Starting phenix.real_space_refine on Wed Sep 25 21:24:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/09_2024/6zn2_11309.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/09_2024/6zn2_11309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/09_2024/6zn2_11309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/09_2024/6zn2_11309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/09_2024/6zn2_11309.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/09_2024/6zn2_11309.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 7192 2.51 5 N 1932 2.21 5 O 2156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11320 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 130 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, F, H, C, E, G Time building chain proxies: 5.52, per 1000 atoms: 0.49 Number of scatterers: 11320 At special positions: 0 Unit cell: (106.05, 87.15, 121.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2156 8.00 N 1932 7.00 C 7192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 58.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.531A pdb=" N ASP A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.546A pdb=" N ARG A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 244 removed outlier: 3.608A pdb=" N ILE A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.698A pdb=" N LEU A 252 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.585A pdb=" N LYS A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.831A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.723A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.852A pdb=" N LEU A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 3.500A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 47 through 57 removed outlier: 4.174A pdb=" N ALA B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 removed outlier: 3.531A pdb=" N ASP C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 212 removed outlier: 3.546A pdb=" N ARG C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.608A pdb=" N ILE C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 removed outlier: 3.698A pdb=" N LEU C 252 " --> pdb=" O CYS C 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.586A pdb=" N LYS C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 removed outlier: 3.831A pdb=" N PHE C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 391 through 394 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.724A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 436 through 451 removed outlier: 3.852A pdb=" N LEU C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 496 removed outlier: 3.581A pdb=" N ARG C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLY C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 485 " --> pdb=" O GLY C 481 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU C 486 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 492 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 496 " --> pdb=" O ALA C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 47 through 57 removed outlier: 4.174A pdb=" N ALA D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 180 removed outlier: 3.531A pdb=" N ASP E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.545A pdb=" N ARG E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 244 removed outlier: 3.608A pdb=" N ILE E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 262 removed outlier: 3.699A pdb=" N LEU E 252 " --> pdb=" O CYS E 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 283 removed outlier: 3.585A pdb=" N LYS E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 305 removed outlier: 3.832A pdb=" N PHE E 299 " --> pdb=" O SER E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 341 through 355 Processing helix chain 'E' and resid 359 through 374 Processing helix chain 'E' and resid 391 through 394 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.722A pdb=" N LEU E 403 " --> pdb=" O LEU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'E' and resid 436 through 451 removed outlier: 3.852A pdb=" N LEU E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 496 removed outlier: 3.582A pdb=" N ARG E 477 " --> pdb=" O GLN E 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY E 481 " --> pdb=" O ARG E 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 485 " --> pdb=" O GLY E 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 486 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA E 490 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS E 491 " --> pdb=" O ASP E 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 492 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 496 " --> pdb=" O ALA E 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 47 through 57 removed outlier: 4.174A pdb=" N ALA F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.530A pdb=" N ASP G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 212 removed