Starting phenix.real_space_refine on Sat Aug 23 09:48:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zn2_11309/08_2025/6zn2_11309.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zn2_11309/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zn2_11309/08_2025/6zn2_11309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zn2_11309/08_2025/6zn2_11309.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zn2_11309/08_2025/6zn2_11309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zn2_11309/08_2025/6zn2_11309.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: C, E, G, D, F, H Time building chain proxies: 2.21, per 1000 atoms: 0.20 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: 1.08 Conformation dependent library (CDL) restraints added in 401.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 1.81 Time building geometry restraints manager: 1.34 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.360 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG G 477 TYR 0.009 0.001 TYR C 243 PHE 0.024 0.001 PHE C 344 TRP 0.018 0.003 TRP E 371 HIS 0.006 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00402 (11592) covalent geometry : angle 0.92922 (15712) hydrogen bonds : bond 0.32640 ( 510) hydrogen bonds : angle 9.39496 ( 1494) *********************** 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 : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LYS cc_start: 0.8656 (mppt) cc_final: 0.8182 (mtpt) REVERT: A 172 GLU cc_start: 0.9163 (pm20) cc_final: 0.8684 (pm20) REVERT: A 186 ASP cc_start: 0.7957 (t0) cc_final: 0.7624 (t0) REVERT: A 208 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9059 (mm-30) REVERT: A 212 GLN cc_start: 0.9353 (pt0) cc_final: 0.9134 (tp40) REVERT: A 242 LEU cc_start: 0.9414 (tp) cc_final: 0.9121 (pp) REVERT: A 341 ASP cc_start: 0.8499 (t0) cc_final: 0.7859 (p0) REVERT: A 379 CYS cc_start: 0.9387 (p) cc_final: 0.9092 (p) REVERT: A 384 GLU cc_start: 0.8308 (pm20) cc_final: 0.8100 (pp20) 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: 0.9237 (t0) REVERT: C 182 LYS cc_start: 0.8687 (pttm) cc_final: 0.8466 (ptpp) REVERT: C 186 ASP cc_start: 0.7997 (t0) cc_final: 0.7646 (t0) REVERT: C 212 GLN cc_start: 0.9385 (pt0) cc_final: 0.9180 (tp40) REVERT: C 242 LEU cc_start: 0.9357 (tp) cc_final: 0.9101 (pp) REVERT: C 243 TYR cc_start: 0.9285 (m-10) cc_final: 0.9078 (m-10) REVERT: C 338 MET cc_start: 0.9048 (mmp) cc_final: 0.8815 (mmp) REVERT: C 341 ASP cc_start: 0.8435 (t0) cc_final: 0.7970 (p0) REVERT: C 393 LEU cc_start: 0.9148 (mp) cc_final: 0.8536 (mp) REVERT: C 463 THR cc_start: 0.8345 (t) cc_final: 0.8069 (t) REVERT: E 182 LYS cc_start: 0.8540 (pttm) cc_final: 0.8294 (ptpp) REVERT: E 186 ASP cc_start: 0.7914 (t0) cc_final: 0.7567 (t0) REVERT: E 212 GLN cc_start: 0.9379 (pt0) cc_final: 0.9175 (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: 0.8325 (mmp) REVERT: E 341 ASP cc_start: 0.8472 (t0) cc_final: 0.7967 (p0) REVERT: E 369 LEU cc_start: 0.8540 (mm) cc_final: 0.8338 (mm) REVERT: E 393 LEU cc_start: 0.9132 (mp) cc_final: 0.8600 (mp) REVERT: E 427 TYR cc_start: 0.8656 (m-80) cc_final: 0.8121 (m-80) REVERT: E 463 THR cc_start: 0.8166 (t) cc_final: 0.7906 (t) REVERT: G 186 ASP cc_start: 0.7918 (t0) cc_final: 0.7613 (t0) REVERT: G 212 GLN cc_start: 0.9366 (pt0) cc_final: 0.9156 (tp40) REVERT: G 242 LEU cc_start: 0.9361 (tp) cc_final: 0.9110 (pp) REVERT: G 341 ASP cc_start: 0.8458 (t0) cc_final: 0.8050 (p0) REVERT: G 393 LEU cc_start: 0.9184 (mp) cc_final: 0.8553 (mp) REVERT: G 427 TYR cc_start: 0.8751 (m-80) cc_final: 0.8171 (m-80) outliers start: 76 outliers final: 33 residues processed: 609 average time/residue: 0.1357 time to fit residues: 110.1600 Evaluate side-chains 454 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 421 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN C 491 HIS E 381 GLN 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 = 0.4019 r_free = 0.4019 target = 0.127762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.096457 restraints weight = 25466.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100320 restraints weight = 17252.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.103232 restraints weight = 12702.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.105396 restraints weight = 9962.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.107121 restraints weight = 8221.080| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 11592 Z= 0.190 Angle : 0.793 10.231 15712 Z= 0.398 Chirality : 0.047 0.150 1684 Planarity : 0.005 0.063 2068 Dihedral : 5.041 21.691 1568 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.84 % Allowed : 3.93 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.22), residues: 1396 helix: -1.17 (0.17), residues: 780 sheet: -0.81 (0.60), residues: 96 loop : -0.76 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 49 TYR 0.016 0.002 TYR C 313 PHE 0.018 0.002 PHE C 278 TRP 0.023 0.003 TRP E 371 HIS 0.011 0.002 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00414 (11592) covalent geometry : angle 0.79253 (15712) hydrogen bonds : bond 0.06243 ( 510) hydrogen bonds : angle 6.29555 ( 1494) *********************** 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 502 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 492 time to evaluate : 0.462 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: A 175 LYS cc_start: 0.7975 (pptt) cc_final: 0.7737 (tttt) REVERT: A 186 ASP cc_start: 0.8096 (t0) cc_final: 0.7748 (t0) REVERT: A 208 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8260 (mm-30) REVERT: A 213 TYR cc_start: 0.8590 (t80) cc_final: 0.8223 (t80) REVERT: A 214 ARG cc_start: 0.8747 (mmp80) cc_final: 0.8476 (mmp80) REVERT: A 239 LEU cc_start: 0.8250 (pp) cc_final: 0.7781 (pp) REVERT: A 246 HIS cc_start: 0.8494 (m-70) cc_final: 0.7966 (m170) REVERT: A 251 HIS cc_start: 0.6566 (m170) cc_final: 0.6262 (m-70) REVERT: A 255 PHE cc_start: 0.9175 (t80) cc_final: 0.8969 (t80) REVERT: A 308 PHE cc_start: 0.8579 (t80) cc_final: 0.8259 (t80) REVERT: A 331 GLU cc_start: 0.8389 (pt0) cc_final: 0.7994 (pt0) REVERT: A 341 ASP cc_start: 0.8476 (t0) cc_final: 0.7888 (p0) REVERT: A 362 GLU cc_start: 0.8998 (mp0) cc_final: 0.8009 (mp0) REVERT: A 369 LEU cc_start: 0.8805 (mm) cc_final: 0.8403 (mm) REVERT: A 393 LEU cc_start: 0.8673 (mp) cc_final: 0.8421 (mp) REVERT: A 413 ASP cc_start: 0.9256 (t0) cc_final: 0.8882 (t0) REVERT: A 482 VAL cc_start: 0.9157 (t) cc_final: 0.8834 (t) REVERT: A 485 GLU cc_start: 0.8932 (mp0) cc_final: 0.8609 (mp0) REVERT: C 174 ASP cc_start: 0.7949 (t70) cc_final: 0.7708 (t0) REVERT: C 175 LYS cc_start: 0.8025 (pptt) cc_final: 0.7620 (tttt) REVERT: C 182 LYS cc_start: 0.8176 (pttm) cc_final: 0.7969 (ptpp) REVERT: C 186 ASP cc_start: 0.8047 (t0) cc_final: 0.7777 (t0) REVERT: C 213 TYR cc_start: 0.8480 (t80) cc_final: 0.8163 (t80) REVERT: C 214 ARG cc_start: 0.8643 (mmp80) cc_final: 0.8331 (mmp80) REVERT: C 239 LEU cc_start: 0.8280 (pp) cc_final: 0.7757 (pp) REVERT: C 246 HIS cc_start: 0.8543 (m-70) cc_final: 0.7935 (m170) REVERT: C 251 HIS cc_start: 0.6853 (m-70) cc_final: 0.6491 (m-70) REVERT: C 308 PHE cc_start: 0.8596 (t80) cc_final: 0.8302 (t80) REVERT: C 338 MET cc_start: 0.7236 (mmp) cc_final: 0.6862 (mmp) REVERT: C 341 ASP cc_start: 0.8700 (t0) cc_final: 0.8104 (p0) REVERT: C 347 PHE cc_start: 0.8670 (t80) cc_final: 0.8358 (t80) REVERT: C 360 ASP cc_start: 0.9145 (m-30) cc_final: 0.8680 (p0) REVERT: C 361 GLU cc_start: 0.9327 (tp30) cc_final: 0.8902 (tm-30) REVERT: C 362 GLU cc_start: 0.8932 (mp0) cc_final: 0.8670 (mp0) REVERT: C 369 LEU cc_start: 0.8568 (mm) cc_final: 0.8168 (mm) REVERT: C 393 LEU cc_start: 0.8778 (mp) cc_final: 0.8411 (mp) REVERT: C 413 ASP cc_start: 0.9185 (t70) cc_final: 0.8855 (t0) REVERT: C 482 VAL cc_start: 0.9022 (t) cc_final: 0.8723 (t) REVERT: C 485 GLU cc_start: 0.8931 (mp0) cc_final: 0.8591 (mp0) REVERT: E 175 LYS cc_start: 0.7993 (pptt) cc_final: 0.7668 (tttt) REVERT: E 182 LYS cc_start: 0.8108 (pttm) cc_final: 0.7839 (ptpp) REVERT: E 186 ASP cc_start: 0.8006 (t0) cc_final: 0.7714 (t0) REVERT: E 213 TYR cc_start: 0.8655 (t80) cc_final: 0.8200 (t80) REVERT: E 239 LEU cc_start: 0.8174 (pp) cc_final: 0.7784 (pp) REVERT: E 246 HIS cc_start: 0.8485 (m-70) cc_final: 0.7611 (m170) REVERT: E 273 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7684 (tp30) REVERT: E 276 SER cc_start: 0.9146 (m) cc_final: 0.8899 (p) REVERT: E 308 PHE cc_start: 0.8581 (t80) cc_final: 0.8234 (t80) REVERT: E 341 ASP cc_start: 0.8712 (t0) cc_final: 0.8117 (p0) REVERT: E 369 LEU cc_start: 0.8728 (mm) cc_final: 0.8236 (mm) REVERT: E 393 LEU cc_start: 0.8823 (mp) cc_final: 0.8448 (mp) REVERT: E 455 PHE cc_start: 0.8106 (p90) cc_final: 0.7749 (p90) REVERT: E 482 VAL cc_start: 0.9104 (t) cc_final: 0.8749 (t) REVERT: E 485 GLU cc_start: 0.8974 (mp0) cc_final: 0.8619 (mp0) REVERT: E 487 ASP cc_start: 0.8614 (m-30) cc_final: 0.8403 (m-30) REVERT: G 172 GLU cc_start: 0.8579 (pm20) cc_final: 0.8088 (pm20) REVERT: G 175 LYS cc_start: 0.7983 (pptt) cc_final: 0.7680 (tttt) REVERT: G 186 ASP cc_start: 0.8072 (t0) cc_final: 0.7758 (t0) REVERT: G 213 TYR cc_start: 0.8543 (t80) cc_final: 0.8172 (t80) REVERT: G 214 ARG cc_start: 0.8664 (mmp80) cc_final: 0.8416 (mmp80) REVERT: G 239 LEU cc_start: 0.8245 (pp) cc_final: 0.7784 (pp) REVERT: G 240 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8460 (mtpp) REVERT: G 246 HIS cc_start: 0.8472 (m-70) cc_final: 0.7601 (m170) REVERT: G 251 HIS cc_start: 0.6693 (m-70) cc_final: 0.6473 (m-70) REVERT: G 308 PHE cc_start: 0.8634 (t80) cc_final: 0.8318 (t80) REVERT: G 338 MET cc_start: 0.6885 (mmp) cc_final: 0.6600 (mmp) REVERT: G 341 ASP cc_start: 0.8723 (t0) cc_final: 0.8187 (p0) REVERT: G 347 PHE cc_start: 0.8690 (t80) cc_final: 0.8319 (t80) REVERT: G 353 LEU cc_start: 0.9061 (mm) cc_final: 0.8846 (mm) REVERT: G 360 ASP cc_start: 0.9214 (m-30) cc_final: 0.8801 (p0) REVERT: G 369 LEU cc_start: 0.8763 (mm) cc_final: 0.8353 (mm) REVERT: G 393 LEU cc_start: 0.8863 (mp) cc_final: 0.8456 (mp) REVERT: G 413 ASP cc_start: 0.9231 (t70) cc_final: 0.8922 (t0) REVERT: G 482 VAL cc_start: 0.9164 (t) cc_final: 0.8832 (t) REVERT: G 485 GLU cc_start: 0.8913 (mp0) cc_final: 0.8561 (mp0) outliers start: 10 outliers final: 0 residues processed: 492 average time/residue: 0.1347 time to fit residues: 89.4905 Evaluate side-chains 403 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.123007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092928 restraints weight = 25995.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096742 restraints weight = 17338.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.099547 restraints weight = 12640.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101712 restraints weight = 9872.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.103144 restraints weight = 8095.188| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 11592 Z= 0.216 Angle : 0.742 9.335 15712 Z= 0.383 Chirality : 0.046 0.188 1684 Planarity : 0.005 0.034 2068 Dihedral : 5.093 25.537 1568 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.17 % Allowed : 6.77 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.22), residues: 1396 helix: -1.16 (0.17), residues: 784 sheet: -1.35 (0.46), residues: 144 loop : -0.58 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 49 TYR 0.017 0.002 TYR C 236 PHE 0.029 0.002 PHE A 372 TRP 0.030 0.003 TRP G 371 HIS 0.012 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00471 (11592) covalent geometry : angle 0.74187 (15712) hydrogen bonds : bond 0.05424 ( 510) hydrogen bonds : angle 6.15274 ( 1494) *********************** 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 481 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 0.466 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: A 166 PHE cc_start: 0.9161 (p90) cc_final: 0.8952 (p90) REVERT: A 175 LYS cc_start: 0.8105 (pptt) cc_final: 0.7780 (tttt) REVERT: A 184 ASP cc_start: 0.8281 (m-30) cc_final: 0.8038 (m-30) REVERT: A 186 ASP cc_start: 0.8165 (t0) cc_final: 0.7838 (t0) REVERT: A 225 THR cc_start: 0.8165 (p) cc_final: 0.7837 (p) REVERT: A 239 LEU cc_start: 0.8597 (pp) cc_final: 0.7686 (pp) REVERT: A 246 HIS cc_start: 0.8644 (m-70) cc_final: 0.8131 (m170) REVERT: A 255 PHE cc_start: 0.9116 (t80) cc_final: 0.8916 (t80) REVERT: A 267 ASP cc_start: 0.9136 (p0) cc_final: 0.8638 (p0) REVERT: A 308 PHE cc_start: 0.8694 (t80) cc_final: 0.8011 (t80) REVERT: A 313 TYR cc_start: 0.8517 (p90) cc_final: 0.8282 (p90) REVERT: A 331 GLU cc_start: 0.8354 (pt0) cc_final: 0.7994 (pt0) REVERT: A 338 MET cc_start: 0.7740 (mmp) cc_final: 0.7442 (mmp) REVERT: A 341 ASP cc_start: 0.8440 (t0) cc_final: 0.8112 (p0) REVERT: A 347 PHE cc_start: 0.8906 (t80) cc_final: 0.8695 (t80) REVERT: A 362 GLU cc_start: 0.8516 (mp0) cc_final: 0.8054 (mp0) REVERT: A 369 LEU cc_start: 0.8966 (mm) cc_final: 0.8556 (mm) REVERT: A 392 LEU cc_start: 0.9278 (mt) cc_final: 0.8726 (mt) REVERT: A 393 LEU cc_start: 0.8610 (mp) cc_final: 0.8238 (mp) REVERT: A 413 ASP cc_start: 0.9344 (t0) cc_final: 0.8957 (t0) REVERT: A 456 SER cc_start: 0.8386 (t) cc_final: 0.8161 (t) REVERT: A 482 VAL cc_start: 0.9184 (t) cc_final: 0.8973 (t) REVERT: A 485 GLU cc_start: 0.8896 (mp0) cc_final: 0.8694 (mp0) REVERT: C 175 LYS cc_start: 0.7991 (pptt) cc_final: 0.7564 (tttt) REVERT: C 186 ASP cc_start: 0.8101 (t0) cc_final: 0.7818 (t0) REVERT: C 239 LEU cc_start: 0.8719 (pp) cc_final: 0.7692 (pp) REVERT: C 246 HIS cc_start: 0.8564 (m-70) cc_final: 0.7614 (m170) REVERT: C 251 HIS cc_start: 0.7245 (m-70) cc_final: 0.6775 (m-70) REVERT: C 255 PHE cc_start: 0.9124 (t80) cc_final: 0.8865 (t80) REVERT: C 267 ASP cc_start: 0.8677 (p0) cc_final: 0.8323 (p0) REVERT: C 308 PHE cc_start: 0.8628 (t80) cc_final: 0.8221 (t80) REVERT: C 313 TYR cc_start: 0.8581 (p90) cc_final: 0.8363 (p90) REVERT: C 341 ASP cc_start: 0.8767 (t0) cc_final: 0.8074 (p0) REVERT: C 347 PHE cc_start: 0.8669 (t80) cc_final: 0.8384 (t80) REVERT: C 360 ASP cc_start: 0.9202 (m-30) cc_final: 0.8710 (p0) REVERT: C 361 GLU cc_start: 0.9393 (tp30) cc_final: 0.8905 (tm-30) REVERT: C 362 GLU cc_start: 0.8986 (mp0) cc_final: 0.8776 (mp0) REVERT: C 369 LEU cc_start: 0.8927 (mm) cc_final: 0.8468 (mm) REVERT: C 393 LEU cc_start: 0.8864 (mp) cc_final: 0.8378 (mp) REVERT: C 447 TYR cc_start: 0.8897 (t80) cc_final: 0.8576 (t80) REVERT: C 455 PHE cc_start: 0.8249 (p90) cc_final: 0.7891 (p90) REVERT: C 456 SER cc_start: 0.8457 (t) cc_final: 0.8074 (t) REVERT: C 482 VAL cc_start: 0.9145 (t) cc_final: 0.8944 (t) REVERT: E 175 LYS cc_start: 0.8103 (pptt) cc_final: 0.7688 (tttt) REVERT: E 186 ASP cc_start: 0.8079 (t0) cc_final: 0.7806 (t0) REVERT: E 239 LEU cc_start: 0.8613 (pp) cc_final: 0.7550 (pp) REVERT: E 246 HIS cc_start: 0.8603 (m-70) cc_final: 0.7718 (m170) REVERT: E 259 GLU cc_start: 0.8915 (pm20) cc_final: 0.8673 (pm20) REVERT: E 273 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7544 (tp30) REVERT: E 276 SER cc_start: 0.9140 (m) cc_final: 0.8933 (p) REVERT: E 308 PHE cc_start: 0.8612 (t80) cc_final: 0.8179 (t80) REVERT: E 313 TYR cc_start: 0.8777 (p90) cc_final: 0.8437 (p90) REVERT: E 338 MET cc_start: 0.7669 (mmp) cc_final: 0.7456 (mmp) REVERT: E 341 ASP cc_start: 0.8756 (t0) cc_final: 0.8200 (p0) REVERT: E 347 PHE cc_start: 0.8867 (t80) cc_final: 0.8614 (t80) REVERT: E 361 GLU cc_start: 0.9333 (tp30) cc_final: 0.8827 (tm-30) REVERT: E 364 GLU cc_start: 0.9380 (mt-10) cc_final: 0.9119 (mt-10) REVERT: E 369 LEU cc_start: 0.9014 (mm) cc_final: 0.8560 (mm) REVERT: E 393 LEU cc_start: 0.8862 (mp) cc_final: 0.8461 (mp) REVERT: E 447 TYR cc_start: 0.8980 (t80) cc_final: 0.8410 (t80) REVERT: E 450 ARG cc_start: 0.9117 (mtt90) cc_final: 0.8643 (ttm110) REVERT: E 456 SER cc_start: 0.8436 (t) cc_final: 0.8188 (t) REVERT: E 482 VAL cc_start: 0.9130 (t) cc_final: 0.8917 (t) REVERT: E 485 GLU cc_start: 0.8986 (mp0) cc_final: 0.8711 (mp0) REVERT: E 487 ASP cc_start: 0.8732 (m-30) cc_final: 0.8340 (m-30) REVERT: G 166 PHE cc_start: 0.8906 (p90) cc_final: 0.8616 (p90) REVERT: G 173 LEU cc_start: 0.8796 (mt) cc_final: 0.8547 (mt) REVERT: G 