Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 00:41:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2g_11624/07_2023/7a2g_11624.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2g_11624/07_2023/7a2g_11624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2g_11624/07_2023/7a2g_11624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2g_11624/07_2023/7a2g_11624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2g_11624/07_2023/7a2g_11624.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a2g_11624/07_2023/7a2g_11624.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.008 sd= 0.048 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 40 5.16 5 C 8520 2.51 5 N 2344 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 217": "OD1" <-> "OD2" Residue "D TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D ASP 350": "OD1" <-> "OD2" Residue "D TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 13408 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3350 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 394} Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3350 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 394} Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3350 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 394} Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3350 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 394} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.58, per 1000 atoms: 0.49 Number of scatterers: 13408 At special positions: 0 Unit cell: (101.85, 119.7, 129.15, 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 40 16.00 O 2500 8.00 N 2344 7.00 C 8520 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 - 3.50 Amino acid : False - 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: 6.52 Conformation dependent library (CDL) restraints added in 2.1 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 16 sheets defined 50.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.991A pdb=" N VAL A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.188A pdb=" N VAL A 180 " --> pdb=" O CYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 225 through 244 removed outlier: 4.080A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.705A pdb=" N ALA A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.743A pdb=" N VAL A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 471 through 496 removed outlier: 3.603A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.930A pdb=" N VAL B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 removed outlier: 3.574A pdb=" N VAL B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 225 through 244 removed outlier: 4.542A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 Processing helix chain 'B' and resid 271 through 283 removed outlier: 4.212A pdb=" N VAL B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 Processing helix chain 'B' and resid 327 through 335 removed outlier: 4.051A pdb=" N LEU B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 341 through 355 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 396 through 404 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 471 through 496 removed outlier: 3.688A pdb=" N GLY B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 removed outlier: 3.886A pdb=" N VAL C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 3.558A pdb=" N VAL C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 174 through 182 removed outlier: 3.829A pdb=" N VAL C 180 " --> pdb=" O CYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 225 through 244 removed outlier: 4.303A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 271 through 284 removed outlier: 4.286A pdb=" N VAL C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.841A pdb=" N LEU C 333 " --> pdb=" O CYS C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 356 removed outlier: 3.632A pdb=" N LEU C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 396 through 404 Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.769A pdb=" N VAL C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 471 through 496 removed outlier: 3.971A pdb=" N GLY C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 3.931A pdb=" N VAL D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 152 removed outlier: 3.522A pdb=" N VAL D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.778A pdb=" N VAL D 180 " --> pdb=" O CYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 225 through 244 removed outlier: 4.027A pdb=" N ALA D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 262 Processing helix chain 'D' and resid 272 through 283 Processing helix chain 'D' and resid 295 through 305 Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.508A pdb=" N LEU D 333 " --> pdb=" O CYS D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 341 through 355 removed outlier: 3.667A pdb=" N SER D 355 " --> pdb=" O ILE D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 396 through 404 Processing helix chain 'D' and resid 413 through 419 removed outlier: 4.120A pdb=" N VAL D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 451 Processing helix chain 'D' and resid 471 through 496 removed outlier: 3.747A pdb=" N GLY D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.483A pdb=" N GLN A 286 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N CYS A 310 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 5.589A 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 