outlier: 3.546A pdb=" N ARG G 200 " --> pdb=" O ASP G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 244 removed outlier: 3.608A pdb=" N ILE G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 262 removed outlier: 3.698A pdb=" N LEU G 252 " --> pdb=" O CYS G 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU G 253 " --> pdb=" O GLY G 249 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 283 removed outlier: 3.585A pdb=" N LYS G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 305 removed outlier: 3.831A pdb=" N PHE G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 335 Processing helix chain 'G' and resid 341 through 355 Processing helix chain 'G' and resid 359 through 374 Processing helix chain 'G' and resid 391 through 394 Processing helix chain 'G' and resid 395 through 403 removed outlier: 3.724A pdb=" N LEU G 403 " --> pdb=" O LEU G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 418 Processing helix chain 'G' and resid 436 through 451 removed outlier: 3.852A pdb=" N LEU G 444 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 496 removed outlier: 3.500A pdb=" N VAL G 475 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG G 477 " --> pdb=" O GLN G 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER G 478 " --> pdb=" O ALA G 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY G 481 " --> pdb=" O ARG G 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 486 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA G 490 " --> pdb=" O LEU G 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS G 491 " --> pdb=" O ASP G 487 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 492 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 496 " --> pdb=" O ALA G 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 47 through 57 removed outlier: 4.174A pdb=" N ALA H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.156A pdb=" N GLN A 286 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS A 310 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ARG A 288 " --> pdb=" O CYS A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 387 removed outlier: 6.219A pdb=" N LEU A 378 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS A 458 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 286 through 289 removed outlier: 6.157A pdb=" N GLN C 286 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS C 310 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ARG C 288 " --> pdb=" O CYS C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 385 through 387 removed outlier: 6.220A pdb=" N LEU C 378 " --> pdb=" O SER C 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS C 458 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 286 through 289 removed outlier: 6.156A pdb=" N GLN E 286 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS E 310 " --> pdb=" O GLN E 286 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ARG E 288 " --> pdb=" O CYS E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 385 through 387 removed outlier: 6.220A pdb=" N LEU E 378 " --> pdb=" O SER E 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS E 458 " --> pdb=" O ASP E 467 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 286 through 289 removed outlier: 6.156A pdb=" N GLN G 286 " --> pdb=" O PHE G 308 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS G 310 " --> pdb=" O GLN G 286 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ARG G 288 " --> pdb=" O CYS G 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 385 through 387 removed outlier: 6.220A pdb=" N LEU G 378 " --> pdb=" O SER G 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS G 458 " --> pdb=" O ASP G 467 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 2.93 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: 0.00 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: 0.300 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.000 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.940 ------------------------------------------------------------------------------- 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= 0.276 Angle : 0.929 14.360 15712 Z= 0.492 Chirality : 0.043 0.190 1684 Planarity : 0.005 0.075 2068 Dihedral : 15.059 73.314 4252 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.35 % Allowed : 3.01 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1396 helix: -0.86 (0.20), residues: 632 sheet: -1.08 (0.43), residues: 160 loop : -0.78 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 371 HIS 0.006 0.001 HIS E 491 PHE 0.024 0.001 PHE C 344 TYR 0.009 0.001 TYR C 243 ARG 0.010 0.001 ARG G 477 *********************** 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 fitting. rotamer outliers: 76 poor density : 569 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LYS cc_start: 0.8656 (mppt) cc_final: 0.8178 (mtpt) REVERT: A 172 GLU cc_start: 0.9163 (pm20) cc_final: 0.8688 (pm20) REVERT: A 186 ASP cc_start: 0.7957 (t0) cc_final: 0.7629 (t0) REVERT: A 208 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9058 (mm-30) REVERT: A 212 GLN cc_start: 0.9353 (pt0) cc_final: 0.9133 (tp40) REVERT: A 242 LEU cc_start: 0.9414 (tp) cc_final: 0.9120 (pp) REVERT: A 341 ASP cc_start: 0.8499 (t0) cc_final: 0.7841 (p0) REVERT: A 379 CYS cc_start: 0.9387 (p) cc_final: 0.9084 (p) REVERT: A 393 LEU cc_start: 0.9209 (mp) cc_final: 0.8580 (mp) REVERT: A 413 ASP cc_start: 0.9513 (t0) cc_final: 0.9236 (t0) REVERT: C 182 LYS cc_start: 0.8687 (pttm) cc_final: 0.8467 (ptpp) REVERT: C 186 ASP cc_start: 0.7997 (t0) cc_final: 0.7650 (t0) REVERT: C 212 GLN cc_start: 0.9385 (pt0) cc_final: 0.9178 (tp40) REVERT: C 242 LEU cc_start: 0.9357 (tp) cc_final: 0.9100 (pp) REVERT: C 243 TYR cc_start: 0.9285 (m-10) cc_final: 0.9077 (m-10) REVERT: C 269 ILE cc_start: 0.8196 (tt) cc_final: 0.7979 (tt) REVERT: C 338 MET cc_start: 0.9048 (mmp) cc_final: 0.8792 (mmp) REVERT: C 341 ASP cc_start: 0.8435 (t0) cc_final: 0.7990 (p0) REVERT: C 393 LEU cc_start: 0.9148 (mp) cc_final: 0.8546 (mp) REVERT: C 463 THR cc_start: 0.8345 (t) cc_final: 0.8060 (t) REVERT: E 182 LYS cc_start: 0.8540 (pttm) cc_final: 0.8299 (ptpp) REVERT: E 186 ASP cc_start: 0.7914 (t0) cc_final: 0.7574 (t0) REVERT: E 212 GLN cc_start: 0.9379 (pt0) cc_final: 0.9173 (tp40) REVERT: E 242 LEU cc_start: 0.9378 (tp) cc_final: 0.9091 (pp) REVERT: E 338 MET cc_start: 0.8688 (mmp) cc_final: 0.8296 (mmp) REVERT: E 341 ASP cc_start: 0.8472 (t0) cc_final: 0.7992 (p0) REVERT: E 349 GLN cc_start: 0.9236 (tt0) cc_final: 0.8929 (tt0) REVERT: E 393 LEU cc_start: 0.9132 (mp) cc_final: 0.8610 (mp) REVERT: E 463 THR cc_start: 0.8166 (t) cc_final: 0.7911 (t) REVERT: G 186 ASP cc_start: 0.7918 (t0) cc_final: 0.7616 (t0) REVERT: G 212 GLN cc_start: 0.9366 (pt0) cc_final: 0.9154 (tp40) REVERT: G 242 LEU cc_start: 0.9361 (tp) cc_final: 0.9111 (pp) REVERT: G 341 ASP cc_start: 0.8458 (t0) cc_final: 0.8061 (p0) REVERT: G 393 LEU cc_start: 0.9184 (mp) cc_final: 0.8563 (mp) outliers start: 76 outliers final: 33 residues processed: 609 average time/residue: 0.2773 time to fit residues: 224.5024 Evaluate side-chains 458 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 425 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN C 491 HIS ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN ** E 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 GLN G 491 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11592 Z= 0.399 Angle : 0.864 11.000 15712 Z= 0.451 Chirality : 0.049 0.175 1684 Planarity : 0.006 0.059 2068 Dihedral : 5.332 24.854 1568 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.67 % Allowed : 5.69 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.22), residues: 1396 helix: -1.52 (0.16), residues: 780 sheet: -1.01 (0.51), residues: 128 loop : -0.67 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP C 371 HIS 0.014 0.003 HIS A 251 PHE 0.023 0.002 PHE E 412 TYR 0.021 0.003 TYR C 264 ARG 0.012 0.001 ARG H 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 500 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LYS cc_start: 0.8832 (mppt) cc_final: 0.8559 (mtpt) REVERT: A 172 GLU cc_start: 0.9202 (pm20) cc_final: 0.8782 (pm20) REVERT: A 186 ASP cc_start: 0.7878 (t0) cc_final: 0.7605 (t0) REVERT: A 208 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9178 (mm-30) REVERT: A 236 TYR cc_start: 0.8872 (t80) cc_final: 0.8617 (t80) REVERT: A 243 TYR cc_start: 0.9186 (m-10) cc_final: 0.8981 (m-10) REVERT: A 251 HIS cc_start: 0.8628 (m170) cc_final: 0.8406 (m-70) REVERT: A 338 MET cc_start: 0.9282 (mmp) cc_final: 0.8563 (mmp) REVERT: A 341 ASP cc_start: 0.8499 (t0) cc_final: 0.7736 (p0) REVERT: A 369 LEU cc_start: 0.9057 (mm) cc_final: 0.8846 (mm) REVERT: A 392 LEU cc_start: 0.9567 (mt) cc_final: 0.9084 (mt) REVERT: A 393 LEU cc_start: 0.9131 (mp) cc_final: 0.8665 (mp) REVERT: A 460 ASP cc_start: 0.9298 (t0) cc_final: 0.9085 (t0) REVERT: A 462 TYR cc_start: 0.8475 (m-80) cc_final: 0.8262 (m-80) REVERT: C 175 LYS cc_start: 0.8426 (pptt) cc_final: 0.8197 (tttt) REVERT: C 186 ASP cc_start: 0.7974 (t0) cc_final: 0.7770 (t0) REVERT: C 221 ARG cc_start: 0.8636 (mmt90) cc_final: 0.8421 (mmm-85) REVERT: C 246 HIS cc_start: 0.8886 (m-70) cc_final: 0.8627 (m170) REVERT: C 338 MET cc_start: 0.9242 (mmp) cc_final: 0.8739 (mmp) REVERT: C 339 LEU cc_start: 0.8818 (pp) cc_final: 0.8514 (pp) REVERT: C 341 ASP cc_start: 0.8603 (t0) cc_final: 0.7705 (p0) REVERT: C 369 LEU cc_start: 0.8943 (mm) cc_final: 0.8700 (mm) REVERT: C 393 LEU cc_start: 0.9092 (mp) cc_final: 0.8717 (mp) REVERT: E 175 LYS cc_start: 0.8393 (pptt) cc_final: 0.8173 (tttt) REVERT: E 243 TYR cc_start: 0.9150 (m-10) cc_final: 0.8917 (m-10) REVERT: E 246 HIS cc_start: 0.8922 (m-70) cc_final: 0.8666 (m170) REVERT: E 339 LEU cc_start: 0.8875 (pp) cc_final: 0.8566 (pp) REVERT: E 341 ASP cc_start: 0.8648 (t0) cc_final: 0.7847 (p0) REVERT: E 361 GLU cc_start: 