175 LYS cc_start: 0.8094 (pptt) cc_final: 0.7708 (tttt) REVERT: G 186 ASP cc_start: 0.8039 (t0) cc_final: 0.7702 (t0) REVERT: G 239 LEU cc_start: 0.8645 (pp) cc_final: 0.7636 (pp) REVERT: G 251 HIS cc_start: 0.7114 (m-70) cc_final: 0.6799 (m90) REVERT: G 267 ASP cc_start: 0.9147 (p0) cc_final: 0.8789 (p0) REVERT: G 308 PHE cc_start: 0.8683 (t80) cc_final: 0.8222 (t80) REVERT: G 310 CYS cc_start: 0.8332 (p) cc_final: 0.7875 (p) REVERT: G 313 TYR cc_start: 0.8527 (p90) cc_final: 0.8265 (p90) REVERT: G 338 MET cc_start: 0.7425 (mmp) cc_final: 0.7167 (mmt) REVERT: G 341 ASP cc_start: 0.8771 (t0) cc_final: 0.8104 (p0) REVERT: G 347 PHE cc_start: 0.8790 (t80) cc_final: 0.8369 (t80) REVERT: G 360 ASP cc_start: 0.9272 (m-30) cc_final: 0.8867 (p0) REVERT: G 361 GLU cc_start: 0.9441 (tp30) cc_final: 0.9052 (tp30) REVERT: G 369 LEU cc_start: 0.8952 (mm) cc_final: 0.8506 (mm) REVERT: G 393 LEU cc_start: 0.8795 (mp) cc_final: 0.8361 (mp) REVERT: G 450 ARG cc_start: 0.9126 (mtt90) cc_final: 0.8676 (ttm110) REVERT: G 455 PHE cc_start: 0.8024 (p90) cc_final: 0.7743 (p90) outliers start: 2 outliers final: 0 residues processed: 479 average time/residue: 0.1154 time to fit residues: 76.5097 Evaluate side-chains 405 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS A 428 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 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** E 491 HIS ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.124108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.094082 restraints weight = 25655.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.098038 restraints weight = 17005.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.100995 restraints weight = 12337.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103147 restraints weight = 9548.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104845 restraints weight = 7794.897| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 11592 Z= 0.176 Angle : 0.733 7.861 15712 Z= 0.374 Chirality : 0.046 0.234 1684 Planarity : 0.005 0.054 2068 Dihedral : 5.126 28.214 1568 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.59 % Allowed : 3.76 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.22), residues: 1396 helix: -1.05 (0.17), residues: 784 sheet: -0.98 (0.48), residues: 136 loop : -0.85 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 297 TYR 0.019 0.002 TYR C 236 PHE 0.027 0.002 PHE C 372 TRP 0.035 0.003 TRP E 371 HIS 0.013 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00392 (11592) covalent geometry : angle 0.73287 (15712) hydrogen bonds : bond 0.04850 ( 510) hydrogen bonds : angle 6.01527 ( 1494) *********************** 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 496 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 489 time to evaluate : 0.412 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: A 166 PHE cc_start: 0.9090 (p90) cc_final: 0.8855 (p90) REVERT: A 169 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8150 (mtpt) REVERT: A 172 GLU cc_start: 0.8591 (pm20) cc_final: 0.8132 (pm20) REVERT: A 175 LYS cc_start: 0.8226 (pptt) cc_final: 0.8024 (tttt) REVERT: A 184 ASP cc_start: 0.8373 (m-30) cc_final: 0.8156 (m-30) REVERT: A 186 ASP cc_start: 0.8227 (t0) cc_final: 0.7878 (t0) REVERT: A 239 LEU cc_start: 0.8640 (pp) cc_final: 0.7699 (pp) REVERT: A 240 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8545 (mtpp) REVERT: A 246 HIS cc_start: 0.8590 (m-70) cc_final: 0.8075 (m170) REVERT: A 265 ARG cc_start: 0.8891 (ttp-110) cc_final: 0.8340 (ttp-110) REVERT: A 267 ASP cc_start: 0.8880 (p0) cc_final: 0.8163 (p0) REVERT: A 308 PHE cc_start: 0.8646 (t80) cc_final: 0.8279 (t80) REVERT: A 313 TYR cc_start: 0.8515 (p90) cc_final: 0.8310 (p90) REVERT: A 331 GLU cc_start: 0.8306 (pt0) cc_final: 0.7835 (mp0) REVERT: A 341 ASP cc_start: 0.8591 (t0) cc_final: 0.7816 (p0) REVERT: A 347 PHE cc_start: 0.8885 (t80) cc_final: 0.8654 (t80) REVERT: A 349 GLN cc_start: 0.8748 (tt0) cc_final: 0.8521 (tt0) REVERT: A 363 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9307 (mp) REVERT: A 369 LEU cc_start: 0.8979 (mm) cc_final: 0.8619 (mm) REVERT: A 393 LEU cc_start: 0.8766 (mp) cc_final: 0.8553 (mp) REVERT: A 413 ASP cc_start: 0.9314 (t0) cc_final: 0.8916 (t0) REVERT: A 445 ARG cc_start: 0.8268 (mmt90) cc_final: 0.7653 (mmt180) REVERT: A 479 LEU cc_start: 0.8392 (mt) cc_final: 0.8187 (mt) REVERT: A 485 GLU cc_start: 0.8892 (mp0) cc_final: 0.8655 (mp0) REVERT: C 175 LYS cc_start: 0.8152 (pptt) cc_final: 0.7856 (tttt) REVERT: C 186 ASP cc_start: 0.8132 (t0) cc_final: 0.7817 (t0) REVERT: C 239 LEU cc_start: 0.8618 (pp) cc_final: 0.7626 (pp) REVERT: C 242 LEU cc_start: 0.8399 (pp) cc_final: 0.7995 (pp) REVERT: C 246 HIS cc_start: 0.8517 (m-70) cc_final: 0.7825 (m170) REVERT: C 255 PHE cc_start: 0.9128 (t80) cc_final: 0.8799 (t80) REVERT: C 297 ARG cc_start: 0.8828 (tpp-160) cc_final: 0.8430 (tpp-160) REVERT: C 308 PHE cc_start: 0.8580 (t80) cc_final: 0.8152 (t80) REVERT: C 313 TYR cc_start: 0.8555 (p90) cc_final: 0.8275 (p90) REVERT: C 338 MET cc_start: 0.7865 (mmp) cc_final: 0.7403 (mmp) REVERT: C 341 ASP cc_start: 0.8798 (t0) cc_final: 0.8095 (p0) REVERT: C 347 PHE cc_start: 0.8768 (t80) cc_final: 0.8361 (t80) REVERT: C 360 ASP cc_start: 0.8895 (m-30) cc_final: 0.8593 (p0) REVERT: C 361 GLU cc_start: 0.9276 (tp30) cc_final: 0.8623 (tm-30) REVERT: C 362 GLU cc_start: 0.8972 (mp0) cc_final: 0.8607 (mp0) REVERT: C 369 LEU cc_start: 0.8974 (mm) cc_final: 0.8577 (mm) REVERT: C 393 LEU cc_start: 0.8792 (mp) cc_final: 0.8449 (mp) REVERT: C 413 ASP cc_start: 0.9209 (t70) cc_final: 0.8922 (t0) REVERT: C 447 TYR cc_start: 0.8922 (t80) cc_final: 0.8662 (t80) REVERT: C 455 PHE cc_start: 0.8178 (p90) cc_final: 0.7854 (p90) REVERT: C 482 VAL cc_start: 0.9145 (t) cc_final: 0.8717 (t) REVERT: C 485 GLU cc_start: 0.8745 (mp0) cc_final: 0.8307 (mp0) REVERT: E 175 LYS cc_start: 0.8260 (pptt) cc_final: 0.7969 (tttt) REVERT: E 186 ASP cc_start: 0.8038 (t0) cc_final: 0.7722 (t0) REVERT: E 225 THR cc_start: 0.8127 (p) cc_final: 0.7791 (p) REVERT: E 239 LEU cc_start: 0.8578 (pp) cc_final: 0.7633 (pp) REVERT: E 242 LEU cc_start: 0.8332 (pp) cc_final: 0.8006 (pp) REVERT: E 246 HIS cc_start: 0.8544 (m-70) cc_final: 0.7816 (m170) REVERT: E 251 HIS cc_start: 0.6938 (m-70) cc_final: 0.6634 (m90) REVERT: E 276 SER cc_start: 0.9252 (m) cc_final: 0.8758 (p) REVERT: E 308 PHE cc_start: 0.8628 (t80) cc_final: 0.8131 (t80) REVERT: E 313 TYR cc_start: 0.8675 (p90) cc_final: 0.8271 (p90) REVERT: E 338 MET cc_start: 0.7507 (mmp) cc_final: 0.7234 (mmt) REVERT: E 341 ASP cc_start: 0.8750 (t0) cc_final: 0.8041 (p0) REVERT: E 347 PHE cc_start: 0.8817 (t80) cc_final: 0.8566 (t80) REVERT: E 349 GLN cc_start: 0.8959 (tt0) cc_final: 0.8606 (tt0) REVERT: E 361 GLU cc_start: 0.9313 (tp30) cc_final: 0.8900 (tm-30) REVERT: E 362 GLU cc_start: 0.9049 (mp0) cc_final: 0.8640 (mp0) REVERT: E 364 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9062 (mt-10) REVERT: E 369 LEU cc_start: 0.9036 (mm) cc_final: 0.8519 (mm) REVERT: E 393 LEU cc_start: 0.8626 (mp) cc_final: 0.8281 (mp) REVERT: E 447 TYR cc_start: 0.8879 (t80) cc_final: 0.8452 (t80) REVERT: E 450 ARG cc_start: 0.8960 (mtt90) cc_final: 0.8598 (ttm110) REVERT: E 455 PHE cc_start: 0.8107 (p90) cc_final: 0.7805 (p90) REVERT: E 456 SER cc_start: 0.8439 (t) cc_final: 0.8133 (t) REVERT: E 480 GLU cc_start: 0.8529 (tt0) cc_final: 0.7942 (tp30) REVERT: E 485 GLU cc_start: 0.8950 (mp0) cc_final: 0.8715 (mp0) REVERT: G 166 PHE cc_start: 0.8875 (p90) cc_final: 0.8575 (p90) REVERT: G 175 LYS cc_start: 0.8215 (pptt) cc_final: 0.7953 (tttt) REVERT: G 186 ASP cc_start: 0.8144 (t0) cc_final: 0.7815 (t0) REVERT: G 239 LEU cc_start: 0.8562 (pp) cc_final: 0.7655 (pp) REVERT: G 240 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8555 (mtpp) REVERT: G 242 LEU cc_start: 0.8318 (pp) cc_final: 0.8091 (pp) REVERT: G 251 HIS cc_start: 0.7052 (m-70) cc_final: 0.6764 (m-70) REVERT: G 255 PHE cc_start: 0.9179 (t80) cc_final: 0.8842 (t80) REVERT: G 265 ARG cc_start: 0.8948 (ttp-110) cc_final: 0.8622 (ttp-110) REVERT: G 267 ASP cc_start: 0.8933 (p0) cc_final: 0.8610 (p0) REVERT: G 299 PHE cc_start: 0.8786 (t80) cc_final: 0.8568 (t80) REVERT: G 308 PHE cc_start: 0.8633 (t80) cc_final: 0.8316 (t80) REVERT: G 310 CYS cc_start: 0.8390 (p) cc_final: 0.7496 (p) REVERT: G 313 TYR cc_start: 0.8525 (p90) cc_final: 0.8294 (p90) REVERT: G 331 GLU cc_start: 0.8309 (pt0) cc_final: 0.7928 (mp0) REVERT: G 338 MET cc_start: 0.7657 (mmp) cc_final: 0.7224 (mmt) REVERT: G 341 ASP cc_start: 0.8750 (t0) cc_final: 0.8084 (p0) REVERT: G 347 PHE cc_start: 0.8884 (t80) cc_final: 0.8310 (t80) REVERT: G 361 GLU cc_start: 0.9334 (tp30) cc_final: 0.8955 (tm-30) REVERT: G 369 LEU cc_start: 0.8942 (mm) cc_final: 0.8559 (mm) REVERT: G 393 LEU cc_start: 0.8798 (mp) cc_final: 0.8433 (mp) REVERT: G 413 ASP cc_start: 0.9286 (t70) cc_final: 0.9011 (t0) REVERT: G 450 ARG cc_start: 0.8995 (mtt90) cc_final: 0.8650 (ttm110) REVERT: G 455 PHE cc_start: 0.7967 (p90) cc_final: 0.7717 (p90) REVERT: G 485 GLU cc_start: 0.8749 (mp0) cc_final: 0.8321 (mp0) outliers start: 7 outliers final: 2 residues processed: 489 average time/residue: 0.1191 time to fit residues: 80.6512 Evaluate side-chains 413 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 410 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 382 ASN A 423 GLN A 428 GLN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN G 271 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.126815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.096356 restraints weight = 24996.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100383 restraints weight = 16715.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103510 restraints weight = 12174.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.105753 restraints weight = 9409.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.107515 restraints weight = 7686.358| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11592 Z= 0.140 Angle : 0.718 9.836 15712 Z= 0.358 Chirality : 0.045 0.231 1684 Planarity : 0.004 0.047 2068 Dihedral : 5.077 29.477 1568 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.22), residues: 1396 helix: -0.95 (0.18), residues: 792 sheet: -0.93 (0.49), residues: 136 loop : -0.72 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.014 0.001 TYR A 236 PHE 0.023 0.002 PHE A 344 TRP 0.041 0.003 TRP A 371 HIS 0.011 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00324 (11592) covalent geometry : angle 0.71788 (15712) hydrogen bonds : bond 0.04632 ( 510) hydrogen bonds : angle 5.90902 ( 1494) *********************** 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 469 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 468 time to evaluate : 0.482 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: A 175 LYS cc_start: 0.8166 (pptt) cc_final: 0.7902 (tttt) REVERT: A 184 ASP cc_start: 0.8210 (m-30) cc_final: 0.7998 (m-30) REVERT: A 186 ASP cc_start: 0.8205 (t0) cc_final: 0.7855 (t0) REVERT: A 239 LEU cc_start: 0.8624 (pp) cc_final: 0.7657 (pp) REVERT: A 251 HIS cc_start: 0.7139 (m-70) cc_final: 0.6925 (m-70) REVERT: A 255 PHE cc_start: 0.9241 (t80) cc_final: 0.9010 (t80) REVERT: A 299 PHE cc_start: 0.8724 (t80) cc_final: 0.8457 (t80) REVERT: A 306 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.8155 (mtp180) REVERT: A 308 PHE cc_start: 0.8672 (t80) cc_final: 0.8354 (t80) REVERT: A 331 GLU cc_start: 0.8308 (pt0) cc_final: 0.7759 (mp0) REVERT: A 338 MET cc_start: 0.8129 (mmp) cc_final: 0.7135 (mmt) REVERT: A 341 ASP cc_start: 0.8536 (t0) cc_final: 0.7723 (p0) REVERT: A 347 PHE cc_start: 0.8908 (t80) cc_final: 0.8622 (t80) REVERT: A 349 GLN cc_start: 0.8713 (tt0) cc_final: 0.8488 (tt0) REVERT: A 362 GLU cc_start: 0.8957 (mp0) cc_final: 0.8693 (mp0) REVERT: A 363 ILE cc_start: 0.9451 (mp) cc_final: 0.9212 (mp) REVERT: A 369 LEU cc_start: 0.8909 (mm) cc_final: 0.8478 (mm) REVERT: A 393 LEU cc_start: 0.8542 (mp) cc_final: 0.8334 (mp) REVERT: A 413 ASP cc_start: 0.9298 (t0) cc_final: 0.8871 (t0) REVERT: A 456 SER cc_start: 0.8252 (t) cc_final: 0.8042 (t) REVERT: A 479 LEU cc_start: 0.8429 (mt) cc_final: 0.8191 (mt) REVERT: A 485 GLU cc_start: 0.8864 (mp0) cc_final: 0.8527 (mp0) REVERT: C 175 LYS cc_start: 0.7997 (pptt) cc_final: 0.7710 (tptt) REVERT: C 186 ASP cc_start: 0.8102 (t0) cc_final: 0.7807 (t0) REVERT: C 239 LEU cc_start: 0.8594 (pp) cc_final: 0.7680 (pp) REVERT: C 246 HIS cc_start: 0.8530 (m-70) cc_final: 0.7607 (m170) REVERT: C 251 HIS cc_start: 0.7100 (m-70) cc_final: 0.6776 (m-70) REVERT: C 267 ASP cc_start: 0.9198 (p0) cc_final: 0.8720 (p0) REVERT: C 297 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8271 (tpp-160) REVERT: C 308 PHE cc_start: 0.8490 (t80) cc_final: 0.8071 (t80) REVERT: C 313 TYR cc_start: 0.8474 (p90) cc_final: 0.8245 (p90) REVERT: C 338 MET cc_start: 0.7924 (mmp) cc_final: 0.7296 (mmt) REVERT: C 341 ASP cc_start: 0.8741 (t0) cc_final: 0.7948 (p0) REVERT: C 347 PHE cc_start: 0.8513 (t80) cc_final: 0.8277 (t80) REVERT: C 361 GLU cc_start: 0.9277 (tp30) cc_final: 0.8519 (tm-30) REVERT: C 362 GLU cc_start: 0.9003 (mp0) cc_final: 0.8270 (mp0) REVERT: C 369 LEU cc_start: 0.8909 (mm) cc_final: 0.8445 (mm) REVERT: C 393 LEU cc_start: 0.8615 (mp) cc_final: 0.8312 (mp) REVERT: C 413 ASP cc_start: 0.9171 (t70) cc_final: 0.8871 (t0) REVERT: C 455 PHE cc_start: 0.8094 (p90) cc_final: 0.7810 (p90) REVERT: C 479 LEU cc_start: 0.8555 (mt) cc_final: 0.8326 (mt) REVERT: C 480 GLU cc_start: 0.8501 (tt0) cc_final: 0.8009 (tp30) REVERT: C 482 VAL cc_start: 0.9102 (t) cc_final: 0.8683 (t) REVERT: C 485 GLU cc_start: 0.8713 (mp0) cc_final: 0.8296 (mp0) REVERT: E 166 PHE cc_start: 0.9063 (p90) cc_final: 0.8853 (p90) REVERT: E 175 LYS cc_start: 0.8025 (pptt) cc_final: 0.7798 (tttt) REVERT: E 184 ASP cc_start: 0.8230 (m-30) cc_final: 0.7840 (m-30) REVERT: E 186 ASP cc_start: 0.8007 (t0) cc_final: 0.7702 (t0) REVERT: E 239 LEU cc_start: 0.8539 (pp) cc_final: 0.7759 (pp) REVERT: E 242 LEU cc_start: 0.8333 (pp) cc_final: 0.8130 (pp) REVERT: E 246 HIS cc_start: 0.8549 (m-70) cc_final: 0.7862 (m170) REVERT: E 251 HIS cc_start: 0.7058 (m-70) cc_final: 0.6783 (m-70) REVERT: E 255 PHE cc_start: 0.9169 (t80) cc_final: 0.8935 (t80) REVERT: E 267 ASP cc_start: 0.9068 (p0) cc_final: 0.8818 (p0) REVERT: E 308 PHE cc_start: 0.8577 (t80) cc_final: 0.8106 (t80) REVERT: E 313 TYR cc_start: 0.8525 (p90) cc_final: 0.8210 (p90) REVERT: E 338 MET cc_start: 0.7656 (mmp) cc_final: 0.7246 (mmt) REVERT: E 341 ASP cc_start: 0.8756 (t0) cc_final: 0.8026 (p0) REVERT: E 347 PHE cc_start: 0.8868 (t80) cc_final: 0.8572 (t80) REVERT: E 349 GLN cc_start: 0.8921 (tt0) cc_final: 0.8494 (tt0) REVERT: E 361 GLU cc_start: 0.9298 (tp30) cc_final: 0.8879 (tm-30) REVERT: E 362 GLU cc_start: 0.9064 (mp0) cc_final: 0.8664 (mp0) REVERT: E 364 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9176 (mt-10) REVERT: E 369 LEU cc_start: 0.8923 (mm) cc_final: 0.8485 (mm) REVERT: E 393 LEU cc_start: 0.8531 (mp) cc_final: 0.8237 (mp) REVERT: E 450 ARG cc_start: 0.8862 (mtt90) cc_final: 0.8588 (ttm110) REVERT: E 455 PHE cc_start: 0.8023 (p90) cc_final: 0.7783 (p90) REVERT: E 456 SER cc_start: 0.8346 (t) cc_final: 0.8131 (t) REVERT: E 480 GLU cc_start: 0.8594 (tt0) cc_final: 0.8093 (tp30) REVERT: E 485 GLU cc_start: 0.9014 (mp0) cc_final: 0.8728 (mp0) REVERT: G 166 PHE cc_start: 0.8862 (p90) cc_final: 0.8479 (p90) REVERT: G 175 LYS cc_start: 0.8158 (pptt) cc_final: 0.7889 (tttt) REVERT: G 184 ASP cc_start: 0.8085 (m-30) cc_final: 0.7851 (m-30) REVERT: G 186 ASP cc_start: 0.8125 (t0) cc_final: 0.7794 (t0) REVERT: G 239 LEU cc_start: 0.8559 (pp) cc_final: 0.7785 (pp) REVERT: G 246 HIS cc_start: 0.8317 (m-70) cc_final: 0.7588 (m170) REVERT: G 248 CYS cc_start: 0.6182 (t) cc_final: 0.5808 (m) REVERT: G 251 HIS cc_start: 0.6928 (m-70) cc_final: 0.6539 (m-70) REVERT: G 308 PHE cc_start: 0.8553 (t80) cc_final: 0.8296 (t80) REVERT: G 310 CYS cc_start: 0.8366 (p) cc_final: 0.7505 (p) REVERT: G 331 GLU cc_start: 0.8264 (pt0) cc_final: 0.7847 (mp0) REVERT: G 338 MET cc_start: 