Starting phenix.real_space_refine on Sun Feb 18 06:48:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/02_2024/7t20_25607_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/02_2024/7t20_25607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/02_2024/7t20_25607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/02_2024/7t20_25607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/02_2024/7t20_25607_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/02_2024/7t20_25607_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 22 5.49 5 Mg 4 5.21 5 S 78 5.16 5 C 13028 2.51 5 N 3752 2.21 5 O 4222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21106 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "B" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "D" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "E" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "F" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "M" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.51, per 1000 atoms: 0.50 Number of scatterers: 21106 At special positions: 0 Unit cell: (118.08, 139.2, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 22 15.00 Mg 4 11.99 O 4222 8.00 N 3752 7.00 C 13028 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: 8.38 Conformation dependent library (CDL) restraints added in 3.7 seconds 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 125 helices and 9 sheets defined 52.3% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 Processing helix chain 'A' and resid 46 through 54 removed outlier: 4.065A pdb=" N ASP A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 97 through 100 No H-bonds generated for 'chain 'A' and resid 97 through 100' Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 119 through 147 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 357 through 375 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 421 through 424 No H-bonds generated for 'chain 'A' and resid 421 through 424' Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 46 through 54 removed outlier: 4.180A pdb=" N ASP B 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 63 through 77 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 97 through 100 No H-bonds generated for 'chain 'B' and resid 97 through 100' Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 147 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 183 through 198 Processing helix chain 'B' and resid 214 through 217 No H-bonds generated for 'chain 'B' and resid 214 through 217' Processing helix chain 'B' and resid 237 through 251 Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 320 through 334 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 357 through 375 Processing helix chain 'B' and resid 388 through 391 No H-bonds generated for 'chain 'B' and resid 388 through 391' Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 421 through 424 No H-bonds generated for 'chain 'B' and resid 421 through 424' Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.954A pdb=" N ASP C 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 63 through 77 Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 119 through 147 Processing helix chain 'C' and resid 154 through 172 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 214 through 217 No H-bonds generated for 'chain 'C' and resid 214 through 217' Processing helix chain 'C' and resid 237 through 250 Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 291 through 307 Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 357 through 375 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 421 through 424 No H-bonds generated for 'chain 'C' and resid 421 through 424' Processing helix chain 'D' and resid 31 through 43 Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.105A pdb=" N ASP D 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 97 through 100 No H-bonds generated for 'chain 'D' and resid 97 through 100' Processing helix chain 'D' and resid 103 through 112 Processing helix chain 'D' and resid 119 through 147 Processing helix chain 'D' and resid 154 through 172 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 237 through 251 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 291 through 307 Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 357 through 375 Processing helix chain 'D' and resid 388 through 391 