0.9713 (tp30) cc_final: 0.9493 (tm-30) REVERT: E 369 LEU cc_start: 0.9011 (mm) cc_final: 0.8753 (mm) REVERT: E 393 LEU cc_start: 0.9121 (mp) cc_final: 0.8786 (mp) REVERT: G 172 GLU cc_start: 0.9301 (pm20) cc_final: 0.8857 (pm20) REVERT: G 186 ASP cc_start: 0.7912 (t0) cc_final: 0.7671 (t0) REVERT: G 242 LEU cc_start: 0.9352 (tp) cc_final: 0.9083 (pp) REVERT: G 243 TYR cc_start: 0.9185 (m-10) cc_final: 0.8921 (m-10) REVERT: G 246 HIS cc_start: 0.8921 (m-70) cc_final: 0.8687 (m170) REVERT: G 310 CYS cc_start: 0.8987 (p) cc_final: 0.8554 (p) REVERT: G 331 GLU cc_start: 0.9340 (pt0) cc_final: 0.9034 (mp0) REVERT: G 338 MET cc_start: 0.8981 (mmp) cc_final: 0.8780 (mmp) REVERT: G 339 LEU cc_start: 0.8800 (pp) cc_final: 0.8570 (pp) REVERT: G 341 ASP cc_start: 0.8654 (t0) cc_final: 0.8056 (p0) REVERT: G 369 LEU cc_start: 0.9013 (mm) cc_final: 0.8787 (mm) REVERT: G 393 LEU cc_start: 0.9043 (mp) cc_final: 0.8694 (mp) outliers start: 8 outliers final: 3 residues processed: 501 average time/residue: 0.2632 time to fit residues: 178.4531 Evaluate side-chains 404 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 401 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 133 optimal weight: 0.0670 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 overall best weight: 2.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 212 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11592 Z= 0.265 Angle : 0.748 8.229 15712 Z= 0.386 Chirality : 0.046 0.178 1684 Planarity : 0.005 0.044 2068 Dihedral : 5.267 27.102 1568 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.33 % Allowed : 4.52 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1396 helix: -1.26 (0.17), residues: 780 sheet: -1.03 (0.47), residues: 136 loop : -0.90 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP G 371 HIS 0.011 0.002 HIS E 251 PHE 0.028 0.002 PHE A 372 TYR 0.019 0.002 TYR A 213 ARG 0.007 0.001 ARG C 297 *********************** 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 473 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 469 time to evaluate : 1.259 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 213 TYR cc_start: 0.9262 (t80) cc_final: 0.8775 (t80) REVERT: A 267 ASP cc_start: 0.9420 (p0) cc_final: 0.9217 (p0) REVERT: A 338 MET cc_start: 0.9277 (mmp) cc_final: 0.8671 (mmp) REVERT: A 341 ASP cc_start: 0.8498 (t0) cc_final: 0.7704 (p0) REVERT: A 369 LEU cc_start: 0.9114 (mm) cc_final: 0.8904 (mm) REVERT: A 393 LEU cc_start: 0.8985 (mp) cc_final: 0.8645 (mp) REVERT: A 462 TYR cc_start: 0.8655 (m-10) cc_final: 0.8254 (m-10) REVERT: C 175 LYS cc_start: 0.8317 (pptt) cc_final: 0.8063 (tttt) REVERT: C 186 ASP cc_start: 0.7902 (t0) cc_final: 0.7691 (t0) REVERT: C 246 HIS cc_start: 0.8885 (m-70) cc_final: 0.8583 (m170) REVERT: C 338 MET cc_start: 0.9206 (mmp) cc_final: 0.8760 (mmp) REVERT: C 341 ASP cc_start: 0.8671 (t0) cc_final: 0.7813 (p0) REVERT: C 361 GLU cc_start: 0.9627 (tp30) cc_final: 0.9383 (tm-30) REVERT: C 369 LEU cc_start: 0.9034 (mm) cc_final: 0.8756 (mm) REVERT: C 393 LEU cc_start: 0.9027 (mp) cc_final: 0.8635 (mp) REVERT: C 455 PHE cc_start: 0.8910 (p90) cc_final: 0.8400 (p90) REVERT: C 456 SER cc_start: 0.8443 (t) cc_final: 0.8106 (t) REVERT: C 462 TYR cc_start: 0.8633 (m-10) cc_final: 0.8411 (m-10) REVERT: E 175 LYS cc_start: 0.8306 (pptt) cc_final: 0.8064 (tttt) REVERT: E 246 HIS cc_start: 0.8921 (m-70) cc_final: 0.8679 (m170) REVERT: E 339 LEU cc_start: 0.8708 (pp) cc_final: 0.8389 (pp) REVERT: E 341 ASP cc_start: 0.8568 (t0) cc_final: 0.7757 (p0) REVERT: E 349 GLN cc_start: 0.9280 (tt0) cc_final: 0.9059 (tt0) REVERT: E 369 LEU cc_start: 0.9090 (mm) cc_final: 0.8801 (mm) REVERT: E 393 LEU cc_start: 0.9076 (mp) cc_final: 0.8706 (mp) REVERT: E 460 ASP cc_start: 0.9137 (t0) cc_final: 0.8936 (t0) REVERT: G 186 ASP cc_start: 0.7904 (t0) cc_final: 0.7648 (t0) REVERT: G 213 TYR cc_start: 0.9278 (t80) cc_final: 0.9000 (t80) REVERT: G 221 ARG cc_start: 0.8673 (mmt90) cc_final: 0.8459 (mmm-85) REVERT: G 235 VAL cc_start: 0.9448 (p) cc_final: 0.9199 (m) REVERT: G 242 LEU cc_start: 0.9335 (tp) cc_final: 0.9110 (pp) REVERT: G 246 HIS cc_start: 0.8932 (m-70) cc_final: 0.8658 (m170) REVERT: G 251 HIS cc_start: 0.8524 (m-70) cc_final: 0.8307 (m-70) REVERT: G 267 ASP cc_start: 0.9405 (p0) cc_final: 0.9196 (p0) REVERT: G 338 MET cc_start: 0.9037 (mmp) cc_final: 0.8335 (mmt) REVERT: G 341 ASP cc_start: 0.8663 (t0) cc_final: 0.7910 (p0) REVERT: G 369 LEU cc_start: 0.9065 (mm) cc_final: 0.8841 (mm) REVERT: G 393 LEU cc_start: 0.9026 (mp) cc_final: 0.8688 (mp) outliers start: 4 outliers final: 1 residues processed: 470 average time/residue: 0.2547 time to fit residues: 162.2861 Evaluate side-chains 405 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 404 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 428 GLN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11592 Z= 0.244 Angle : 0.731 8.753 15712 Z= 0.374 Chirality : 0.046 0.197 