378 through 381 Processing sheet with id=AA3, first strand: chain 'A' and resid 410 through 411 removed outlier: 6.928A pdb=" N ARG A 410 " --> pdb=" O VAL A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 456 through 459 Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.426A pdb=" N GLN B 286 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS B 310 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG B 288 " --> pdb=" O CYS B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AA7, first strand: chain 'B' and resid 409 through 411 removed outlier: 6.980A pdb=" N ARG B 410 " --> pdb=" O VAL B 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 456 through 459 Processing sheet with id=AA9, first strand: chain 'C' and resid 286 through 289 removed outlier: 6.137A pdb=" N GLN C 286 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS C 310 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG C 288 " --> pdb=" O CYS C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 409 through 411 removed outlier: 6.959A pdb=" N ARG C 410 " --> pdb=" O VAL C 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 456 through 459 Processing sheet with id=AB3, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB4, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.225A pdb=" N GLN D 286 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N CYS D 310 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG D 288 " --> pdb=" O CYS D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 378 through 381 Processing sheet with id=AB6, first strand: chain 'D' and resid 409 through 411 removed outlier: 6.907A pdb=" N ARG D 410 " --> pdb=" O VAL D 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 456 through 459 588 hydrogen bonds defined for protein. 1728 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: 3.91 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4370 1.33 - 1.45: 2195 1.45 - 1.57: 7123 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 13740 Sorted by residual: bond pdb=" CA ILE A 219 " pdb=" CB ILE A 219 " ideal model delta sigma weight residual 1.541 1.515 0.027 1.24e-02 6.50e+03 4.62e+00 bond pdb=" CA ILE B 219 " pdb=" CB ILE B 219 " ideal model delta sigma weight residual 1.540 1.515 0.025 1.23e-02 6.61e+03 4.06e+00 bond pdb=" CA ILE C 219 " pdb=" CB ILE C 219 " ideal model delta sigma weight residual 1.540 1.518 0.022 1.23e-02 6.61e+03 3.28e+00 bond pdb=" C ARG C 120 " pdb=" N PRO C 121 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" N SER C 323 " pdb=" CA SER C 323 " ideal model delta sigma weight residual 1.458 1.439 0.020 1.25e-02 6.40e+03 2.51e+00 ... (remaining 13735 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.76: 335 105.76 - 112.81: 7235 112.81 - 119.87: 4592 119.87 - 126.92: 6270 126.92 - 133.98: 192 Bond angle restraints: 18624 Sorted by residual: angle pdb=" N SER A 394 " pdb=" CA SER A 394 " pdb=" C SER A 394 " ideal model delta sigma weight residual 114.31 107.90 6.41 1.29e+00 6.01e-01 2.47e+01 angle pdb=" N SER B 394 " pdb=" CA SER B 394 " pdb=" C SER B 394 " ideal model delta sigma weight residual 113.97 107.86 6.11 1.28e+00 6.10e-01 2.28e+01 angle pdb=" N GLY D 263 " pdb=" CA GLY D 263 " pdb=" C GLY D 263 " ideal model delta sigma weight residual 115.63 109.80 5.83 1.49e+00 4.50e-01 1.53e+01 angle pdb=" N VAL A 136 " pdb=" CA VAL A 136 " pdb=" C VAL A 136 " ideal model delta sigma weight residual 108.53 104.36 4.17 1.22e+00 6.72e-01 1.17e+01 angle pdb=" C ALA A 95 " pdb=" N LEU A 96 " pdb=" CA LEU A 96 " ideal model delta sigma weight residual 121.54 127.93 -6.39 1.91e+00 2.74e-01 1.12e+01 ... (remaining 18619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7310 17.72 - 35.43: 813 35.43 - 53.15: 124 53.15 - 70.87: 20 70.87 - 88.58: 17 Dihedral angle restraints: 8284 sinusoidal: 3368 harmonic: 4916 Sorted by residual: dihedral pdb=" CA VAL D 163 " pdb=" C VAL D 163 " pdb=" N PRO D 164 " pdb=" CA PRO D 164 " ideal model delta harmonic sigma weight residual -180.00 -146.80 -33.20 0 5.00e+00 4.00e-02 4.41e+01 dihedral pdb=" CA VAL C 163 " pdb=" C VAL C 163 " pdb=" N PRO C 164 " pdb=" CA PRO C 164 " ideal model delta harmonic sigma weight residual -180.00 -147.11 -32.89 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA LEU C 293 " pdb=" C LEU C 293 " pdb=" N LEU C 294 " pdb=" CA LEU C 294 " ideal model delta harmonic sigma weight residual -180.00 -147.68 -32.32 0 5.00e+00 4.00e-02 4.18e+01 ... (remaining 8281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1337 0.041 - 0.081: 525 0.081 - 0.122: 118 0.122 - 0.162: 18 0.162 - 0.203: 2 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CG LEU A 393 " pdb=" CB LEU A 393 " pdb=" CD1 LEU A 393 " pdb=" CD2 LEU A 393 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU C 189 " pdb=" CB LEU C 189 " pdb=" CD1 LEU C 189 " pdb=" CD2 LEU C 189 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA VAL A 136 " pdb=" N VAL A 136 " pdb=" C VAL A 136 " pdb=" CB VAL A 136 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 1997 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO C 164 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 413 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 414 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 164 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.028 5.00e-02 4.00e+02 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 342 2.47 - 3.08: 11983 3.08 - 3.69: 25480 3.69 - 4.29: 34407 4.29 - 4.90: 