp) REVERT: G 251 HIS cc_start: 0.7048 (m-70) cc_final: 0.6802 (m-70) REVERT: G 255 PHE cc_start: 0.9062 (t80) cc_final: 0.8512 (t80) REVERT: G 259 GLU cc_start: 0.9071 (pm20) cc_final: 0.8610 (pm20) REVERT: G 267 ASP cc_start: 0.9172 (p0) cc_final: 0.8357 (p0) REVERT: G 308 PHE cc_start: 0.8575 (t80) cc_final: 0.8125 (t80) REVERT: G 338 MET cc_start: 0.8065 (mmp) cc_final: 0.7074 (mmt) REVERT: G 341 ASP cc_start: 0.8871 (t0) cc_final: 0.8055 (p0) REVERT: G 347 PHE cc_start: 0.8921 (t80) cc_final: 0.8369 (t80) REVERT: G 350 ASP cc_start: 0.8422 (m-30) cc_final: 0.8213 (m-30) REVERT: G 362 GLU cc_start: 0.9076 (mp0) cc_final: 0.8782 (mp0) REVERT: G 369 LEU cc_start: 0.8997 (mm) cc_final: 0.8562 (mm) REVERT: G 427 TYR cc_start: 0.8087 (m-80) cc_final: 0.7536 (m-80) REVERT: G 450 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8557 (ttm110) REVERT: G 480 GLU cc_start: 0.8551 (tt0) cc_final: 0.8154 (tp30) REVERT: G 487 ASP cc_start: 0.8789 (m-30) cc_final: 0.8498 (m-30) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.2438 time to fit residues: 150.8923 Evaluate side-chains 383 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 96 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** G 428 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 = 0.122034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093009 restraints weight = 25390.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.096982 restraints weight = 16583.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099887 restraints weight = 11902.441| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11592 Z= 0.151 Angle : 0.789 11.779 15712 Z= 0.396 Chirality : 0.047 0.236 1684 Planarity : 0.005 0.056 2068 Dihedral : 5.436 31.036 1568 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -1.63 (0.21), residues: 1396 helix: -0.85 (0.18), residues: 796 sheet: -1.47 (0.50), residues: 96 loop : -1.10 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP A 371 HIS 0.018 0.002 HIS C 401 PHE 0.018 0.002 PHE G 376 TYR 0.015 0.002 TYR C 243 ARG 0.010 0.001 ARG G 265 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 510) hydrogen bonds : angle 5.84736 ( 1494) covalent geometry : bond 0.00335 (11592) covalent geometry : angle 0.78940 (15712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.200 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: A 175 LYS cc_start: 0.7937 (pptt) cc_final: 0.7654 (tttt) REVERT: A 184 ASP cc_start: 0.8294 (m-30) cc_final: 0.8007 (m-30) REVERT: A 186 ASP cc_start: 0.8201 (t0) cc_final: 0.7895 (t0) REVERT: A 239 LEU cc_start: 0.8532 (pp) cc_final: 0.7768 (pp) REVERT: A 240 LYS cc_start: 0.9080 (tttt) cc_final: 0.8707 (tttt) REVERT: A 255 PHE cc_start: 0.9065 (t80) cc_final: 0.8702 (t80) REVERT: A 259 GLU cc_start: 0.8900 (pm20) cc_final: 0.8564 (pm20) REVERT: A 297 ARG cc_start: 0.8176 (mmt90) cc_final: 0.7925 (mmt90) REVERT: A 308 PHE cc_start: 0.8667 (t80) cc_final: 0.8044 (t80) REVERT: A 338 MET cc_start: 0.8433 (mmp) cc_final: 0.7248 (mmp) REVERT: A 341 ASP cc_start: 0.8716 (t0) cc_final: 0.8098 (p0) REVERT: A 347 PHE cc_start: 0.8910 (t80) cc_final: 0.8610 (t80) REVERT: A 363 ILE cc_start: 0.9487 (mm) cc_final: 0.9279 (mm) REVERT: A 369 LEU cc_start: 0.9027 (mm) cc_final: 0.8601 (mm) REVERT: A 413 ASP cc_start: 0.9335 (t0) cc_final: 0.8843 (t0) REVERT: A 441 LYS cc_start: 0.8948 (tttm) cc_final: 0.8684 (tttm) REVERT: A 445 ARG cc_start: 0.8732 (ttm170) cc_final: 0.8297 (mmm160) REVERT: A 480 GLU cc_start: 0.8530 (tt0) cc_final: 0.8142 (tp30) REVERT: A 482 VAL cc_start: 0.9299 (t) cc_final: 0.9050 (t) REVERT: A 485 GLU cc_start: 0.8764 (mp0) cc_final: 0.8384 (mp0) REVERT: A 487 ASP cc_start: 0.8668 (m-30) cc_final: 0.8429 (m-30) REVERT: C 175 LYS cc_start: 0.7890 (pptt) cc_final: 0.7621 (mttt) REVERT: C 239 LEU cc_start: 0.8718 (pp) cc_final: 0.8303 (pp) REVERT: C 255 PHE cc_start: 0.9015 (t80) cc_final: 0.8605 (t80) REVERT: C 259 GLU cc_start: 0.9049 (pm20) cc_final: 0.8820 (pm20) REVERT: C 267 ASP cc_start: 0.8941 (p0) cc_final: 0.8703 (p0) REVERT: C 280 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8245 (ttpt) REVERT: C 308 PHE cc_start: 0.8567 (t80) cc_final: 0.8064 (t80) REVERT: C 347 PHE cc_start: 0.8877 (t80) cc_final: 0.8611 (t80) REVERT: C 349 GLN cc_start: 0.8809 (tt0) cc_final: 0.8278 (tp40) REVERT: C 361 GLU cc_start: 0.9321 (tp30) cc_final: 0.8626 (tm-30) REVERT: C 362 GLU cc_start: 0.8908 (mp0) cc_final: 0.8553 (mp0) REVERT: C 369 LEU cc_start: 0.8942 (mm) cc_final: 0.8482 (mm) REVERT: C 455 PHE cc_start: 0.8057 (p90) cc_final: 0.7809 (p90) REVERT: C 480 GLU cc_start: 0.8503 (tt0) cc_final: 0.8218 (tp30) REVERT: C 483 GLN cc_start: 0.9114 (pm20) cc_final: 0.8892 (pm20) REVERT: C 485 GLU cc_start: 0.8722 (mp0) cc_final: 0.8395 (mp0) REVERT: E 175 LYS cc_start: 0.7910 (pptt) cc_final: 0.7636 (tttt) REVERT: E 213 TYR cc_start: 0.8247 (t80) cc_final: 0.7819 (t80) REVERT: E 239 LEU cc_start: 0.8592 (pp) cc_final: 0.8135 (pp) REVERT: E 251 HIS cc_start: 0.7149 (m-70) cc_final: 0.6793 (m-70) REVERT: E 308 PHE cc_start: 0.8553 (t80) cc_final: 0.8058 (t80) REVERT: E 313 TYR cc_start: 0.8551 (p90) cc_final: 0.8342 (p90) REVERT: E 327 ASP cc_start: 0.7465 (p0) cc_final: 0.6883 (p0) REVERT: E 347 PHE cc_start: 0.8958 (t80) cc_final: 0.8629 (t80) REVERT: E 349 GLN cc_start: 0.8736 (tt0) cc_final: 0.8391 (tt0) REVERT: E 361 GLU cc_start: 0.9188 (tp30) cc_final: 0.8831 (tm-30) REVERT: E 362 GLU cc_start: 0.9081 (mp0) cc_final: 0.8578 (mp0) REVERT: E 364 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9181 (mt-10) REVERT: E 369 LEU cc_start: 0.8994 (mm) cc_final: 0.8598 (mm) REVERT: E 427 TYR cc_start: 0.8188 (m-80) cc_final: 0.7595 (m-80) REVERT: E 443 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8132 (mtpt) REVERT: E 455 PHE cc_start: 0.7949 (p90) cc_final: 0.7735 (p90) REVERT: E 480 GLU cc_start: 0.8544 (tt0) cc_final: 0.8157 (tp30) REVERT: E 485 GLU cc_start: 0.8915 (mp0) cc_final: 0.8632 (mp0) REVERT: G 166 PHE cc_start: 0.9198 (p90) cc_final: 0.8850 (p90) REVERT: G 171 SER cc_start: 0.8844 (m) cc_final: 0.8571 (p) REVERT: G 172 GLU cc_start: 0.8573 (mp0) cc_final: 0.8309 (mp0) REVERT: G 175 LYS cc_start: 0.7761 (pptt) cc_final: 0.7452 (tttt) REVERT: G 184 ASP cc_start: 0.8106 (m-30) cc_final: 0.7803 (m-30) REVERT: G 186 ASP cc_start: 0.8086 (t0) cc_final: 0.7808 (t0) REVERT: G 213 TYR cc_start: 0.8468 (t80) cc_final: 0.8158 (t80) REVERT: G 239 LEU cc_start: 0.8577 (pp) cc_final: 0.8144 (pp) REVERT: G 251 HIS cc_start: 0.7145 (m-70) cc_final: 0.6893 (m-70) REVERT: G 297 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8480 (tpp-160) REVERT: G 308 PHE cc_start: 0.8491 (t80) cc_final: 0.8161 (t80) REVERT: G 310 CYS cc_start: 0.8835 (p) cc_final: 0.8509 (p) REVERT: G 327 ASP cc_start: 0.7187 (p0) cc_final: 0.6972 (p0) REVERT: G 338 MET cc_start: 0.8069 (mmp) cc_final: 0.6987 (mmt) REVERT: G 341 ASP cc_start: 0.8816 (t0) cc_final: 0.8010 (p0) REVERT: G 346 GLN cc_start: 0.8629 (tp40) cc_final: 0.8406 (tp-100) REVERT: G 347 PHE cc_start: 0.8880 (t80) cc_final: 0.8346 (t80) REVERT: G 349 GLN cc_start: 0.8819 (tt0) cc_final: 0.8589 (tt0) REVERT: G 369 LEU cc_start: 0.8890 (mm) cc_final: 0.8591 (mm) REVERT: G 413 ASP cc_start: 0.9246 (t70) cc_final: 0.9022 (t0) REVERT: G 427 TYR cc_start: 0.8096 (m-80) cc_final: 0.7508 (m-80) REVERT: G 480 GLU cc_start: 0.8559 (tt0) cc_final: 0.8271 (tp30) REVERT: G 485 GLU cc_start: 0.8738 (mp0) cc_final: 0.8485 (mp0) REVERT: G 487 ASP cc_start: 0.8599 (m-30) cc_final: 0.8372 (m-30) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.2713 time to fit residues: 174.4507 Evaluate side-chains 400 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** G 428 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 = 0.3861 r_free = 0.3861 target = 0.117870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.090133 restraints weight = 26187.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093941 restraints weight = 16786.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.096745 restraints weight = 11932.586| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 11592 Z= 0.223 Angle : 0.828 10.241 15712 Z= 0.427 Chirality : 0.048 0.173 1684 Planarity : 0.006 0.060 2068 Dihedral : 5.652 30.949 1568 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % 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: -1.79 (0.21), residues: 1396 helix: -0.80 (0.18), residues: 796 sheet: -1.24 (0.41), residues: 140 loop : -1.58 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.005 TRP A 371 HIS 0.014 0.002 HIS C 401 PHE 0.025 0.002 PHE A 305 TYR 0.015 0.002 TYR E 236 ARG 0.016 0.001 ARG G 265 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 510) hydrogen bonds : angle 6.21118 ( 1494) covalent geometry : bond 0.00473 (11592) covalent geometry : angle 0.82753 (15712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.831 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: A 166 PHE cc_start: 0.9219 (p90) cc_final: 0.8961 (p90) REVERT: A 171 SER cc_start: 0.8811 (m) cc_final: 0.8432 (p) REVERT: A 172 GLU cc_start: 0.8608 (mp0) cc_final: 0.8286 (mp0) REVERT: A 175 LYS cc_start: 0.7975 (pptt) cc_final: 0.7715 (tttt) REVERT: A 184 ASP cc_start: 