No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 407 through 411 Processing helix chain 'D' and resid 421 through 424 No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'E' and resid 31 through 43 Processing helix chain 'E' and resid 46 through 54 removed outlier: 4.042A pdb=" N ASP E 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 59 No H-bonds generated for 'chain 'E' and resid 57 through 59' Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 84 through 93 Processing helix chain 'E' and resid 97 through 100 No H-bonds generated for 'chain 'E' and resid 97 through 100' Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 119 through 147 Processing helix chain 'E' and resid 154 through 175 removed outlier: 3.712A pdb=" N ASN E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 214 through 217 No H-bonds generated for 'chain 'E' and resid 214 through 217' Processing helix chain 'E' and resid 237 through 251 Processing helix chain 'E' and resid 265 through 277 Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 291 through 307 Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 357 through 375 Processing helix chain 'E' and resid 388 through 391 No H-bonds generated for 'chain 'E' and resid 388 through 391' Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 421 through 424 No H-bonds generated for 'chain 'E' and resid 421 through 424' Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 46 through 54 removed outlier: 4.048A pdb=" N ASP F 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 63 through 77 Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'F' and resid 97 through 100 No H-bonds generated for 'chain 'F' and resid 97 through 100' Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 119 through 147 Processing helix chain 'F' and resid 154 through 172 removed outlier: 3.822A pdb=" N ARG F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 214 through 217 No H-bonds generated for 'chain 'F' and resid 214 through 217' Processing helix chain 'F' and resid 237 through 250 Processing helix chain 'F' and resid 265 through 277 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 291 through 307 Processing helix chain 'F' and resid 320 through 334 Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 357 through 375 Processing helix chain 'F' and resid 388 through 391 No H-bonds generated for 'chain 'F' and resid 388 through 391' Processing helix chain 'F' and resid 407 through 411 Processing helix chain 'F' and resid 421 through 424 No H-bonds generated for 'chain 'F' and resid 421 through 424' Processing sheet with id= A, first strand: chain 'A' and resid 378 through 384 removed outlier: 5.935A pdb=" N ASP A 225 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA A 381 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 227 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N SER A 383 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 229 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU A 414 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA A 230 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N MET A 416 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 256 through 258 Processing sheet with id= C, first strand: chain 'B' and resid 459 through 462 removed outlier: 6.813A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 379 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL B 229 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA B 381 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 340 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 459 through 462 removed outlier: 6.334A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 418 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 379 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL C 229 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA C 381 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE C 340 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU C 382 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE C 342 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.499A pdb=" N VAL D 379 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL D 229 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA D 381 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ALA D 231 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER D 383 " --> pdb=" O