49923 Nonbonded interactions: 122135 Sorted by model distance: nonbonded pdb=" OE2 GLU B 375 " pdb="FE FE B 501 " model vdw 1.869 2.260 nonbonded pdb="FE FE D 501 " pdb=" O HOH D 601 " model vdw 1.873 2.260 nonbonded pdb="FE FE B 501 " pdb=" O HOH B 601 " model vdw 1.876 2.260 nonbonded pdb="FE FE A 501 " pdb=" O HOH A 601 " model vdw 1.891 2.260 nonbonded pdb=" NE2 HIS B 335 " pdb="FE FE B 501 " model vdw 1.908 2.340 ... (remaining 122130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.030 Extract box with map and model: 2.590 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.400 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.006 0.045 13740 Z= 0.377 Angle : 0.858 10.143 18624 Z= 0.514 Chirality : 0.044 0.203 2000 Planarity : 0.006 0.063 2456 Dihedral : 15.223 88.583 5108 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 47.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.33 % Favored : 83.43 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.19 % 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: -5.55 (0.15), residues: 1672 helix: -2.79 (0.14), residues: 764 sheet: -3.64 (0.35), residues: 152 loop : -4.72 (0.16), residues: 756 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 1.507 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 outliers start: 7 outliers final: 3 residues processed: 214 average time/residue: 0.3092 time to fit residues: 91.3034 Evaluate side-chains 161 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1186 time to fit residues: 2.8055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.0670 chunk 152 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN C 111 HIS ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN D 111 HIS ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 HIS ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 349 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 13740 Z= 0.214 Angle : 0.720 8.853 18624 Z= 0.370 Chirality : 0.043 0.177 2000 Planarity : 0.005 0.046 2456 Dihedral : 5.806 30.535 1868 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 30.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.62 % Favored : 87.20 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.00 % 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: -3.68 (0.18), residues: 1672 helix: -1.05 (0.16), residues: 796 sheet: -3.40 (0.36), residues: 144 loop : -3.92 (0.19), residues: 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 1.618 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 outliers start: 4 outliers final: 1 residues processed: 228 average time/residue: 0.3176 time to fit residues: 100.4967 Evaluate side-chains 151 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1306 time to fit residues: 2.2065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 50.0000 chunk 47 optimal weight: 9.9990 chunk 126 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 0.0980 chunk 136 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 chunk 122 optimal weight: 3.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 13740 Z= 0.238 Angle : 0.706 11.102 18624 Z= 0.363 Chirality : 0.043 0.184 2000 Planarity : 0.005 0.047 2456 Dihedral : 5.585 30.675 1868 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 32.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.98 % Favored : 86.84 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -3.12 (0.19), residues: 1672 helix: -0.51 (0.17), residues: 792 sheet: -3.41 (0.33), residues: 192 loop : -3.59 (0.21), residues: 688 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.480 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 outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2799 time to fit residues: 79.9083 Evaluate side-chains 143 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 43 optimal weight: 50.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** A 312 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** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 13740 Z= 0.281 Angle : 0.718 12.129 18624 Z= 0.372 Chirality : 0.043 0.217 2000 Planarity : 0.005 0.053 2456 Dihedral : 5.630 30.671 1868 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 35.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.86 % Favored : 87.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -2.71 (0.20), residues: 1672 helix: -0.27 (0.18), residues: 772 sheet: -3.13 (0.39), residues: 144 loop : -3.25 (0.21), residues: 756 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.590 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 outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2938 time to fit residues: 85.4930 Evaluate side-chains 144 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 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** B 111 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 HIS ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13740 Z= 0.216 Angle : 0.692 10.471 18624 Z= 0.354 Chirality : 0.043 0.168 2000 Planarity : 0.005 0.046 2456 Dihedral : 5.437 29.197 1868 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 31.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.84 % Favored : 88.04 % Rotamer Outliers : 0.14 % 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: -2.48 (0.20), residues: 1672 helix: -0.12 (0.18), residues: 808 sheet: -4.06 (0.41), residues: 104 loop : -3.07 (0.22), residues: 760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.695 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 outliers start: 2 outliers final: 1 residues processed: 209 average time/residue: 0.2774 time to fit residues: 84.0214 Evaluate side-chains 145 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1686 time to fit residues: 2.4710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 0.0370 overall best weight: 4.