0.8313 (m-30) cc_final: 0.8012 (m-30) REVERT: A 186 ASP cc_start: 0.8145 (t0) cc_final: 0.7853 (t0) REVERT: A 236 TYR cc_start: 0.9014 (t80) cc_final: 0.8694 (t80) REVERT: A 239 LEU cc_start: 0.8644 (pp) cc_final: 0.7837 (pp) REVERT: A 297 ARG cc_start: 0.8205 (mmt90) cc_final: 0.7962 (mmt90) REVERT: A 308 PHE cc_start: 0.8730 (t80) cc_final: 0.8035 (t80) REVERT: A 338 MET cc_start: 0.8321 (mmp) cc_final: 0.7772 (mmp) REVERT: A 343 THR cc_start: 0.8833 (p) cc_final: 0.8618 (p) REVERT: A 347 PHE cc_start: 0.8978 (t80) cc_final: 0.8665 (t80) REVERT: A 349 GLN cc_start: 0.8808 (tt0) cc_final: 0.8221 (tt0) REVERT: A 363 ILE cc_start: 0.9523 (mm) cc_final: 0.9293 (mm) REVERT: A 369 LEU cc_start: 0.9016 (mm) cc_final: 0.8716 (mm) REVERT: A 413 ASP cc_start: 0.9413 (t0) cc_final: 0.9067 (t0) REVERT: A 466 ILE cc_start: 0.8741 (mm) cc_final: 0.8441 (mm) REVERT: A 480 GLU cc_start: 0.8475 (tt0) cc_final: 0.8199 (tp30) REVERT: A 487 ASP cc_start: 0.8808 (m-30) cc_final: 0.8536 (m-30) REVERT: C 166 PHE cc_start: 0.9204 (p90) cc_final: 0.8956 (p90) REVERT: C 175 LYS cc_start: 0.7972 (pptt) cc_final: 0.7659 (tttt) REVERT: C 184 ASP cc_start: 0.8191 (m-30) cc_final: 0.7930 (m-30) REVERT: C 239 LEU cc_start: 0.8711 (pp) cc_final: 0.8255 (pp) REVERT: C 251 HIS cc_start: 0.7282 (m90) cc_final: 0.7070 (m90) REVERT: C 255 PHE cc_start: 0.9037 (t80) cc_final: 0.8501 (t80) REVERT: C 259 GLU cc_start: 0.9063 (pm20) cc_final: 0.8761 (pm20) REVERT: C 273 GLU cc_start: 0.8129 (tp30) cc_final: 0.6998 (tm-30) REVERT: C 308 PHE cc_start: 0.8600 (t80) cc_final: 0.8039 (t80) REVERT: C 313 TYR cc_start: 0.8592 (p90) cc_final: 0.8366 (p90) REVERT: C 347 PHE cc_start: 0.8923 (t80) cc_final: 0.8595 (t80) REVERT: C 361 GLU cc_start: 0.9320 (tp30) cc_final: 0.8650 (tm-30) REVERT: C 362 GLU cc_start: 0.8912 (mp0) cc_final: 0.8647 (mp0) REVERT: C 369 LEU cc_start: 0.9013 (mm) cc_final: 0.8721 (mm) REVERT: C 413 ASP cc_start: 0.9214 (t70) cc_final: 0.8946 (t70) REVERT: C 427 TYR cc_start: 0.8130 (m-80) cc_final: 0.7571 (m-80) REVERT: C 455 PHE cc_start: 0.8117 (p90) cc_final: 0.7881 (p90) REVERT: C 479 LEU cc_start: 0.9121 (mm) cc_final: 0.8822 (mm) REVERT: C 480 GLU cc_start: 0.8518 (tt0) cc_final: 0.8170 (tp30) REVERT: E 166 PHE cc_start: 0.9250 (p90) cc_final: 0.9014 (p90) REVERT: E 175 LYS cc_start: 0.7935 (pptt) cc_final: 0.7611 (tttt) REVERT: E 213 TYR cc_start: 0.8354 (t80) cc_final: 0.7939 (t80) REVERT: E 221 ARG cc_start: 0.8207 (mmt90) cc_final: 0.7921 (mmt90) REVERT: E 239 LEU cc_start: 0.8617 (pp) cc_final: 0.8167 (pp) REVERT: E 251 HIS cc_start: 0.7218 (m-70) cc_final: 0.6887 (m-70) REVERT: E 308 PHE cc_start: 0.8615 (t80) cc_final: 0.8022 (t80) REVERT: E 347 PHE cc_start: 0.8978 (t80) cc_final: 0.8680 (t80) REVERT: E 361 GLU cc_start: 0.9126 (tp30) cc_final: 0.8746 (tm-30) REVERT: E 362 GLU cc_start: 0.9053 (mp0) cc_final: 0.8737 (mp0) REVERT: E 364 GLU cc_start: 0.9383 (mt-10) cc_final: 0.9085 (mt-10) REVERT: E 369 LEU cc_start: 0.9072 (mm) cc_final: 0.8719 (mm) REVERT: E 427 TYR cc_start: 0.8133 (m-80) cc_final: 0.7539 (m-80) REVERT: E 443 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8221 (mtpt) REVERT: E 480 GLU cc_start: 0.8591 (tt0) cc_final: 0.8062 (tp30) REVERT: E 483 GLN cc_start: 0.9070 (pm20) cc_final: 0.8491 (pm20) REVERT: G 166 PHE cc_start: 0.9276 (p90) cc_final: 0.8950 (p90) REVERT: G 171 SER cc_start: 0.8957 (m) cc_final: 0.8628 (p) REVERT: G 172 GLU cc_start: 0.8601 (mp0) cc_final: 0.8266 (mp0) REVERT: G 175 LYS cc_start: 0.7812 (pptt) cc_final: 0.7528 (tttt) REVERT: G 213 TYR cc_start: 0.8575 (t80) cc_final: 0.8149 (t80) REVERT: G 239 LEU cc_start: 0.8641 (pp) cc_final: 0.8238 (pp) REVERT: G 251 HIS cc_start: 0.7186 (m-70) cc_final: 0.6981 (m-70) REVERT: G 255 PHE cc_start: 0.9144 (t80) cc_final: 0.8826 (t80) REVERT: G 259 GLU cc_start: 0.9056 (pm20) cc_final: 0.8841 (pm20) REVERT: G 266 GLU cc_start: 0.8471 (pp20) cc_final: 0.7812 (pp20) REVERT: G 297 ARG cc_start: 0.8818 (tpp-160) cc_final: 0.8513 (tpp-160) REVERT: G 308 PHE cc_start: 0.8578 (t80) cc_final: 0.8167 (t80) REVERT: G 338 MET cc_start: 0.8115 (mmp) cc_final: 0.7742 (mmp) REVERT: G 346 GLN cc_start: 0.8689 (tp40) cc_final: 0.8019 (tp40) REVERT: G 347 PHE cc_start: 0.8868 (t80) cc_final: 0.8344 (t80) REVERT: G 350 ASP cc_start: 0.8433 (m-30) cc_final: 0.8205 (m-30) REVERT: G 362 GLU cc_start: 0.9084 (mp0) cc_final: 0.8799 (mp0) REVERT: G 369 LEU cc_start: 0.8955 (mm) cc_final: 0.8624 (mm) REVERT: G 427 TYR cc_start: 0.8092 (m-80) cc_final: 0.7510 (m-80) REVERT: G 480 GLU cc_start: 0.8547 (tt0) cc_final: 0.8194 (tp30) REVERT: G 487 ASP cc_start: 0.8739 (m-30) cc_final: 0.8512 (m-30) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.2357 time to fit residues: 149.4731 Evaluate side-chains 394 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 36 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** G 428 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 = 0.3920 r_free = 0.3920 target = 0.122358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.093791 restraints weight = 25227.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097753 restraints weight = 16289.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100666 restraints weight = 11643.875| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11592 Z= 0.145 Angle : 0.807 12.667 15712 Z= 0.401 Chirality : 0.046 0.164 1684 Planarity : 0.005 0.063 2068 Dihedral : 5.418 30.465 1568 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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: -1.67 (0.22), residues: 1396 helix: -0.75 (0.18), residues: 788 sheet: -0.94 (0.43), residues: 140 loop : -1.53 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP A 371 HIS 0.017 0.002 HIS G 401 PHE 0.017 0.002 PHE C 305 TYR 0.012 0.001 TYR C 243 ARG 0.013 0.001 ARG G 450 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 510) hydrogen bonds : angle 5.84439 ( 1494) covalent geometry : bond 0.00327 (11592) covalent geometry : angle 0.80651 (15712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4501.44 seconds wall clock time: 79 minutes 28.54 seconds (4768.54 seconds total)