0.7657 (mmp) cc_final: 0.7385 (mmp) REVERT: G 341 ASP cc_start: 0.8632 (t0) cc_final: 0.7929 (p0) REVERT: G 347 PHE cc_start: 0.8763 (t80) cc_final: 0.8204 (t80) REVERT: G 350 ASP cc_start: 0.8257 (m-30) cc_final: 0.7998 (m-30) REVERT: G 361 GLU cc_start: 0.9376 (tp30) cc_final: 0.8729 (tm-30) REVERT: G 362 GLU cc_start: 0.8910 (mp0) cc_final: 0.8445 (mp0) REVERT: G 369 LEU cc_start: 0.8907 (mm) cc_final: 0.8461 (mm) REVERT: G 393 LEU cc_start: 0.8660 (mp) cc_final: 0.8344 (mp) REVERT: G 413 ASP cc_start: 0.9220 (t70) cc_final: 0.8936 (t0) REVERT: G 450 ARG cc_start: 0.8975 (mtt90) cc_final: 0.8626 (ttm110) REVERT: G 455 PHE cc_start: 0.7868 (p90) cc_final: 0.7651 (p90) REVERT: G 480 GLU cc_start: 0.8473 (tt0) cc_final: 0.7869 (tp30) REVERT: G 482 VAL cc_start: 0.9138 (t) cc_final: 0.8723 (t) REVERT: G 485 GLU cc_start: 0.8690 (mp0) cc_final: 0.8300 (mp0) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.1166 time to fit residues: 76.1425 Evaluate side-chains 410 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 107 optimal weight: 0.1980 chunk 97 optimal weight: 0.0370 chunk 78 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN C 178 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 286 GLN E 271 GLN G 271 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.128025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.097478 restraints weight = 25160.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.101445 restraints weight = 16957.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.104469 restraints weight = 12459.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.106732 restraints weight = 9723.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.108483 restraints weight = 7981.363| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11592 Z= 0.138 Angle : 0.759 10.535 15712 Z= 0.375 Chirality : 0.046 0.225 1684 Planarity : 0.004 0.071 2068 Dihedral : 5.083 29.173 1568 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.22), residues: 1396 helix: -1.02 (0.18), residues: 788 sheet: -0.98 (0.48), residues: 136 loop : -0.76 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 297 TYR 0.017 0.002 TYR A 213 PHE 0.018 0.002 PHE A 344 TRP 0.046 0.003 TRP A 371 HIS 0.014 0.002 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00312 (11592) covalent geometry : angle 0.75887 (15712) hydrogen bonds : bond 0.04465 ( 510) hydrogen bonds : angle 5.80415 ( 1494) *********************** 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 469 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.439 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 172 GLU cc_start: 0.8613 (pm20) cc_final: 0.8199 (pm20) REVERT: A 175 LYS cc_start: 0.8123 (pptt) cc_final: 0.7907 (tttt) REVERT: A 184 ASP cc_start: 0.8224 (m-30) cc_final: 0.7958 (m-30) REVERT: A 186 ASP cc_start: 0.8245 (t0) cc_final: 0.7887 (t0) REVERT: A 213 TYR cc_start: 0.8328 (t80) cc_final: 0.8054 (t80) REVERT: A 236 TYR cc_start: 0.8015 (t80) cc_final: 0.7805 (t80) REVERT: A 239 LEU cc_start: 0.8609 (pp) cc_final: 0.7682 (pp) REVERT: A 255 PHE cc_start: 0.9108 (t80) cc_final: 0.8856 (t80) REVERT: A 297 ARG cc_start: 0.8714 (tpp-160) cc_final: 0.8373 (tpp-160) REVERT: A 299 PHE cc_start: 0.8627 (t80) cc_final: 0.8219 (t80) REVERT: A 306 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.8099 (mtp180) REVERT: A 308 PHE cc_start: 0.8665 (t80) cc_final: 0.8374 (t80) REVERT: A 331 GLU cc_start: 0.8253 (pt0) cc_final: 0.7714 (mp0) REVERT: A 338 MET cc_start: 0.8143 (mmp) cc_final: 0.7509 (mmp) REVERT: A 341 ASP cc_start: 0.8518 (t0) cc_final: 0.7686 (p0) REVERT: A 349 GLN cc_start: 0.8739 (tt0) cc_final: 0.8452 (tt0) REVERT: A 369 LEU cc_start: 0.8877 (mm) cc_final: 0.8534 (mm) REVERT: A 413 ASP cc_start: 0.9296 (t0) cc_final: 0.8807 (t0) REVERT: A 456 SER cc_start: 0.8144 (t) cc_final: 0.7939 (t) REVERT: A 479 LEU cc_start: 0.8502 (mt) cc_final: 0.8291 (mt) REVERT: A 485 GLU cc_start: 0.8878 (mp0) cc_final: 0.8497 (mp0) REVERT: C 175 LYS cc_start: 0.8065 (pptt) cc_final: 0.7832 (mttm) REVERT: C 239 LEU cc_start: 0.8586 (pp) cc_final: 0.7766 (pp) REVERT: C 240 LYS cc_start: 0.9120 (tptm) cc_final: 0.8910 (mmmm) REVERT: C 242 LEU cc_start: 0.8311 (pp) cc_final: 0.8099 (pp) REVERT: C 246 HIS cc_start: 0.8381 (m-70) cc_final: 0.7792 (m170) REVERT: C 251 HIS cc_start: 0.7215 (m-70) cc_final: 0.6882 (m-70) REVERT: C 255 PHE cc_start: 0.9144 (t80) cc_final: 0.8851 (t80) REVERT: C 288 ARG cc_start: 0.8641 (tpt-90) cc_final: 0.8294 (tpt90) REVERT: C 299 PHE cc_start: 0.8468 (t80) cc_final: 0.8065 (t80) REVERT: C 308 PHE cc_start: 0.8521 (t80) cc_final: 0.8098 (t80) REVERT: C 338 MET cc_start: 0.7968 (mmp) cc_final: 0.7527 (mmp) REVERT: C 341 ASP cc_start: 0.8607 (t0) cc_final: 0.7970 (p0) REVERT: C 347 PHE cc_start: 0.8634 (t80) cc_final: 0.8234 (t80) REVERT: C 361 GLU cc_start: 0.9287 (tp30) cc_final: 0.8749 (tm-30) REVERT: C 364 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8965 (mt-10) REVERT: C 369 LEU cc_start: 0.8856 (mm) cc_final: 0.8497 (mm) REVERT: C 393 LEU cc_start: 0.8498 (mp) cc_final: 0.8280 (mp) REVERT: C 455 PHE cc_start: 0.8023 (p90) cc_final: 0.7768 (p90) REVERT: C 480 GLU cc_start: 0.8469 (tt0) cc_final: 0.7923 (tp30) REVERT: C 482 VAL cc_start: 0.9000 (t) cc_final: 0.8590 (t) REVERT: C 485 GLU cc_start: 0.8610 (mp0) cc_final: 0.8240 (mp0) REVERT: E 175 LYS cc_start: 0.7931 (pptt) cc_final: 0.7729 (tttt) REVERT: E 184 ASP cc_start: 0.7890 (m-30) cc_final: 0.7681 (m-30) REVERT: E 186 ASP cc_start: 0.8022 (t0) cc_final: 0.7727 (t0) REVERT: E 239 LEU cc_start: 0.8616 (pp) cc_final: 0.7894 (pp) REVERT: E 240 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8733 (mtpt) REVERT: E 242 LEU cc_start: 0.8255 (pp) cc_final: 0.8052 (pp) REVERT: E 251 HIS cc_start: 0.6922 (m-70) cc_final: 0.6574 (m-70) REVERT: E 255 PHE cc_start: 0.9018 (t80) cc_final: 0.8766 (t80) REVERT: E 308 PHE cc_start: 0.8535 (t80) cc_final: 0.8055 (t80) REVERT: E 313 TYR cc_start: 0.8562 (p90) cc_final: 0.8280 (p90) REVERT: E 338 MET cc_start: 0.7650 (mmp) cc_final: 0.7119 (mmt) REVERT: E 341 ASP cc_start: 0.8667 (t0) cc_final: 0.8004 (p0) REVERT: E 349 GLN cc_start: 0.8886 (tt0) cc_final: 0.8502 (tt0) REVERT: E 361 GLU cc_start: 0.9269 (tp30) cc_final: 0.8764 (tm-30) REVERT: E 364 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9149 (mt-10) REVERT: E 369 LEU cc_start: 0.8923 (mm) cc_final: 0.8442 (mm) REVERT: E 393 LEU cc_start: 0.8476 (mp) cc_final: 0.8194 (mp) REVERT: E 455 PHE cc_start: 0.7944 (p90) cc_final: 0.7697 (p90) REVERT: E 456 SER cc_start: 0.8251 (t) cc_final: 0.8045 (t) REVERT: E 480 GLU cc_start: 0.8517 (tt0) cc_final: 0.8153 (tp30) REVERT: E 485 GLU cc_start: 0.8998 (mp0) cc_final: 0.8659 (mp0) REVERT: G 166 PHE cc_start: 0.8790 (p90) cc_final: 0.8448 (p90) REVERT: G 175 LYS cc_start: 0.7976 (pptt) cc_final: 0.7633 (tttt) REVERT: G 184 ASP cc_start: 0.7588 (m-30) cc_final: 0.7345 (m-30) REVERT: G 186 ASP cc_start: 0.8124 (t0) cc_final: 0.7784 (t0) REVERT: G 239 LEU cc_start: 0.8560 (pp) cc_final: 0.7822 (pp) REVERT: G 240 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8785 (mtpt) REVERT: G 255 PHE cc_start: 0.9123 (t80) cc_final: 0.8859 (t80) REVERT: G 267 ASP cc_start: 0.9129 (p0) cc_final: 0.8641 (p0) REVERT: G 297 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8295 (mmt90) REVERT: G 308 PHE cc_start: 0.8568 (t80) cc_final: 0.8304 (t80) REVERT: G 310 CYS cc_start: 0.8411 (p) cc_final: 0.7528 (p) REVERT: G 313 TYR cc_start: 0.8499 (p90) cc_final: 0.8294 (p90) REVERT: G 331 GLU cc_start: 0.8216 (pt0) cc_final: 0.7818 (mp0) REVERT: G 338 MET cc_start: 0.7672 (mmp) cc_final: 0.6985 (mmt) REVERT: G 341 ASP cc_start: 0.8656 (t0) cc_final: 0.8049 (p0) REVERT: G 346 GLN cc_start: 0.8705 (tp40) cc_final: 0.7963 (tp40) REVERT: G 347 PHE cc_start: 0.8681 (t80) cc_final: 0.8159 (t80) REVERT: G 361 GLU cc_start: 0.9386 (tp30) cc_final: 0.8859 (tm-30) REVERT: G 362 GLU cc_start: 0.8918 (mp0) cc_final: 0.8541 (mp0) REVERT: G 369 LEU cc_start: 0.8777 (mm) cc_final: 0.8429 (mm) REVERT: G 413 ASP cc_start: 0.9186 (t70) cc_final: 0.8890 (t0) REVERT: G 450 ARG cc_start: 0.8946 (mtt90) cc_final: 0.8679 (ttm110) REVERT: G 480 GLU cc_start: 0.8462 (tt0) cc_final: 0.7922 (tp30) REVERT: G 482 VAL cc_start: 0.9148 (t) cc_final: 0.8732 (t) REVERT: G 485 GLU cc_start: 0.8666 (mp0) cc_final: 0.8261 (mp0) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.1239 time to fit residues: 79.4074 Evaluate side-chains 419 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.125557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.095214 restraints weight = 25440.