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 13740 Z= 0.241 Angle : 0.712 11.140 18624 Z= 0.366 Chirality : 0.043 0.183 2000 Planarity : 0.005 0.047 2456 Dihedral : 5.505 29.440 1868 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 32.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.02 % Favored : 87.92 % Rotamer Outliers : 0.00 % 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: -2.41 (0.20), residues: 1672 helix: -0.08 (0.18), residues: 800 sheet: -3.15 (0.36), residues: 184 loop : -3.01 (0.23), residues: 688 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.552 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 outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2666 time to fit residues: 79.2111 Evaluate side-chains 141 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 30.0000 chunk 161 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 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** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 13740 Z= 0.246 Angle : 0.722 15.580 18624 Z= 0.368 Chirality : 0.043 0.179 2000 Planarity : 0.005 0.050 2456 Dihedral : 5.483 28.956 1868 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 32.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.08 % Favored : 87.86 % Rotamer Outliers : 0.00 % 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: -2.29 (0.21), residues: 1672 helix: -0.06 (0.18), residues: 808 sheet: -3.14 (0.36), residues: 184 loop : -2.86 (0.24), residues: 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.869 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 outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2762 time to fit residues: 82.4995 Evaluate side-chains 142 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 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** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 13740 Z= 0.270 Angle : 0.735 13.826 18624 Z= 0.378 Chirality : 0.043 0.174 2000 Planarity : 0.005 0.061 2456 Dihedral : 5.525 29.184 1868 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 35.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer Outliers : 0.00 % 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: -2.32 (0.21), residues: 1672 helix: -0.17 (0.18), residues: 804 sheet: -3.19 (0.36), residues: 184 loop : -2.72 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.606 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 outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2685 time to fit residues: 76.7055 Evaluate side-chains 142 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 159 optimal weight: 0.0370 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13740 Z= 0.195 Angle : 0.723 12.032 18624 Z= 0.365 Chirality : 0.044 0.173 2000 Planarity : 0.005 0.045 2456 Dihedral : 5.316 26.977 1868 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer Outliers : 0.00 % 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: -2.08 (0.21), residues: 1672 helix: 0.09 (0.18), residues: 804 sheet: -3.13 (0.39), residues: 144 loop : -2.77 (0.23), residues: 724 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.705 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 outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2657 time to fit residues: 79.2568 Evaluate side-chains 146 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.0060 chunk 110 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13740 Z= 0.228 Angle : 0.725 13.067 18624 Z= 0.369 Chirality : 0.043 0.215 2000 Planarity : 0.005 0.052 2456 Dihedral : 5.338 28.153 1868 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 30.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer Outliers : 0.00 % 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: -2.00 (0.21), residues: 1672 helix: 0.15 (0.18), residues: 804 sheet: -3.23 (0.35), residues: 184 loop : -2.59 (0.24), residues: 684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.601 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 outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2573 time to fit residues: 72.1872 Evaluate side-chains 142 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.075618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.050057 restraints weight = 69850.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051717 restraints weight = 49254.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052941 restraints weight = 37375.047| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 13740 Z= 0.257 Angle : 0.736 11.770 18624 Z= 0.376 Chirality : 0.043 0.166 2000 Planarity : 0.005 0.052 2456 Dihedral : 5.395 28.027 1868 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 32.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer Outliers : 0.00 % 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: -2.12 (0.21), residues: 1672 helix: -0.01 (0.18), residues: 804 sheet: -3.31 (0.35), residues: 184 loop : -2.54 (0.25), residues: 684 =============================================================================== Job complete usr+sys time: 2429.60 seconds wall clock time: 45 minutes 54.11 seconds (2754.11 seconds total)