ALA D 231 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 459 through 462 removed outlier: 6.581A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 226 through 230 removed outlier: 6.697A pdb=" N VAL E 379 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL E 229 " --> pdb=" O VAL E 379 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 381 " --> pdb=" O VAL E 229 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 459 through 462 removed outlier: 6.680A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 459 through 462 removed outlier: 6.720A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 379 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL F 229 " --> pdb=" O VAL F 379 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA F 381 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE F 340 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU F 382 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE F 342 " --> pdb=" O LEU F 382 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2964 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: 6.39 Time building geometry restraints manager: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6851 1.34 - 1.45: 2267 1.45 - 1.57: 12106 1.57 - 1.69: 40 1.69 - 1.81: 159 Bond restraints: 21423 Sorted by residual: bond pdb=" O3A ANP E1001 " pdb=" PB ANP E1001 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" O3A ANP C1001 " pdb=" PB ANP C1001 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" O3A ANP D1001 " pdb=" PB ANP D1001 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" O3A ANP F1001 " pdb=" PB ANP F1001 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" N3B ANP E1001 " pdb=" PG ANP E1001 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 21418 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.93: 666 106.93 - 113.69: 11999 113.69 - 120.45: 7206 120.45 - 127.21: 8980 127.21 - 133.96: 184 Bond angle restraints: 29035 Sorted by residual: angle pdb=" PB ANP E1001 " pdb=" N3B ANP E1001 " pdb=" PG ANP E1001 " ideal model delta sigma weight residual 126.95 107.47 19.48 3.00e+00 1.11e-01 4.22e+01 angle pdb=" PB ANP C1001 " pdb=" N3B ANP C1001 " pdb=" PG ANP C1001 " ideal model delta sigma weight residual 126.95 109.26 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" PB ANP D1001 " pdb=" N3B ANP D1001 " pdb=" PG ANP D1001 " ideal model delta sigma weight residual 126.95 111.63 15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" PB ANP F1001 " pdb=" N3B ANP F1001 " pdb=" PG ANP F1001 " ideal model delta sigma weight residual 126.95 111.98 14.97 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C SER D 234 " pdb=" CA SER D 234 " pdb=" CB SER D 234 " ideal model delta sigma weight residual 117.23 111.21 6.02 1.36e+00 5.41e-01 1.96e+01 ... (remaining 29030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 13005 31.79 - 63.58: 245 63.58 - 95.38: 42 95.38 - 127.17: 0 127.17 - 158.96: 1 Dihedral angle restraints: 13293 sinusoidal: 5589 harmonic: 7704 Sorted by residual: dihedral pdb=" CA TYR E 344 " pdb=" C TYR E 344 " pdb=" N LEU E 345 " pdb=" CA LEU E 345 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" O1A ANP C1001 " pdb=" O3A ANP C1001 " pdb=" PA ANP C1001 " pdb=" PB ANP C1001 " ideal model delta sinusoidal sigma weight residual 83.11 -75.85 158.96 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA TYR B 344 " pdb=" C TYR B 344 " pdb=" N LEU B 345 " pdb=" CA LEU B 345 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 13290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2788 0.055 - 0.110: 468 0.110 - 0.165: 30 0.165 - 0.220: 0 0.220 - 0.275: 4 Chirality restraints: 3290 Sorted by residual: chirality pdb=" C3' ANP E1001 " pdb=" C2' ANP E1001 " pdb=" C4' ANP E1001 " pdb=" O3' ANP E1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP C1001 " pdb=" C2' ANP C1001 " pdb=" C4' ANP C1001 " pdb=" O3' ANP C1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP F1001 " pdb=" C2' ANP F1001 " pdb=" C4' ANP F1001 " pdb=" O3' ANP F1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3287 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 232 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO D 233 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 233 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 233 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 