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099170 restraints weight = 17038.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.102129 restraints weight = 12445.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.104340 restraints weight = 9684.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.106009 restraints weight = 7932.623| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11592 Z= 0.159 Angle : 0.723 10.544 15712 Z= 0.366 Chirality : 0.045 0.210 1684 Planarity : 0.005 0.042 2068 Dihedral : 5.019 29.600 1568 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.08 % Allowed : 2.76 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.22), residues: 1396 helix: -1.01 (0.18), residues: 792 sheet: -0.89 (0.56), residues: 96 loop : -0.94 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 265 TYR 0.016 0.002 TYR A 213 PHE 0.024 0.002 PHE G 376 TRP 0.051 0.004 TRP C 371 HIS 0.013 0.002 HIS G 401 Details of bonding type rmsd covalent geometry : bond 0.00352 (11592) covalent geometry : angle 0.72335 (15712) hydrogen bonds : bond 0.04307 ( 510) hydrogen bonds : angle 5.91348 ( 1494) *********************** 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 454 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.468 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: 0.9138 (p90) cc_final: 0.8897 (p90) REVERT: A 172 GLU cc_start: 0.8637 (pm20) cc_final: 0.8243 (pm20) REVERT: A 184 ASP cc_start: 0.8185 (m-30) cc_final: 0.7890 (m-30) REVERT: A 186 ASP cc_start: 0.8222 (t0) cc_final: 0.7862 (t0) REVERT: A 239 LEU cc_start: 0.8601 (pp) cc_final: 0.7719 (pp) REVERT: A 299 PHE cc_start: 0.8663 (t80) cc_final: 0.8303 (t80) REVERT: A 308 PHE cc_start: 0.8754 (t80) cc_final: 0.8045 (t80) REVERT: A 313 TYR cc_start: 0.8605 (p90) cc_final: 0.8377 (p90) REVERT: A 331 GLU cc_start: 0.8357 (pt0) cc_final: 0.7948 (pt0) REVERT: A 338 MET cc_start: 0.8204 (mmp) cc_final: 0.7748 (mmp) REVERT: A 341 ASP cc_start: 0.8585 (t0) cc_final: 0.7759 (p0) REVERT: A 347 PHE cc_start: 0.8931 (t80) cc_final: 0.8661 (t80) REVERT: A 362 GLU cc_start: 0.8943 (mp0) cc_final: 0.8692 (mp0) REVERT: A 363 ILE cc_start: 0.9453 (mp) cc_final: 0.8866 (mp) REVERT: A 369 LEU cc_start: 0.8926 (mm) cc_final: 0.8539 (mm) REVERT: A 413 ASP cc_start: 0.9291 (t0) cc_final: 0.8859 (t0) REVERT: A 485 GLU cc_start: 0.8899 (mp0) cc_final: 0.8572 (mp0) REVERT: C 175 LYS cc_start: 0.8035 (pptt) cc_final: 0.7728 (mttm) REVERT: C 184 ASP cc_start: 0.7974 (m-30) cc_final: 0.7753 (m-30) REVERT: C 239 LEU cc_start: 0.8693 (pp) cc_final: 0.8013 (pp) REVERT: C 240 LYS cc_start: 0.9203 (tptm) cc_final: 0.8786 (mmmm) REVERT: C 242 LEU cc_start: 0.8310 (pp) cc_final: 0.8025 (pp) REVERT: C 246 HIS cc_start: 0.8407 (m-70) cc_final: 0.7634 (m170) REVERT: C 251 HIS cc_start: 0.7285 (m-70) cc_final: 0.6875 (m-70) REVERT: C 255 PHE cc_start: 0.9037 (t80) cc_final: 0.8653 (t80) REVERT: C 288 ARG cc_start: 0.8725 (tpt-90) cc_final: 0.8469 (tpt90) REVERT: C 299 PHE cc_start: 0.8544 (t80) cc_final: 0.8210 (t80) REVERT: C 300 LEU cc_start: 0.7895 (pp) cc_final: 0.7480 (pp) REVERT: C 308 PHE cc_start: 0.8581 (t80) cc_final: 0.8079 (t80) REVERT: C 313 TYR cc_start: 0.8675 (p90) cc_final: 0.8344 (p90) REVERT: C 338 MET cc_start: 0.8057 (mmp) cc_final: 0.7418 (mmt) REVERT: C 341 ASP cc_start: 0.8660 (t0) cc_final: 0.8016 (p0) REVERT: C 347 PHE cc_start: 0.8758 (t80) cc_final: 0.8338 (t80) REVERT: C 361 GLU cc_start: 0.9366 (tp30) cc_final: 0.8836 (tm-30) REVERT: C 363 ILE cc_start: 0.9370 (mp) cc_final: 0.8664 (mp) REVERT: C 364 GLU cc_start: 0.9243 (mt-10) cc_final: 0.9038 (mt-10) REVERT: C 369 LEU cc_start: 0.8910 (mm) cc_final: 0.8510 (mm) REVERT: C 393 LEU cc_start: 0.8496 (mp) cc_final: 0.8275 (mp) REVERT: C 413 ASP cc_start: 0.9223 (t70) cc_final: 0.8939 (t0) REVERT: C 455 PHE cc_start: 0.8114 (p90) cc_final: 0.7836 (p90) REVERT: C 480 GLU cc_start: 0.8510 (tt0) cc_final: 0.8024 (tp30) REVERT: C 482 VAL cc_start: 0.9130 (t) cc_final: 0.8854 (t) REVERT: C 485 GLU cc_start: 0.8626 (mp0) cc_final: 0.8336 (mp0) REVERT: E 175 LYS cc_start: 0.7954 (pptt) cc_final: 0.7730 (tttt) REVERT: E 239 LEU cc_start: 0.8649 (pp) cc_final: 0.8042 (pp) REVERT: E 242 LEU cc_start: 0.8316 (pp) cc_final: 0.8109 (pp) REVERT: E 251 HIS cc_start: 0.6941 (m-70) cc_final: 0.6538 (m-70) REVERT: E 276 SER cc_start: 0.9253 (m) cc_final: 0.8725 (p) REVERT: E 308 PHE cc_start: 0.8629 (t80) cc_final: 0.8067 (t80) REVERT: E 313 TYR cc_start: 0.8669 (p90) cc_final: 0.8340 (p90) REVERT: E 338 MET cc_start: 0.7800 (mmp) cc_final: 0.7242 (mmt) REVERT: E 341 ASP cc_start: 0.8743 (t0) cc_final: 0.8115 (p0) REVERT: E 347 PHE cc_start: 0.8916 (t80) cc_final: 0.8620 (t80) REVERT: E 349 GLN cc_start: 0.8921 (tt0) cc_final: 0.8517 (tt0) REVERT: E 361 GLU cc_start: 0.9323 (tp30) cc_final: 0.8802 (tm-30) REVERT: E 364 GLU cc_start: 0.9393 (mt-10) cc_final: 0.9154 (mt-10) REVERT: E 369 LEU cc_start: 0.9006 (mm) cc_final: 0.8505 (mm) REVERT: E 393 LEU cc_start: 0.8506 (mp) cc_final: 0.8223 (mp) REVERT: E 455 PHE cc_start: 0.8075 (p90) cc_final: 0.7795 (p90) REVERT: E 456 SER cc_start: 0.8209 (t) cc_final: 0.7995 (t) REVERT: E 480 GLU cc_start: 0.8659 (tt0) cc_final: 0.8187 (tp30) REVERT: E 485 GLU cc_start: 0.9023 (mp0) cc_final: 0.8674 (mp0) REVERT: G 166 PHE cc_start: 0.8943 (p90) cc_final: 0.8576 (p90) REVERT: G 175 LYS cc_start: 0.8030 (pptt) cc_final: 0.7686 (tttt) REVERT: G 184 ASP cc_start: 0.7615 (m-30) cc_final: 0.7391 (m-30) REVERT: G 186 ASP cc_start: 0.8112 (t0) cc_final: 0.7778 (t0) REVERT: G 214 ARG cc_start: 0.8711 (mmp80) cc_final: 0.8334 (mmp80) REVERT: G 239 LEU cc_start: 0.8635 (pp) cc_final: 0.8205 (pp) REVERT: G 251 HIS cc_start: 0.7180 (m-70) cc_final: 0.6869 (m-70) REVERT: G 255 PHE cc_start: 0.9026 (t80) cc_final: 0.8760 (t80) REVERT: G 308 PHE cc_start: 0.8627 (t80) cc_final: 0.8039 (t80) REVERT: G 313 TYR cc_start: 0.8562 (p90) cc_final: 0.8301 (p90) REVERT: G 338 MET cc_start: 0.7814 (mmp) cc_final: 0.7341 (mmp) REVERT: G 341 ASP cc_start: 0.8670 (t0) cc_final: 0.8125 (p0) REVERT: G 347 PHE cc_start: 0.8823 (t80) cc_final: 0.8278 (t80) REVERT: G 350 ASP cc_start: 0.8335 (m-30) cc_final: 0.8129 (m-30) REVERT: G 353 LEU cc_start: 0.9077 (mm) cc_final: 0.8871 (mm) REVERT: G 369 LEU cc_start: 0.8893 (mm) cc_final: 0.8502 (mm) REVERT: G 413 ASP cc_start: 0.9221 (t70) cc_final: 0.8946 (t0) REVERT: G 437 PHE cc_start: 0.8778 (m-80) cc_final: 0.8504 (m-80) REVERT: G 479 LEU cc_start: 0.8527 (mt) cc_final: 0.8099 (mt) REVERT: G 480 GLU cc_start: 0.8575 (tt0) cc_final: 0.8259 (tp30) REVERT: G 485 GLU cc_start: 0.8725 (mp0) cc_final: 0.8337 (mp0) REVERT: H 49 ARG cc_start: 0.8472 (mpp80) cc_final: 0.8246 (mpp80) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.1188 time to fit residues: 74.8214 Evaluate side-chains 399 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS G 246 HIS ** G 251 HIS ** 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 = 0.3958 r_free = 0.3958 target = 0.125275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095125 restraints weight = 25510.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099036 restraints weight = 17015.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101970 restraints weight = 12386.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.104138 restraints weight = 9641.