1684 Planarity : 0.005 0.045 2068 Dihedral : 5.226 28.991 1568 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.59 % Allowed : 4.35 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.22), residues: 1396 helix: -1.06 (0.17), residues: 776 sheet: -0.84 (0.47), residues: 136 loop : -0.83 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 371 HIS 0.013 0.002 HIS A 251 PHE 0.019 0.002 PHE A 372 TYR 0.019 0.002 TYR C 236 ARG 0.009 0.001 ARG G 450 *********************** 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 474 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 467 time to evaluate : 1.144 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 213 TYR cc_start: 0.9201 (t80) cc_final: 0.8956 (t80) REVERT: A 308 PHE cc_start: 0.8962 (t80) cc_final: 0.8751 (t80) REVERT: A 338 MET cc_start: 0.9332 (mmp) cc_final: 0.8705 (mmp) REVERT: A 341 ASP cc_start: 0.8485 (t0) cc_final: 0.7758 (p0) REVERT: A 369 LEU cc_start: 0.9082 (mm) cc_final: 0.8876 (mm) REVERT: A 393 LEU cc_start: 0.9050 (mp) cc_final: 0.8800 (mp) REVERT: C 246 HIS cc_start: 0.8795 (m-70) cc_final: 0.8542 (m170) REVERT: C 251 HIS cc_start: 0.8561 (m-70) cc_final: 0.8350 (m-70) REVERT: C 338 MET cc_start: 0.9222 (mmp) cc_final: 0.8779 (mmt) REVERT: C 341 ASP cc_start: 0.8682 (t0) cc_final: 0.7956 (p0) REVERT: C 361 GLU cc_start: 0.9627 (tp30) cc_final: 0.9396 (tm-30) REVERT: C 369 LEU cc_start: 0.9004 (mm) cc_final: 0.8762 (mm) REVERT: C 393 LEU cc_start: 0.8942 (mp) cc_final: 0.8589 (mp) REVERT: C 455 PHE cc_start: 0.8823 (p90) cc_final: 0.8306 (p90) REVERT: C 456 SER cc_start: 0.8453 (t) cc_final: 0.8151 (t) REVERT: C 462 TYR cc_start: 0.8741 (m-10) cc_final: 0.8364 (m-10) REVERT: E 246 HIS cc_start: 0.9007 (m-70) cc_final: 0.8769 (m170) REVERT: E 251 HIS cc_start: 0.8473 (m-70) cc_final: 0.8271 (m-70) REVERT: E 338 MET cc_start: 0.9063 (mmp) cc_final: 0.8752 (mmp) REVERT: E 341 ASP cc_start: 0.8623 (t0) cc_final: 0.7915 (p0) REVERT: E 369 LEU cc_start: 0.9078 (mm) cc_final: 0.8830 (mm) REVERT: E 393 LEU cc_start: 0.8970 (mp) cc_final: 0.8662 (mp) REVERT: G 186 ASP cc_start: 0.7901 (t0) cc_final: 0.7672 (t0) REVERT: G 213 TYR cc_start: 0.9306 (t80) cc_final: 0.9008 (t80) REVERT: G 242 LEU cc_start: 0.9256 (tp) cc_final: 0.9008 (pp) REVERT: G 246 HIS cc_start: 0.8955 (m-70) cc_final: 0.8657 (m170) REVERT: G 251 HIS cc_start: 0.8575 (m-70) cc_final: 0.8374 (m-70) REVERT: G 338 MET cc_start: 0.9093 (mmp) cc_final: 0.8533 (mmp) REVERT: G 341 ASP cc_start: 0.8674 (t0) cc_final: 0.7917 (p0) REVERT: G 369 LEU cc_start: 0.8985 (mm) cc_final: 0.8777 (mm) REVERT: G 393 LEU cc_start: 0.8947 (mp) cc_final: 0.8595 (mp) outliers start: 7 outliers final: 4 residues processed: 469 average time/residue: 0.2393 time to fit residues: 154.7524 Evaluate side-chains 405 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 401 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.0270 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- 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 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 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 ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 11592 Z= 0.275 Angle : 0.731 7.848 15712 Z= 0.378 Chirality : 0.047 0.245 1684 Planarity : 0.005 0.035 2068 Dihedral : 5.317 31.660 1568 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1396 helix: -0.99 (0.18), residues: 780 sheet: -0.65 (0.56), residues: 96 loop : -1.02 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 371 HIS 0.013 0.002 HIS E 401 PHE 0.021 0.002 PHE C 299 TYR 0.014 0.002 TYR C 236 ARG 0.006 0.001 ARG G 445 *********************** 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 447 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 444 time to evaluate : 1.335 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: A 213 TYR cc_start: 0.9300 (t80) cc_final: 0.9041 (t80) REVERT: A 308 PHE cc_start: 0.8967 (t80) cc_final: 0.8747 (t80) REVERT: A 338 MET cc_start: 0.9311 (mmp) cc_final: 0.8187 (mmp) REVERT: A 341 ASP cc_start: 0.8669 (t0) cc_final: 0.7844 (p0) REVERT: A 369 LEU cc_start: 0.9067 (mm) cc_final: 0.8839 (mm) REVERT: A 393 LEU cc_start: 0.9144 (mp) cc_final: 0.8898 (mp) REVERT: C 246 HIS cc_start: 0.8881 (m-70) cc_final: 0.8637 (m170) REVERT: C 338 MET cc_start: 0.9264 (mmp) cc_final: 0.8728 (mmp) REVERT: C 341 ASP cc_start: 0.8780 (t0) cc_final: 0.7968 (p0) REVERT: C 361 GLU cc_start: 0.9637 (tp30) cc_final: 0.9420 (tm-30) REVERT: C 369 LEU cc_start: 0.9026 (mm) cc_final: 0.8774 (mm) REVERT: C 393 LEU cc_start: 0.8955 (mp) cc_final: 0.8702 (mp) REVERT: C 455 PHE cc_start: 0.8887 (p90) cc_final: 0.8383 (p90) REVERT: C 462 TYR cc_start: 0.8859 (m-10) cc_final: 0.8381 (m-10) REVERT: E 213 TYR cc_start: 0.9148 (t80) cc_final: 0.8769 (t80) REVERT: E 246 HIS cc_start: 0.8999 (m-70) cc_final: 0.8740 (m170) REVERT: E 338 MET cc_start: 0.9117 (mmp) cc_final: 0.8462 (mmp) REVERT: E 341 ASP cc_start: 