63 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 63 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO E 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " -0.021 5.00e-02 4.00e+02 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 389 2.64 - 3.21: 19355 3.21 - 3.77: 36594 3.77 - 4.34: 48913 4.34 - 4.90: 77411 Nonbonded interactions: 182662 Sorted by model distance: nonbonded pdb=" OG1 THR D 238 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb=" OG1 THR E 238 " pdb="MG MG E1002 " model vdw 2.079 2.170 nonbonded pdb=" O2G ANP C1001 " pdb="MG MG C1002 " model vdw 2.079 2.170 nonbonded pdb=" O2B ANP D1001 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb=" O2G ANP E1001 " pdb="MG MG E1002 " model vdw 2.079 2.170 ... (remaining 182657 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' and resid 25 through 464) selection = (chain 'C' and resid 25 through 464) selection = (chain 'D' and resid 25 through 464) selection = (chain 'E' and resid 25 through 464) selection = (chain 'F' and resid 25 through 464) } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.090 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 54.250 Find NCS groups from input model: 1.530 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.148 21423 Z= 0.250 Angle : 0.635 19.484 29035 Z= 0.350 Chirality : 0.039 0.275 3290 Planarity : 0.004 0.052 3812 Dihedral : 12.589 158.959 8301 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.27 % Favored : 97.58 % Rotamer: Outliers : 3.24 % Allowed : 4.88 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.16), residues: 2649 helix: 1.78 (0.13), residues: 1473 sheet: -2.17 (0.25), residues: 314 loop : -0.79 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 457 HIS 0.002 0.001 HIS D 334 PHE 0.010 0.001 PHE D 166 TYR 0.023 0.001 TYR F 344 ARG 0.002 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 403 time to evaluate : 2.668 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ILE cc_start: 0.9283 (mm) cc_final: 0.9003 (pt) REVERT: A 339 LEU cc_start: 0.8704 (tp) cc_final: 0.8473 (mp) REVERT: A 347 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8305 (mm) REVERT: B 50 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.9159 (p0) REVERT: B 235 MET cc_start: 0.4420 (mmt) cc_final: 0.3816 (mmm) REVERT: B 268 ILE cc_start: 0.9261 (mm) cc_final: 0.9029 (pt) REVERT: B 345 LEU cc_start: 0.9479 (mt) cc_final: 0.9258 (mt) REVERT: C 212 ASP cc_start: 0.9566 (OUTLIER) cc_final: 0.9215 (p0) REVERT: C 371 LEU cc_start: 0.9607 (tp) cc_final: 0.9306 (tp) REVERT: D 235 MET cc_start: 0.7917 (mmt) cc_final: 0.7340 (mmm) REVERT: D 240 PHE cc_start: 0.9386 (t80) cc_final: 0.9102 (t80) REVERT: D 263 MET cc_start: 0.8874 (mtp) cc_final: 0.8663 (mtt) REVERT: D 382 LEU cc_start: 0.9143 (mt) cc_final: 0.8885 (mt) REVERT: D 411 ASP cc_start: 0.7797 (m-30) cc_final: 0.7343 (t0) REVERT: E 49 ASP cc_start: 0.9578 (OUTLIER) cc_final: 0.9367 (p0) REVERT: E 315 SER cc_start: 0.8694 (m) cc_final: 0.8336 (p) REVERT: E 390 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8703 (mp0) REVERT: F 105 TYR cc_start: 0.9314 (t80) cc_final: 0.9094 (t80) REVERT: F 159 ASP cc_start: 0.9401 (m-30) cc_final: 0.9016 (p0) REVERT: F 263 MET cc_start: 0.8659 (mtt) cc_final: 0.8141 (mtt) REVERT: F 382 LEU cc_start: 0.8597 (mt) cc_final: 0.7882 (mp) REVERT: F 389 LEU cc_start: 0.9198 (tt) cc_final: 0.8948 (tt) outliers start: 73 outliers final: 15 residues processed: 471 average time/residue: 0.3795 time to fit residues: 263.8380 Evaluate side-chains 265 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 10.0000 chunk 200 optimal weight: 0.0040 chunk 111 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 135 optimal weight: 0.0980 chunk 107 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 240 optimal weight: 10.0000 overall best weight: 3.