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.105773 restraints weight = 7925.918| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11592 Z= 0.157 Angle : 0.739 11.013 15712 Z= 0.375 Chirality : 0.046 0.200 1684 Planarity : 0.006 0.134 2068 Dihedral : 5.081 30.909 1568 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.22), residues: 1396 helix: -1.06 (0.17), residues: 792 sheet: -0.56 (0.57), residues: 88 loop : -1.05 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 297 TYR 0.013 0.002 TYR A 236 PHE 0.018 0.002 PHE G 376 TRP 0.054 0.004 TRP C 371 HIS 0.014 0.002 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00358 (11592) covalent geometry : angle 0.73932 (15712) hydrogen bonds : bond 0.04294 ( 510) hydrogen bonds : angle 5.90370 ( 1494) *********************** 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 448 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 0.455 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: A 184 ASP cc_start: 0.8141 (m-30) cc_final: 0.7830 (m-30) REVERT: A 186 ASP cc_start: 0.8228 (t0) cc_final: 0.7861 (t0) REVERT: A 219 ILE cc_start: 0.8733 (mt) cc_final: 0.8292 (mt) REVERT: A 239 LEU cc_start: 0.8578 (pp) cc_final: 0.7746 (pp) REVERT: A 273 GLU cc_start: 0.7961 (tp30) cc_final: 0.7706 (tp30) REVERT: A 299 PHE cc_start: 0.8557 (t80) cc_final: 0.8195 (t80) REVERT: A 308 PHE cc_start: 0.8747 (t80) cc_final: 0.8161 (t80) REVERT: A 313 TYR cc_start: 0.8625 (p90) cc_final: 0.8387 (p90) REVERT: A 338 MET cc_start: 0.8156 (mmp) cc_final: 0.7545 (mmp) REVERT: A 341 ASP cc_start: 0.8580 (t0) cc_final: 0.7880 (p0) REVERT: A 347 PHE cc_start: 0.8915 (t80) cc_final: 0.8705 (t80) REVERT: A 369 LEU cc_start: 0.8924 (mm) cc_final: 0.8497 (mm) REVERT: A 413 ASP cc_start: 0.9295 (t0) cc_final: 0.8856 (t0) REVERT: A 445 ARG cc_start: 0.8646 (mmt180) cc_final: 0.8336 (mmt180) REVERT: A 485 GLU cc_start: 0.8915 (mp0) cc_final: 0.8586 (mp0) REVERT: A 487 ASP cc_start: 0.8481 (m-30) cc_final: 0.8216 (m-30) REVERT: C 166 PHE cc_start: 0.9070 (p90) cc_final: 0.8854 (p90) REVERT: C 175 LYS cc_start: 0.7957 (pptt) cc_final: 0.7698 (mttm) REVERT: C 239 LEU cc_start: 0.8704 (pp) cc_final: 0.8097 (pp) REVERT: C 251 HIS cc_start: 0.7273 (m-70) cc_final: 0.7005 (m-70) REVERT: C 255 PHE cc_start: 0.9081 (t80) cc_final: 0.8442 (t80) REVERT: C 259 GLU cc_start: 0.9011 (pm20) cc_final: 0.8613 (pm20) REVERT: C 288 ARG cc_start: 0.8734 (tpt-90) cc_final: 0.8503 (tpt90) REVERT: C 308 PHE cc_start: 0.8611 (t80) cc_final: 0.8096 (t80) REVERT: C 313 TYR cc_start: 0.8702 (p90) cc_final: 0.8437 (p90) REVERT: C 338 MET cc_start: 0.8079 (mmp) cc_final: 0.7470 (mmp) REVERT: C 341 ASP cc_start: 0.8683 (t0) cc_final: 0.8093 (p0) REVERT: C 347 PHE cc_start: 0.8780 (t80) cc_final: 0.8287 (t80) REVERT: C 350 ASP cc_start: 0.8241 (m-30) cc_final: 0.7988 (m-30) REVERT: C 361 GLU cc_start: 0.9344 (tp30) cc_final: 0.8751 (tm-30) REVERT: C 369 LEU cc_start: 0.8903 (mm) cc_final: 0.8457 (mm) REVERT: C 455 PHE cc_start: 0.8083 (p90) cc_final: 0.7815 (p90) REVERT: C 480 GLU cc_start: 0.8511 (tt0) cc_final: 0.8199 (tp30) REVERT: C 485 GLU cc_start: 0.8613 (mp0) cc_final: 0.8393 (mp0) REVERT: E 175 LYS cc_start: 0.7978 (pptt) cc_final: 0.7708 (tttt) REVERT: E 184 ASP cc_start: 0.7996 (m-30) cc_final: 0.7789 (m-30) REVERT: E 186 ASP cc_start: 0.7986 (t0) cc_final: 0.7693 (t0) REVERT: E 213 TYR cc_start: 0.8526 (t80) cc_final: 0.8273 (t80) REVERT: E 239 LEU cc_start: 0.8636 (pp) cc_final: 0.8139 (pp) REVERT: E 251 HIS cc_start: 0.7130 (m-70) cc_final: 0.6724 (m90) REVERT: E 255 PHE cc_start: 0.9153 (t80) cc_final: 0.8951 (t80) REVERT: E 276 SER cc_start: 0.9198 (m) cc_final: 0.8756 (p) REVERT: E 308 PHE cc_start: 0.8613 (t80) cc_final: 0.8053 (t80) REVERT: E 313 TYR cc_start: 0.8648 (p90) cc_final: 0.8292 (p90) REVERT: E 327 ASP cc_start: 0.7176 (p0) cc_final: 0.6882 (p0) REVERT: E 341 ASP cc_start: 0.8716 (t0) cc_final: 0.8151 (p0) REVERT: E 347 PHE cc_start: 0.8994 (t80) cc_final: 0.8627 (t80) REVERT: E 349 GLN cc_start: 0.8921 (tt0) cc_final: 0.8530 (tt0) REVERT: E 361 GLU cc_start: 0.9335 (tp30) cc_final: 0.8728 (tm-30) REVERT: E 362 GLU cc_start: 0.9054 (mp0) cc_final: 0.8756 (mp0) REVERT: E 364 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9150 (mt-10) REVERT: E 369 LEU cc_start: 0.8964 (mm) cc_final: 0.8560 (mm) REVERT: E 455 PHE cc_start: 0.8070 (p90) cc_final: 0.7773 (p90) REVERT: E 456 SER cc_start: 0.8245 (t) cc_final: 0.8013 (t) REVERT: E 480 GLU cc_start: 0.8588 (tt0) cc_final: 0.8236 (tp30) REVERT: E 485 GLU cc_start: 0.9002 (mp0) cc_final: 0.8599 (mp0) REVERT: G 166 PHE cc_start: 0.9020 (p90) cc_final: 0.8611 (p90) REVERT: G 171 SER cc_start: 0.8685 (m) cc_final: 0.8313 (p) REVERT: G 175 LYS cc_start: 0.7928 (pptt) cc_final: 0.7618 (tttt) REVERT: G 184 ASP cc_start: 0.7835 (m-30) cc_final: 0.7588 (m-30) REVERT: G 214 ARG cc_start: 0.8704 (mmp80) cc_final: 0.8445 (mmp80) REVERT: G 239 LEU cc_start: 0.8623 (pp) cc_final: 0.8257 (pp) REVERT: G 251 HIS cc_start: 0.7196 (m-70) cc_final: 0.6822 (m-70) REVERT: G 255 PHE cc_start: 0.9017 (t80) cc_final: 0.8358 (t80) REVERT: G 259 GLU cc_start: 0.8964 (pm20) cc_final: 0.8557 (pm20) REVERT: G 297 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8236 (mmt90) REVERT: G 308 PHE cc_start: 0.8635 (t80) cc_final: 0.7902 (t80) REVERT: G 313 TYR cc_start: 0.8634 (p90) cc_final: 0.8377 (p90) REVERT: G 331 GLU cc_start: 0.8341 (pt0) cc_final: 0.8067 (pt0) REVERT: G 338 MET cc_start: 0.7819 (mmp) cc_final: 0.7127 (mmt) REVERT: G 341 ASP cc_start: 0.8663 (t0) cc_final: 0.8149 (p0) REVERT: G 347 PHE cc_start: 0.8842 (t80) cc_final: 0.8297 (t80) REVERT: G 350 ASP cc_start: 0.8297 (m-30) cc_final: 0.8093 (m-30) REVERT: G 353 LEU cc_start: 0.9021 (mm) cc_final: 0.8804 (mm) REVERT: G 369 LEU cc_start: 0.8900 (mm) cc_final: 0.8455 (mm) REVERT: G 480 GLU cc_start: 0.8607 (tt0) cc_final: 0.8263 (tp30) REVERT: G 482 VAL cc_start: 0.9195 (t) cc_final: 0.8984 (t) REVERT: G 485 GLU cc_start: 0.8668 (mp0) cc_final: 0.8321 (mp0) REVERT: G 487 ASP cc_start: 0.8490 (m-30) cc_final: 0.8268 (m-30) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.1173 time to fit residues: 72.8841 Evaluate side-chains 407 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 38 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS G 246 HIS ** G 251 HIS ** 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 = 0.3934 r_free = 0.3934 target = 0.123594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093857 restraints weight = 25457.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.097731 restraints weight = 16844.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100673 restraints weight = 12245.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.102874 restraints weight = 9474.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.104541 restraints weight = 7728.775| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11592 Z= 0.166 Angle : 0.784 11.528 15712 Z= 0.394 Chirality : 0.046 0.175 1684 Planarity : 0.005 0.096 2068 Dihedral : 5.134 31.525 1568 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.22), residues: 1396 helix: -1.07 (0.17), residues: 788 sheet: -0.66 (0.57), residues: 88 loop : -1.03 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 477 TYR 0.014 0.002 TYR A 236 PHE 0.018 0.002 PHE E 376 TRP 0.059 0.005 TRP C 371 HIS 0.016 0.002 HIS G 401 Details of bonding type rmsd covalent geometry : bond 0.00383 (11592) covalent geometry : angle 0.78450 (15712) hydrogen bonds : bond 0.04430 ( 510) hydrogen bonds : angle 5.93081 ( 1494) *********************** 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 446 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.474 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: A 166 PHE cc_start: 0.9162 (p90) cc_final: 0.8947 (p90) REVERT: A 184 ASP cc_start: 0.8135 (m-30) cc_final: 0.7807 (m-30) REVERT: A 186 ASP cc_start: 0.8213 (t0) cc_final: 0.7848 (t0) REVERT: A 214 ARG cc_start: 0.8699 (mmp80) cc_final: 0.8493 (mmp80) REVERT: A 239 LEU cc_start: 0.8613 (pp) cc_final: 0.7815 (pp) REVERT: A 299 PHE cc_start: 0.8525 (t80) cc_final: 0.8133 (t80) REVERT: A 308 PHE cc_start: 0.8719 (t80) cc_final: 0.8111 (t80) REVERT: A 313 TYR cc_start: 0.8697 (p90) cc_final: 0.8456 (p90) REVERT: A 338 MET cc_start: 0.8246 (mmp) cc_final: 0.7091 (mmt) REVERT: A 341 ASP cc_start: 0.8629 (t0) cc_final: 0.7878 (p0) REVERT: A 347 PHE cc_start: 0.8996 (t80) cc_final: 0.8606 (t80) REVERT: A 369 LEU cc_start: 0.8945 (mm) cc_final: 0.8519 (mm) REVERT: A 413 ASP cc_start: 0.9301 (t0) cc_final: 0.8861 (t0) REVERT: A 480 GLU cc_start: 0.8432 (tp30) cc_final: 0.8228 (tp30) REVERT: A 485 GLU cc_start: 0.8966 (mp0) cc_final: 0.8625 (mp0) REVERT: A 487 ASP cc_start: 0.8540 (m-30) cc_final: 0.8261 (m-30) REVERT: C 174 ASP cc_start: 0.7871 (t70) cc_final: 0.7655 (t70) REVERT: C 175 LYS cc_start: 0.7945 (pptt) cc_final: 0.7707 (mttm) REVERT: C 184 ASP cc_start: 0.8034 (m-30) cc_final: 0.7805 (m-30) REVERT: C 239 LEU cc_start: 0.8716 (pp) cc_final: 0.8169 (pp) REVERT: C 240 LYS cc_start: 0.9147 (tptm) cc_final: 0.8721 (mmmm) REVERT: C 251 HIS cc_start: 0.7285 (m-70) cc_final: 0.7059 (m-70) REVERT: C 255 PHE cc_start: 0.9126 (t80) cc_final: 0.8920 (t80) REVERT: C 288 ARG cc_start: 0.8755 (tpt-90) cc_final: 0.8432 (tpt90) REVERT: C 308 PHE cc_start: 0.8575 (t80) cc_final: 0.8020 (t80) REVERT: C 313 TYR cc_start: 0.8725 (p90) cc_final: 0.8390 (p90) REVERT: C 327 ASP cc_start: 0.7032 (p0) cc_final: 0.6827 (p0) REVERT: C 338 MET cc_start: 0.8157 (mmp) cc_final: 0.7737 (mmp) REVERT: C 341 ASP cc_start: 0.8728 (t0) cc_final: 0.8078 (p0) REVERT: C 347 PHE cc_start: 0.8834 (t80) cc_final: 0.8339 (t80) REVERT: C 350 ASP cc_start: 0.8259 (m-30) cc_final: 0.8024 (m-30) REVERT: C 361 GLU cc_start: 0.9374 (tp30) cc_final: 0.8851 (tm-30) REVERT: C 364 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8971 (mt-10) REVERT: C 366 LEU cc_start: 0.8888 (pt) cc_final: 0.8678 (pt) REVERT: C 369 LEU cc_start: 0.8897 (mm) cc_final: 0.8439 (mm) REVERT: C 413 ASP cc_start: 0.9188 (t70) cc_final: 0.8959 (t0) REVERT: C 455 PHE cc_start: 0.8108 (p90) cc_final: 0.7833 (p90) REVERT: C 480 GLU cc_start: 0.8659 (tt0) cc_final: 0.8318 (tp30) REVERT: C 487 ASP cc_start: 0.8620 (m-30) cc_final: 0.8356 (m-30) REVERT: E 175 LYS cc_start: 0.8010 (pptt) cc_final: 0.7734 (tttt) REVERT: E 184 ASP cc_start: 0.7855 (m-30) cc_final: 0.7616 (m-30) REVERT: E 213 TYR cc_start: 0.8498 (t80) cc_final: 0.8245 (t80) REVERT: E 239 LEU cc_start: 0.8641 (pp) cc_final: 0.8195 (pp) REVERT: E 251 HIS cc_start: 0.7166 (m-70) cc_final: 0.6859 (m-70) REVERT: E 255 PHE cc_start: 0.9134 (t80) cc_final: 0.8916 (t80) REVERT: E 276 SER cc_start: 0.9146 (m) cc_final: 0.8730 (p) REVERT: E 308 PHE cc_start: 0.8649 (t80) cc_final: 0.8070 (t80) REVERT: E 313 TYR cc_start: 0.8694 (p90) cc_final: 0.8415 (p90) REVERT: E 338 MET cc_start: 0.8108 (mmp) cc_final: 0.7633 (mmp) REVERT: E 341 ASP cc_start: 0.8729 (t0) cc_final: 0.8111 (p0) REVERT: E 347 PHE cc_start: 0.8960 (t80) cc_final: 0.8635 (t80) REVERT: E 349 GLN cc_start: 0.8906 (tt0) cc_final: 0.8549 (tt0) REVERT: E 361 GLU cc_start: 0.9323 (tp30) cc_final: 0.8749 (tm-30) REVERT: E 362 GLU cc_start: 0.9031 (mp0) cc_final: 0.8690 (mp0) REVERT: E 364 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9147 (mt-10) REVERT: E 369 LEU cc_start: 0.8964 (mm) cc_final: 0.8548 (mm) REVERT: E 427 TYR cc_start: 0.8139 (m-80) cc_final: 0.7582 (m-80) REVERT: E 443 LYS cc_start: 0.8590 (mtpt) cc_final: 0.7928 (mtpt) REVERT: E 455 PHE cc_start: 0.8021 (p90) cc_final: 0.7759 (p90) REVERT: E 480 GLU cc_start: 0.8524 (tt0) cc_final: 0.8160 (tp30) REVERT: E 485 GLU cc_start: 0.8865 (mp0) cc_final: 0.8471 (mp0) REVERT: G 166 PHE cc_start: 0.9063 (p90) cc_final: 0.8662 (p90) REVERT: G 171 SER cc_start: 0.8683 (m) cc_final: 0.8437 (p) REVERT: G 172 GLU cc_start: 0.8500 (mp0) cc_final: 0.8144 (mp0) REVERT: G 175 LYS cc_start: 0.8011 (pptt) cc_final: 0.7768 (tttt) REVERT: G 184 ASP cc_start: 0.7844 (m-30) cc_final: 0.7617 (m-30) REVERT: G 214 ARG cc_start: 0.8702 (mmp80) cc_final: 0.8455 (mmp80) REVERT: G 239 LEU cc_start: 0.8621 (pp) cc_final: 0.8309 (pp) REVERT: G 240 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8621 (mmmm) REVERT: G 251 HIS cc_start: 0.7123 (m-70) cc_final: 0.6843 (m-70) REVERT: G 255 PHE cc_start: 0.9132 (t80) cc_final: 0.8759 (t80) REVERT: G 300 LEU cc_start: 0.7970 (pp) cc_final: 0.7436 (pp) REVERT: G 308 PHE cc_start: 0.8668 (t80) cc_final: 0.8025 (t80) REVERT: G 313 TYR cc_start: 0.8646 (p90) cc_final: 0.8376 (p90) REVERT: G 338 MET cc_start: 0.7845 (mmp) cc_final: 0.7176 (mmp) REVERT: G 341 ASP cc_start: 0.8677 (t0) cc_final: 0.8136 (p0) REVERT: G 346 GLN cc_start: 0.8795 (tp40) cc_final: 0.8064 (tp40) REVERT: G 347 PHE cc_start: 0.8925 (t80) cc_final: 0.8361 (t80) REVERT: G 350 ASP cc_start: 0.8313 (m-30) cc_final: 0.8106 (m-30) REVERT: G 353 LEU cc_start: 0.9048 (mm) cc_final: 0.8819 (mm) REVERT: G 363 ILE cc_start: 0.9463 (pt) cc_final: 0.9262 (pt) REVERT: G 369 LEU cc_start: 0.8918 (mm) cc_final: 0.8506 (mm) REVERT: G 413 ASP cc_start: 0.9232 (t70) cc_final: 0.8977 (t0) REVERT: G 437 PHE cc_start: 0.8837 (m-80) cc_final: 0.8612 (m-80) REVERT: G 455 PHE cc_start: 0.7892 (p90) cc_final: 0.7689 (p90) REVERT: G 480 GLU cc_start: 0.8553 (tt0) cc_final: 0.8135 (tp30) REVERT: G 485 GLU cc_start: 0.8726 (mp0) cc_final: 0.8421 (mp0) REVERT: G 487 ASP cc_start: 0.8596 (m-30) cc_final: 0.8271 (m-30) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1136 time to fit residues: 70.8148 Evaluate side-chains 402 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0507 > 50: distance: 1 - 14: 3.033 distance: 58 - 80: 12.708 distance: 62 - 88: 24.376 distance: 73 - 80: 12.554 distance: 74 - 105: 16.440 distance: 80 - 81: 15.845 distance: 81 - 82: 11.870 distance: 81 - 84: 34.751 distance: 82 - 83: 23.093 distance: 82 - 88: 23.252 distance: 83 - 116: 27.431 distance: 84 - 85: 24.124 distance: 85 - 86: 9.114 distance: 85 - 87: 10.433 distance: 88 - 89: 7.301 distance: 89 - 90: 5.514 distance: 89 - 92: 13.613 distance: 90 - 91: 35.811 distance: 90 - 97: 22.690 distance: 91 - 122: 48.739 distance: 92 - 93: 17.491 distance: 93 - 94: 19.397 distance: 94 - 95: 5.829 distance: 95 - 96: 12.909 distance: 97 - 98: 11.562 distance: 98 - 99: 33.040 distance: 98 - 101: 24.912 distance: 99 - 100: 27.273 distance: 99 - 105: 16.755 distance: 100 - 134: 33.888 distance: 101 - 102: 13.658 distance: 102 - 103: 30.424 distance: 102 - 104: 20.287 distance: 105 - 106: 24.643 distance: 106 - 107: 10.301 distance: 106 - 109: 24.029 distance: 107 - 108: 14.741 distance: 107 - 116: 14.640 distance: 108 - 139: 29.611 distance: 109 - 110: 15.272 distance: 110 - 111: 17.004 distance: 111 - 112: 12.522 distance: 112 - 113: 6.286 distance: 113 - 114: 23.690 distance: 113 - 115: 24.085 distance: 116 - 117: 17.364 distance: 117 - 118: 23.627 distance: 117 - 120: 24.375 distance: 118 - 119: 19.953 distance: 118 - 122: 7.372 distance: 119 - 145: 31.729 distance: 120 - 121: 17.060 distance: 122 - 123: 16.476 distance: 123 - 124: 11.294 distance: 123 - 126: 8.883 distance: 124 - 125: 20.882 distance: 124 - 134: 14.451 distance: 125 - 156: 42.900 distance: 126 - 127: 15.137 distance: 127 - 128: 4.042 distance: 127 - 129: 5.214 distance: 128 - 130: 13.203 distance: 129 - 131: 14.881 distance: 130 - 132: 11.035 distance: 131 - 132: 8.766 distance: 132 - 133: 6.318 distance: 134 - 135: 16.552 distance: 135 - 136: 25.699 distance: 135 - 138: 14.395 distance: 136 - 137: 13.743 distance: 136 - 139: 14.982 distance: 139 - 140: 11.585 distance: 140 - 141: 8.390 distance: 140 - 143: 23.683 distance: 141 - 142: 15.358 distance: 141 - 145: 3.490 distance: 143 - 144: 8.307 distance: 145 - 146: 5.116 distance: 146 - 147: 12.349 distance: 146 - 149: 8.122 distance: 147 - 148: 5.036 distance: 147 - 156: 10.454 distance: 149 - 150: 11.785 distance: 150 - 151: 19.434 distance: 151 - 152: 7.751 distance: 152 - 153: 7.109 distance: 153 - 154: 7.771 distance: 153 - 155: 7.437 distance: 156 - 157: 17.580 distance: 157 - 158: 28.704 distance: 157 - 160: 25.216 distance: 158 - 164: 34.289 distance: 160 - 161: 9.359 distance: 160 - 162: 15.438 distance: 161 - 163: 20.606