0.8671 (t0) cc_final: 0.7863 (p0) REVERT: E 369 LEU cc_start: 0.9131 (mm) cc_final: 0.8869 (mm) REVERT: E 393 LEU cc_start: 0.8966 (mp) cc_final: 0.8672 (mp) REVERT: E 460 ASP cc_start: 0.9241 (t0) cc_final: 0.9007 (t0) REVERT: G 213 TYR cc_start: 0.9330 (t80) cc_final: 0.9102 (t80) REVERT: G 221 ARG cc_start: 0.8636 (mmt90) cc_final: 0.8383 (mmm-85) REVERT: G 251 HIS cc_start: 0.8680 (m-70) cc_final: 0.8427 (m-70) REVERT: G 338 MET cc_start: 0.9121 (mmp) cc_final: 0.8263 (mmt) REVERT: G 341 ASP cc_start: 0.8718 (t0) cc_final: 0.7930 (p0) REVERT: G 369 LEU cc_start: 0.9030 (mm) cc_final: 0.8799 (mm) REVERT: G 393 LEU cc_start: 0.8953 (mp) cc_final: 0.8608 (mp) outliers start: 3 outliers final: 1 residues processed: 444 average time/residue: 0.2399 time to fit residues: 146.5603 Evaluate side-chains 403 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 131 optimal weight: 0.1980 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 0.0270 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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 423 GLN A 428 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11592 Z= 0.209 Angle : 0.743 9.659 15712 Z= 0.370 Chirality : 0.045 0.221 1684 Planarity : 0.005 0.046 2068 Dihedral : 5.248 32.019 1568 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.17 % Allowed : 2.76 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1396 helix: -0.91 (0.18), residues: 784 sheet: -0.88 (0.47), residues: 136 loop : -0.75 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP E 371 HIS 0.014 0.002 HIS G 401 PHE 0.025 0.002 PHE E 344 TYR 0.020 0.002 TYR C 213 ARG 0.012 0.001 ARG A 221 *********************** 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 467 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 465 time to evaluate : 1.348 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 174 ASP cc_start: 0.8782 (t70) cc_final: 0.8541 (t0) REVERT: A 186 ASP cc_start: 0.7852 (t0) cc_final: 0.7571 (t0) REVERT: A 338 MET cc_start: 0.9354 (mmp) cc_final: 0.8673 (mmt) REVERT: A 341 ASP cc_start: 0.8575 (t0) cc_final: 0.7732 (p0) REVERT: A 349 GLN cc_start: 0.8762 (mt0) cc_final: 0.8258 (mm110) REVERT: A 393 LEU cc_start: 0.9113 (mp) cc_final: 0.8843 (mp) REVERT: A 422 TYR cc_start: 0.8509 (p90) cc_final: 0.8299 (p90) REVERT: A 462 TYR cc_start: 0.8783 (m-10) cc_final: 0.8133 (m-10) REVERT: C 213 TYR cc_start: 0.9371 (t80) cc_final: 0.9153 (t80) REVERT: C 246 HIS cc_start: 0.8785 (m-70) cc_final: 0.8546 (m170) REVERT: C 267 ASP cc_start: 0.9478 (p0) cc_final: 0.9235 (p0) REVERT: C 338 MET cc_start: 0.9265 (mmp) cc_final: 0.8839 (mmp) REVERT: C 341 ASP cc_start: 0.8705 (t0) cc_final: 0.7919 (p0) REVERT: C 361 GLU cc_start: 0.9629 (tp30) cc_final: 0.9429 (tm-30) REVERT: C 362 GLU cc_start: 0.9690 (mp0) cc_final: 0.9475 (mp0) REVERT: C 369 LEU cc_start: 0.8894 (mm) cc_final: 0.8676 (mm) REVERT: C 393 LEU cc_start: 0.8811 (mp) cc_final: 0.8575 (mp) REVERT: C 455 PHE cc_start: 0.8820 (p90) cc_final: 0.8341 (p90) REVERT: C 462 TYR cc_start: 0.8815 (m-10) cc_final: 0.8250 (m-10) REVERT: E 213 TYR cc_start: 0.9165 (t80) cc_final: 0.8802 (t80) REVERT: E 338 MET cc_start: 0.9156 (mmp) cc_final: 0.8649 (mmp) REVERT: E 341 ASP cc_start: 0.8708 (t0) cc_final: 0.8023 (p0) REVERT: E 369 LEU cc_start: 0.9057 (mm) cc_final: 0.8786 (mm) REVERT: E 393 LEU cc_start: 0.8588 (mp) cc_final: 0.8367 (mp) REVERT: E 455 PHE cc_start: 0.8778 (p90) cc_final: 0.8344 (p90) REVERT: G 213 TYR cc_start: 0.9341 (t80) cc_final: 0.9040 (t80) REVERT: G 338 MET cc_start: 0.9087 (mmp) cc_final: 0.8322 (mmt) REVERT: G 341 ASP cc_start: 0.8690 (t0) cc_final: 0.8012 (p0) REVERT: G 393 LEU cc_start: 0.8952 (mp) cc_final: 0.8725 (mp) outliers start: 2 outliers final: 0 residues processed: 467 average time/residue: 0.2357 time to fit residues: 152.0623 Evaluate side-chains 401 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 C 178 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 HIS ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5884 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= 0.235 Angle : 0.740 9.941 15712 Z= 0.373 Chirality : 0.046 0.202 1684 Planarity : 0.005 0.040 2068 Dihedral : 5.185 30.912 1568 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1396 helix: -0.89 (0.18), residues: 784 sheet: -0.75 (0.55), residues: 96 loop : -0.94 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 371 HIS 0.015 0.002 HIS C 401 PHE 0.021 0.002 PHE C 376 TYR 0.028 0.002 TYR A 213 ARG 0.010 0.001 ARG G 221 *********************** 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 445 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 1.256 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 213 TYR cc_start: 0.9352 (t80) cc_final: 0.9034 (t80) REVERT: A 338 MET cc_start: 0.9261 (mmp) cc_final: 0.8390 (mmp) REVERT: A 341 ASP cc_start: 0.8595 (t0) cc_final: 0.7747 (p0) REVERT: A 349 GLN cc_start: 0.8841 (mt0) cc_final: 0.8322 (mm110) REVERT: A 393 LEU cc_start: 0.8940 (mp) cc_final: 0.8732 (mp) REVERT: A 459 PHE cc_start: 0.8887 (t80) cc_final: 0.8659 (t80) REVERT: C 246 HIS cc_start: 0.8745 (m-70) cc_final: 0.8516 (m170) REVERT: C 300 LEU cc_start: 0.8541 (pp) cc_final: 0.8334 (pp) REVERT: C 338 MET cc_start: 0.9256 (mmp) cc_final: 0.8763 (mmp) REVERT: C 341 ASP cc_start: 0.8697 (t0) cc_final: 0.7970 (p0) REVERT: C 361 GLU cc_start: 0.9624 (tp30) cc_final: 0.9424 (tm-30) REVERT: C 362 GLU cc_start: 0.9623 (mp0) cc_final: 0.9422 (mp0) REVERT: C 369 LEU cc_start: 0.8916 (mm) cc_final: 0.8679 (mm) REVERT: C 393 LEU cc_start: 0.8749 (mp) cc_final: 0.8532 (mp) REVERT: C 455 PHE cc_start: 0.8851 (p90) cc_final: 0.8391 (p90) REVERT: C 460 ASP cc_start: 0.9286 (t0) cc_final: 0.9020 (t0) REVERT: C 462 TYR cc_start: 0.8802 (m-10) cc_final: 0.8281 (m-10) REVERT: E 213 TYR cc_start: 0.9179 (t80) cc_final: 0.8833 (t80) REVERT: E 267 ASP cc_start: 0.9396 (p0) cc_final: 0.9155 (p0) REVERT: E 341 ASP cc_start: 0.8672 (t0) cc_final: 0.7970 (p0) REVERT: E 369 LEU cc_start: 0.9004 (mm) cc_final: 0.8773 (mm) REVERT: E 455 PHE cc_start: 0.8817 (p90) cc_final: 0.8387 (p90) REVERT: E 456 SER cc_start: 0.8441 (t) cc_final: 0.8177 (t) REVERT: G 213 TYR cc_start: 0.9361 (t80) cc_final: 0.8946 (t80) REVERT: G 266 GLU cc_start: 0.8185 (pm20) cc_final: 0.7974 (pm20) REVERT: G 267 ASP cc_start: 0.9341 (p0) cc_final: 0.9139 (p0) REVERT: G 338 MET cc_start: 0.9057 (mmp) cc_final: 0.8750 (mmp) REVERT: G 341 ASP cc_start: 0.8736 (t0) cc_final: 0.8128 (p0) REVERT: G 393 LEU cc_start: 0.8889 (mp) cc_final: 0.8655 (mp) REVERT: G 427 TYR cc_start: 0.8479 (m-80) cc_final: 0.7922 (m-80) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.2399 time to fit residues: 147.2711 Evaluate side-chains 396 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 0.0770 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 chunk 125 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 11592 Z= 0.223 Angle : 0.766 11.100 15712 Z= 0.380 Chirality : 0.046 0.180 1684 Planarity : 0.005 0.051 2068 Dihedral : 5.196 30.396 1568 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.22), residues: 1396 helix: -0.99 (0.18), residues: 792 sheet: -0.88 (0.53), residues: 96 loop : -0.90 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP E 371 HIS 0.016 0.002 HIS E 401 PHE 0.020 0.002 PHE G 376 TYR 0.023 0.002 TYR A 213 ARG 0.014 0.001 ARG C 477 *********************** 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 441 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.7771 (t0) cc_final: 0.7519 (t0) REVERT: A 213 TYR cc_start: 0.9337 (t80) cc_final: 0.9054 (t80) REVERT: A 338 MET cc_start: 0.9300 (mmp) cc_final: 0.8523 (mmp) REVERT: A 341 ASP cc_start: 0.8457 (t0) cc_final: 0.7583 (p0) REVERT: A 349 GLN cc_start: 0.8838 (mt0) cc_final: 0.8325 (mm110) REVERT: A 455 PHE cc_start: 0.8716 (p90) cc_final: 0.8328 (p90) REVERT: A 459 PHE cc_start: 0.8880 (t80) cc_final: 0.8642 (t80) REVERT: C 213 TYR cc_start: 0.9363 (t80) cc_final: 0.9078 (t80) REVERT: C 297 ARG cc_start: 0.8902 (mmp80) cc_final: 0.8697 (mmp80) REVERT: C 338 MET cc_start: 0.9307 (mmp) cc_final: 0.8759 (mmp) REVERT: C 341 ASP cc_start: 0.8661 (t0) cc_final: 0.7986 (p0) REVERT: C 346 GLN cc_start: 0.9072 (tp40) cc_final: 0.8702 (tp40) REVERT: C 369 LEU cc_start: 0.8868 (mm) cc_final: 0.8615 (mm) REVERT: C 393 LEU cc_start: 0.8639 (mp) cc_final: 0.8418 (mp) REVERT: C 455 PHE cc_start: 0.8816 (p90) cc_final: 0.8362 (p90) REVERT: C 456 SER cc_start: 0.8424 (t) cc_final: 0.8197 (t) REVERT: C 460 ASP cc_start: 0.9271 (t0) cc_final: 0.8965 (t0) REVERT: C 462 TYR cc_start: 0.8730 (m-10) cc_final: 0.8270 (m-10) REVERT: E 213 TYR cc_start: 0.9161 (t80) cc_final: 0.8796 (t80) REVERT: E 321 MET cc_start: 0.8038 (pmm) cc_final: 0.7440 (tpt) REVERT: E 338 MET cc_start: 0.9173 (mmp) cc_final: 0.8665 (mmp) REVERT: E 341 ASP cc_start: 0.8585 (t0) cc_final: 0.7798 (p0) REVERT: E 369 LEU cc_start: 0.8987 (mm) cc_final: 0.8747 (mm) REVERT: E 455 PHE cc_start: 0.8800 (p90) cc_final: 0.8384 (p90) REVERT: E 456 SER cc_start: 0.8386 (t) cc_final: 0.8133 (t) REVERT: G 213 TYR cc_start: 0.9337 (t80) cc_final: 0.8989 (t80) REVERT: G 267 ASP cc_start: 0.9504 (p0) cc_final: 0.9241 (p0) REVERT: G 297 ARG cc_start: 0.9006 (tpp80) cc_final: 0.8791 (mmt90) REVERT: G 338 MET cc_start: 0.9101 (mmp) cc_final: 0.8764 (mmp) REVERT: G 341 ASP cc_start: 0.8699 (t0) cc_final: 0.7979 (p0) REVERT: G 393 LEU cc_start: 0.8751 (mp) cc_final: 0.8520 (mp) REVERT: G 427 TYR cc_start: 0.8455 (m-80) cc_final: 0.7897 (m-80) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.2410 time to fit residues: 146.9157 Evaluate side-chains 396 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 11592 Z= 0.316 Angle : 0.798 9.401 15712 Z= 0.416 Chirality : 0.048 0.223 1684 Planarity : 0.006 0.138 2068 Dihedral : 5.423 30.696 1568 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1396 