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 425 HIS C 96 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS D 252 GLN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21423 Z= 0.194 Angle : 0.527 7.799 29035 Z= 0.274 Chirality : 0.039 0.176 3290 Planarity : 0.004 0.061 3812 Dihedral : 9.038 175.566 3150 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.53 % Favored : 97.32 % Rotamer: Outliers : 0.31 % Allowed : 2.13 % Favored : 97.56 % 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: 1.24 (0.17), residues: 2649 helix: 2.17 (0.13), residues: 1475 sheet: -1.88 (0.26), residues: 332 loop : -0.38 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 457 HIS 0.008 0.001 HIS D 65 PHE 0.021 0.002 PHE A 460 TYR 0.025 0.002 TYR F 344 ARG 0.011 0.001 ARG D 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 295 time to evaluate : 2.540 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8578 (tp) cc_final: 0.8246 (pp) REVERT: A 341 MET cc_start: 0.5842 (ttt) cc_final: 0.5480 (tpp) REVERT: B 172 ARG cc_start: 0.6919 (tpt170) cc_final: 0.6668 (tpt170) REVERT: B 235 MET cc_start: 0.4603 (mmt) cc_final: 0.4169 (mmm) REVERT: B 268 ILE cc_start: 0.9320 (mm) cc_final: 0.9100 (pt) REVERT: B 348 MET cc_start: 0.9185 (mmm) cc_final: 0.8769 (tpt) REVERT: C 126 VAL cc_start: 0.9601 (t) cc_final: 0.9371 (p) REVERT: C 371 LEU cc_start: 0.9633 (tp) cc_final: 0.9360 (tp) REVERT: D 105 TYR cc_start: 0.8620 (t80) cc_final: 0.8361 (t80) REVERT: D 235 MET cc_start: 0.7955 (mmt) cc_final: 0.7442 (mmm) REVERT: D 240 PHE cc_start: 0.9366 (t80) cc_final: 0.8978 (t80) REVERT: D 263 MET cc_start: 0.8946 (mtp) cc_final: 0.8628 (mtm) REVERT: D 291 ASP cc_start: 0.9313 (t0) cc_final: 0.8913 (p0) REVERT: D 411 ASP cc_start: 0.7961 (m-30) cc_final: 0.7227 (t0) REVERT: E 291 ASP cc_start: 0.9250 (t0) cc_final: 0.8872 (p0) REVERT: E 315 SER cc_start: 0.8868 (m) cc_final: 0.8619 (p) REVERT: F 105 TYR cc_start: 0.9318 (t80) cc_final: 0.9042 (t80) REVERT: F 235 MET cc_start: 0.7872 (tpt) cc_final: 0.6634 (mtp) REVERT: F 240 PHE cc_start: 0.9504 (t80) cc_final: 0.9288 (t80) REVERT: F 263 MET cc_start: 0.8643 (mtt) cc_final: 0.8227 (mtt) REVERT: F 347 LEU cc_start: 0.9632 (mt) cc_final: 0.9394 (mt) REVERT: F 389 LEU cc_start: 0.9255 (tt) cc_final: 0.9002 (tt) outliers start: 7 outliers final: 3 residues processed: 301 average time/residue: 0.3870 time to fit residues: 170.9519 Evaluate side-chains 213 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 163 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 260 optimal weight: 0.0060 chunk 214 optimal weight: 50.0000 chunk 239 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN B 112 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** F 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21423 Z= 0.228 Angle : 0.558 8.528 29035 Z= 0.294 Chirality : 0.039 0.182 3290 Planarity : 0.004 0.066 3812 Dihedral : 7.664 151.854 3150 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.02 % Favored : 96.87 % Rotamer: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % 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: 1.08 (0.17), residues: 2649 helix: 1.90 (0.13), residues: 1477 sheet: -1.73 (0.25), residues: 335 loop : -0.27 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 48 HIS 0.006 0.001 HIS E 67 PHE 0.021 0.002 PHE F 259 TYR 0.025 0.002 TYR A 344 ARG 0.013 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 2.607 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: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.4705 (mmt) cc_final: 0.4355 (mmm) REVERT: B 242 MET cc_start: 0.8052 (ptt) cc_final: 0.7756 (ppp) REVERT: B 270 MET cc_start: 0.8782 (mmt) cc_final: 0.8512 (mmt) REVERT: B 348 MET cc_start: 0.9499 (mmm) cc_final: 0.9284 (tpt) REVERT: C 155 GLU cc_start: 0.9393 (mp0) cc_final: 0.9190 (mp0) REVERT: C 172 ARG cc_start: 0.8837 (tmt170) cc_final: 0.8389 (ttt180) REVERT: C 240 PHE cc_start: 0.9480 (t80) cc_final: 0.9223 (t80) REVERT: C 257 LEU cc_start: 0.9528 (tt) cc_final: 0.9310 (tt) REVERT: C 371 LEU cc_start: 0.9607 (tp) cc_final: 0.9294 (tp) REVERT: C 415 ILE cc_start: 0.9795 (mt) cc_final: 0.9395 (mp) REVERT: D 105 TYR cc_start: 0.8727 (t80) cc_final: 0.8288 (t80) REVERT: D 235 MET cc_start: 0.8148 (mmt) cc_final: 0.7564 (mmm) REVERT: D 240 PHE cc_start: 0.9309 (t80) cc_final: 0.8926 (t80) REVERT: D 263 MET cc_start: 0.8892 (mtp) cc_final: 0.8590 (mtm) REVERT: D 373 LYS cc_start: 0.9361 (mttt) cc_final: 0.9116 (ptpt) REVERT: E 142 ILE cc_start: 0.9282 (mm) cc_final: 0.8905 (mm) REVERT: E 315 SER cc_start: 0.9018 (m) cc_final: 0.8685 (p) REVERT: F 42 MET cc_start: 0.7992 (ttp) cc_final: 0.7643 (ptm) REVERT: F 105 TYR cc_start: 0.9379 (t80) cc_final: 0.8954 (t80) REVERT: F 235 MET cc_start: 0.8000 (tpt) cc_final: 0.6852 (mtp) REVERT: F 242 MET cc_start: 0.9272 (ptm) cc_final: 0.8780 (ppp) REVERT: F 263 MET cc_start: 0.8500 (mtt) cc_final: 0.7678 (mmm) REVERT: F 270 MET cc_start: 0.9608 (ttt) cc_final: 0.8501 (tmm) REVERT: F 418 ILE cc_start: 0.8921 (mp) cc_final: 0.8635 (mp) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.3918 time to fit residues: 156.1356 Evaluate side-chains 198 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 30.0000 chunk 181 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 256 optimal weight: 50.0000 chunk 126 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN B 443 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21423 Z= 0.228 Angle : 0.548 8.290 29035 Z= 0.290 Chirality : 0.039 0.185 3290 Planarity : 0.004 0.044 3812 Dihedral : 7.245 144.721 3150 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 1.16 (0.17), residues: 2649 helix: 1.96 (0.13), residues: 1467 sheet: -1.35 (0.26), residues: 335 loop : -0.36 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 48 HIS 0.004 0.001 HIS A 67 PHE 0.019 0.002 PHE E 60 TYR 0.017 0.002 TYR E 311 ARG 0.019 0.001 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.697 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: B 172 ARG cc_start: 0.7594 (tpt170) cc_final: 0.7228 (tpt170) REVERT: B 235 MET cc_start: 0.4532 (mmt) cc_final: 0.4287 (mmm) REVERT: B 242 MET cc_start: 0.8270 (ptt) cc_final: 0.7809 (ppp) REVERT: B 268 ILE cc_start: 0.9334 (mm) cc_final: 0.9049 (pt) REVERT: B 270 MET cc_start: 0.8858 (mmt) cc_final: 0.8623 (mmt) REVERT: B 348 MET cc_start: 0.9540 (mmm) cc_final: 0.9230 (tpt) REVERT: C 172 ARG cc_start: 0.8909 (tmt170) cc_final: 0.8454 (ttt180) REVERT: C 257 LEU cc_start: 0.9564 (tt) cc_final: 0.9287 (tt) REVERT: C 371 LEU cc_start: 0.9606 (tp) cc_final: 0.9312 (tp) REVERT: C 415 ILE cc_start: 0.9467 (mt) cc_final: 0.9133 (mp) REVERT: D 105 TYR cc_start: 0.8738 (t80) cc_final: 0.8361 (t80) REVERT: D 235 MET cc_start: 0.8277 (mmt) cc_final: 0.7571 (mmm) REVERT: D 240 PHE cc_start: 0.9312 (t80) cc_final: 0.8885 (t80) REVERT: D 263 MET cc_start: 0.8929 (mtp) cc_final: 0.8634 (mtm) REVERT: D 323 VAL cc_start: 0.9416 (t) cc_final: 0.9130 (p) REVERT: D 348 MET cc_start: 0.9262 (tpt) cc_final: 0.8939 (tpp) REVERT: D 373 LYS cc_start: 0.9378 (mttt) cc_final: 0.8990 (ptpp) REVERT: E 271 ARG cc_start: 0.8350 (mtt180) cc_final: 0.7773 (ptp-110) REVERT: E 315 SER cc_start: 0.9052 (m) cc_final: 0.8722 (p) REVERT: F 42 MET cc_start: 0.8118 (ttp) cc_final: 0.7469 (ptm) REVERT: F 105 TYR cc_start: 0.9381 (t80) cc_final: 0.9017 (t80) REVERT: F 235 MET cc_start: 0.7932 (tpp) cc_final: 0.7515 (mtp) REVERT: F 263 MET cc_start: 0.8418 (mtt) cc_final: 0.7784 (mmm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3738 time to fit residues: 140.9474 Evaluate side-chains 182 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 177 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 229 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN ** F 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21423 Z= 0.144 Angle : 0.494 8.139 29035 Z= 0.254 Chirality : 0.039 0.169 3290 Planarity : 0.003 0.077 3812 Dihedral : 6.795 142.125 3150 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 0.18 % Allowed : 1.15 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2649 helix: 2.14 (0.14), residues: 1467 sheet: -1.05 (0.27), residues: 332 loop : -0.32 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 457 HIS 0.002 0.001 HIS B 67 PHE 0.022 0.001 PHE E 166 TYR 0.016 0.001 TYR E 344 ARG 0.011 0.000 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 2.715 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: A 60 PHE cc_start: 0.7888 (m-80) cc_final: 0.7485 (m-80) REVERT: A 339 LEU cc_start: 0.8372 (mt) cc_final: 0.8088 (pp) REVERT: A 416 MET cc_start: 0.9207 (mmm) cc_final: 0.8635 (mmm) REVERT: B 235 MET cc_start: 0.4164 (mmt) cc_final: 0.3888 (mmm) REVERT: B 268 ILE cc_start: 0.9297 (mm) cc_final: 0.9057 (pt) REVERT: C 126 VAL cc_start: 0.9624 (t) cc_final: 0.9365 (p) REVERT: C 155 GLU cc_start: 0.9292 (mp0) cc_final: 0.9064 (mp0) REVERT: C 172 ARG cc_start: 0.8801 (tmt170) cc_final: 0.8325 (ttt180) REVERT: C 371 LEU cc_start: 0.9617 (tp) cc_final: 0.9415 (pp) REVERT: C 415 ILE cc_start: 0.9412 (mt) cc_final: 0.9123 (mp) REVERT: D 105 TYR cc_start: 0.8645 (t80) cc_final: 0.8315 (t80) REVERT: D 226 LEU cc_start: 0.9418 (tp) cc_final: 0.9092 (mp) REVERT: D 235 MET cc_start: 0.8198 (mmt) cc_final: 0.7515 (mmm) REVERT: D 240 PHE cc_start: 0.9260 (t80) cc_final: 0.8867 (t80) REVERT: D 263 MET cc_start: 0.8961 (mtp) cc_final: 0.8645 (mtm) REVERT: D 357 ARG cc_start: 0.9228 (tpt170) cc_final: 0.8989 (tpt170) REVERT: D 376 ASN cc_start: 0.9482 (t0) cc_final: 0.9204 (m-40) REVERT: D 416 MET cc_start: 0.8686 (mmm) cc_final: 0.8214 (mmm) REVERT: E 291 ASP cc_start: 0.9263 (t0) cc_final: 0.8767 (p0) REVERT: E 315 SER cc_start: 0.9017 (m) cc_final: 0.8726 (p) REVERT: E 414 LEU cc_start: 0.8549 (mt) cc_final: 0.8344 (mt) REVERT: F 42 MET cc_start: 0.8079 (ttp) cc_final: 0.7336 (ptm) REVERT: F 105 TYR cc_start: 0.9340 (t80) cc_final: 0.9004 (t80) REVERT: F 242 MET cc_start: 0.9391 (ptm) cc_final: 0.9039 (ppp) REVERT: F 263 MET cc_start: 0.8393 (mtt) cc_final: 0.7771 (mmm) REVERT: F 270 MET cc_start: 0.9508 (ttt) cc_final: 0.8303 (tmm) outliers start: 4 outliers final: 2 residues processed: 252 average time/residue: 0.3639 time to fit residues: 140.4259 Evaluate side-chains 194 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 30.0000 chunk 230 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 63 optimal weight: 7.9990 chunk 256 optimal weight: 40.0000 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 134 optimal weight: 0.2980 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** F 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21423 Z= 0.244 Angle : 0.583 8.896 29035 Z= 0.306 Chirality : 0.040 0.201 3290 Planarity : 0.004 0.054 3812 Dihedral : 6.820 133.849 3150 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2649 helix: 1.99 (0.14), residues: 1448 sheet: -0.83 (0.28), residues: 330 loop : -0.44 (0.23), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 457 HIS 0.005 0.001 HIS A 67 PHE 0.025 0.002 PHE F 259 TYR 0.020 0.002 TYR A 344 ARG 0.015 0.001 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8215 (m-80) cc_final: 0.7638 (m-80) REVERT: A 416 MET cc_start: 0.9215 (mmm) cc_final: 0.8714 (mmm) REVERT: B 235 MET cc_start: 0.4601 (mmt) cc_final: 0.4363 (mmm) REVERT: B 270 MET cc_start: 0.8802 (mmm) cc_final: 0.8541 (mmm) REVERT: B 348 MET cc_start: 0.9394 (tpt) cc_final: 0.8891 (tpt) REVERT: C 172 ARG cc_start: 0.8897 (tmt170) cc_final: 0.8621 (ttt180) REVERT: C 371 LEU cc_start: 0.9610 (tp) cc_final: 0.9317 (tp) REVERT: C 415 ILE cc_start: 0.9465 (mt) cc_final: 0.9174 (mp) REVERT: D 105 TYR cc_start: 0.8787 (t80) cc_final: 0.8491 (t80) REVERT: D 235 MET cc_start: 0.8323 (mmt) cc_final: 0.7551 (mmm) REVERT: D 240 PHE cc_start: 0.9323 (t80) cc_final: 0.8908 (t80) REVERT: D 263 MET cc_start: 0.8918 (mtp) cc_final: 0.8648 (mtm) REVERT: D 269 MET cc_start: 0.9258 (ttm) cc_final: 0.9042 (ttm) REVERT: D 416 MET cc_start: 0.8855 (mmm) cc_final: 0.8430 (mmm) REVERT: E 315 SER cc_start: 0.9039 (m) cc_final: 0.8820 (p) REVERT: E 339 LEU cc_start: 0.9361 (tp) cc_final: 0.9124 (tp) REVERT: E 416 MET cc_start: 0.8632 (mmm) cc_final: 0.8093 (mmm) REVERT: E 417 PHE cc_start: 0.8323 (m-80) cc_final: 0.7829 (m-80) REVERT: F 42 MET cc_start: 0.8223 (ttp) cc_final: 0.7485 (ptm) REVERT: F 105 TYR cc_start: 0.9394 (t80) cc_final: 0.9100 (t80) REVERT: F 235 MET cc_start: 0.7717 (tpt) cc_final: 0.7201 (mmm) REVERT: F 242 MET cc_start: 0.9472 (ptm) cc_final: 0.9113 (ppp) REVERT: F 263 MET cc_start: 0.8431 (mtt) cc_final: 0.7862 (mmm) REVERT: F 348 MET cc_start: 0.9489 (mpp) cc_final: 0.9281 (mpp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3348 time to fit residues: 120.8370 Evaluate side-chains 179 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 255 optimal weight: 30.0000 chunk 159 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21423 Z= 0.197 Angle : 0.531 10.288 29035 Z= 0.278 Chirality : 0.039 0.149 3290 Planarity : 0.004 0.048 3812 Dihedral : 6.785 131.669 3150 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: 1.29 (0.17), residues: 2649 helix: 2.00 (0.14), residues: 1441 sheet: -0.71 (0.28), residues: 335 loop : -0.37 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 457 HIS 0.003 0.001 HIS E 29 PHE 0.016 0.002 PHE F 259 TYR 0.013 0.001 TYR E 311 ARG 0.008 0.001 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.496 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: A 60 PHE cc_start: 0.8064 (m-80) cc_final: 0.7481 (m-80) REVERT: A 416 MET cc_start: 0.9152 (mmm) cc_final: 0.8753 (mmm) REVERT: B 235 MET cc_start: 0.4397 (mmt) cc_final: 0.4167 (mmm) REVERT: B 270 MET cc_start: 0.8770 (mmm) cc_final: 0.8555 (mmm) REVERT: B 