helix: -1.09 (0.17), residues: 788 sheet: -1.26 (0.50), residues: 96 loop : -1.01 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP E 371 HIS 0.016 0.003 HIS C 401 PHE 0.024 0.002 PHE G 376 TYR 0.022 0.002 TYR E 236 ARG 0.010 0.001 ARG G 265 *********************** 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 429 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 1.276 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 213 TYR cc_start: 0.9399 (t80) cc_final: 0.9112 (t80) REVERT: A 338 MET cc_start: 0.9281 (mmp) cc_final: 0.8545 (mmp) REVERT: A 341 ASP cc_start: 0.8578 (t0) cc_final: 0.7715 (p0) REVERT: A 349 GLN cc_start: 0.8939 (mt0) cc_final: 0.8479 (mm110) REVERT: C 213 TYR cc_start: 0.9368 (t80) cc_final: 0.9105 (t80) REVERT: C 267 ASP cc_start: 0.9445 (p0) cc_final: 0.9240 (p0) REVERT: C 308 PHE cc_start: 0.8879 (t80) cc_final: 0.8679 (t80) REVERT: C 369 LEU cc_start: 0.9031 (mm) cc_final: 0.8799 (mm) REVERT: E 213 TYR cc_start: 0.9237 (t80) cc_final: 0.8860 (t80) REVERT: E 349 GLN cc_start: 0.9307 (tt0) cc_final: 0.9088 (tt0) REVERT: E 369 LEU cc_start: 0.9133 (mm) cc_final: 0.8931 (mm) REVERT: E 427 TYR cc_start: 0.8413 (m-80) cc_final: 0.7891 (m-80) REVERT: G 171 SER cc_start: 0.8902 (m) cc_final: 0.8667 (p) REVERT: G 213 TYR cc_start: 0.9320 (t80) cc_final: 0.9008 (t80) REVERT: G 349 GLN cc_start: 0.9283 (tt0) cc_final: 0.8795 (tp40) REVERT: G 427 TYR cc_start: 0.8396 (m-80) cc_final: 0.7864 (m-80) REVERT: G 453 ARG cc_start: 0.9312 (ptp-110) cc_final: 0.8922 (ttm110) REVERT: G 460 ASP cc_start: 0.9238 (t0) cc_final: 0.8924 (t0) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.2303 time to fit residues: 137.8457 Evaluate side-chains 378 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS E 178 HIS ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11592 Z= 0.230 Angle : 0.812 12.135 15712 Z= 0.407 Chirality : 0.048 0.210 1684 Planarity : 0.006 0.106 2068 Dihedral : 5.343 30.948 1568 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.22), residues: 1396 helix: -0.99 (0.17), residues: 804 sheet: -1.25 (0.50), residues: 96 loop : -1.12 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP E 371 HIS 0.016 0.002 HIS G 401 PHE 0.031 0.002 PHE G 255 TYR 0.020 0.002 TYR A 213 ARG 0.008 0.001 ARG C 297 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.7726 (t0) cc_final: 0.7462 (t0) REVERT: A 213 TYR cc_start: 0.9349 (t80) cc_final: 0.9118 (t80) REVERT: A 338 MET cc_start: 0.9305 (mmp) cc_final: 0.8280 (mmp) REVERT: A 341 ASP cc_start: 0.8445 (t0) cc_final: 0.7735 (p0) REVERT: A 349 GLN cc_start: 0.8879 (mt0) cc_final: 0.8376 (mm110) REVERT: C 213 TYR cc_start: 0.9442 (t80) cc_final: 0.9206 (t80) REVERT: C 267 ASP cc_start: 0.9449 (p0) cc_final: 0.9236 (p0) REVERT: C 455 PHE cc_start: 0.8854 (p90) cc_final: 0.8399 (p90) REVERT: C 462 TYR cc_start: 0.8759 (m-10) cc_final: 0.8471 (m-10) REVERT: E 213 TYR cc_start: 0.9216 (t80) cc_final: 0.8842 (t80) REVERT: E 341 ASP cc_start: 0.8577 (t0) cc_final: 0.7963 (p0) REVERT: E 369 LEU cc_start: 0.9042 (mm) cc_final: 0.8817 (mm) REVERT: E 427 TYR cc_start: 0.8384 (m-80) cc_final: 0.7860 (m-80) REVERT: E 455 PHE cc_start: 0.8803 (p90) cc_final: 0.8397 (p90) REVERT: G 171 SER cc_start: 0.8832 (m) cc_final: 0.8592 (p) REVERT: G 213 TYR cc_start: 0.9316 (t80) cc_final: 0.9031 (t80) REVERT: G 338 MET cc_start: 0.9085 (mmp) cc_final: 0.8728 (mmp) REVERT: G 341 ASP cc_start: 0.8596 (t0) cc_final: 0.8075 (p0) REVERT: G 349 GLN cc_start: 0.9162 (tt0) cc_final: 0.8682 (tp40) REVERT: G 427 TYR cc_start: 0.8426 (m-80) cc_final: 0.7892 (m-80) REVERT: G 453 ARG cc_start: 0.9261 (ptp-110) cc_final: 0.8753 (ttm170) REVERT: G 460 ASP cc_start: 0.9230 (t0) cc_final: 0.9026 (t0) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.2421 time to fit residues: 147.9474 Evaluate side-chains 386 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 108 optimal weight: 0.0070 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS C 246 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.124551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.095874 restraints weight = 24934.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099794 restraints weight = 16466.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.102654 restraints weight = 11890.122| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11592 Z= 0.222 Angle : 0.805 12.218 15712 Z= 0.402 Chirality : 0.046 0.167 1684 Planarity : 0.005 0.072 2068 Dihedral : 5.265 29.144 1568 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.22), residues: 1396 helix: -1.00 (0.17), residues: 808 sheet: -1.31 (0.49), residues: 96 loop : -0.99 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP C 371 HIS 0.016 0.002 HIS C 401 PHE 0.022 0.002 PHE A 305 TYR 0.021 0.002 TYR A 213 ARG 0.008 0.001 ARG C 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3187.52 seconds wall clock time: 57 minutes 4.37 seconds (3424.37 seconds total)