348 MET cc_start: 0.9322 (tpt) cc_final: 0.9015 (tpt) REVERT: C 172 ARG cc_start: 0.8901 (tmt170) cc_final: 0.8630 (ttt180) REVERT: C 371 LEU cc_start: 0.9596 (tp) cc_final: 0.9358 (tp) REVERT: C 415 ILE cc_start: 0.9491 (mt) cc_final: 0.9242 (mp) REVERT: D 105 TYR cc_start: 0.8789 (t80) cc_final: 0.8507 (t80) REVERT: D 235 MET cc_start: 0.8334 (mmt) cc_final: 0.7573 (mmm) REVERT: D 240 PHE cc_start: 0.9298 (t80) cc_final: 0.8866 (t80) REVERT: D 263 MET cc_start: 0.8911 (mtp) cc_final: 0.8711 (ttm) REVERT: D 268 ILE cc_start: 0.9726 (mm) cc_final: 0.9133 (mm) REVERT: D 323 VAL cc_start: 0.9416 (t) cc_final: 0.8988 (p) REVERT: D 348 MET cc_start: 0.9233 (tpt) cc_final: 0.8991 (tpt) REVERT: D 376 ASN cc_start: 0.9485 (t0) cc_final: 0.9269 (m110) REVERT: D 416 MET cc_start: 0.8856 (mmm) cc_final: 0.8486 (mmm) REVERT: E 242 MET cc_start: 0.8763 (ppp) cc_final: 0.8167 (ppp) REVERT: E 315 SER cc_start: 0.9079 (m) cc_final: 0.8840 (p) REVERT: E 416 MET cc_start: 0.8509 (mmm) cc_final: 0.7952 (mmm) REVERT: E 417 PHE cc_start: 0.8305 (m-80) cc_final: 0.7981 (m-80) REVERT: F 42 MET cc_start: 0.8356 (ttp) cc_final: 0.8007 (tmm) REVERT: F 105 TYR cc_start: 0.9374 (t80) cc_final: 0.9128 (t80) REVERT: F 242 MET cc_start: 0.9418 (ptm) cc_final: 0.9061 (ppp) REVERT: F 263 MET cc_start: 0.8386 (mtt) cc_final: 0.7929 (mmm) REVERT: F 348 MET cc_start: 0.9510 (mpp) cc_final: 0.9155 (mpp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3526 time to fit residues: 130.1880 Evaluate side-chains 180 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 174 optimal weight: 30.0000 chunk 126 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 462 ASN ** 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: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21423 Z= 0.148 Angle : 0.511 9.873 29035 Z= 0.265 Chirality : 0.040 0.172 3290 Planarity : 0.004 0.123 3812 Dihedral : 6.698 132.122 3150 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.17), residues: 2649 helix: 2.06 (0.14), residues: 1449 sheet: -0.55 (0.29), residues: 333 loop : -0.31 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 457 HIS 0.002 0.001 HIS E 29 PHE 0.030 0.002 PHE E 166 TYR 0.012 0.001 TYR B 344 ARG 0.017 0.000 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.650 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: A 60 PHE cc_start: 0.7921 (m-80) cc_final: 0.7375 (m-80) REVERT: A 263 MET cc_start: 0.6809 (mpp) cc_final: 0.6324 (mpp) REVERT: A 416 MET cc_start: 0.9135 (mmm) cc_final: 0.8765 (mmm) REVERT: B 235 MET cc_start: 0.4243 (mmt) cc_final: 0.3709 (mmm) REVERT: B 270 MET cc_start: 0.8717 (mmm) cc_final: 0.8487 (mmm) REVERT: B 348 MET cc_start: 0.9238 (tpt) cc_final: 0.9012 (tpt) REVERT: C 126 VAL cc_start: 0.9685 (t) cc_final: 0.9450 (p) REVERT: C 172 ARG cc_start: 0.8869 (tmt170) cc_final: 0.8592 (ttt180) REVERT: C 371 LEU cc_start: 0.9581 (tp) cc_final: 0.9354 (pp) REVERT: D 235 MET cc_start: 0.8244 (mmt) cc_final: 0.7492 (mmm) REVERT: D 263 MET cc_start: 0.9269 (mtp) cc_final: 0.8939 (mpp) REVERT: D 348 MET cc_start: 0.9232 (tpt) cc_final: 0.8974 (tpt) REVERT: D 376 ASN cc_start: 0.9429 (t0) cc_final: 0.9189 (m-40) REVERT: D 416 MET cc_start: 0.8789 (mmm) cc_final: 0.8379 (mmm) REVERT: E 315 SER cc_start: 0.8969 (m) cc_final: 0.8750 (p) REVERT: E 416 MET cc_start: 0.8470 (mmm) cc_final: 0.8049 (mmm) REVERT: E 417 PHE cc_start: 0.8181 (m-80) cc_final: 0.7845 (m-80) REVERT: F 42 MET cc_start: 0.8355 (ttp) cc_final: 0.7993 (tmm) REVERT: F 105 TYR cc_start: 0.9349 (t80) cc_final: 0.9099 (t80) REVERT: F 242 MET cc_start: 0.9412 (ptm) cc_final: 0.9032 (ppp) REVERT: F 263 MET cc_start: 0.8405 (mtt) cc_final: 0.7968 (mmm) REVERT: F 348 MET cc_start: 0.9517 (mpp) cc_final: 0.9292 (mpp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3586 time to fit residues: 130.1103 Evaluate side-chains 177 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 223 optimal weight: 0.0970 chunk 238 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21423 Z= 0.155 Angle : 0.512 10.743 29035 Z= 0.266 Chirality : 0.039 0.164 3290 Planarity : 0.003 0.072 3812 Dihedral : 6.645 131.380 3150 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 1.45 (0.17), residues: 2649 helix: 2.05 (0.14), residues: 1448 sheet: -0.38 (0.30), residues: 328 loop : -0.30 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 457 HIS 0.002 0.001 HIS B 67 PHE 0.033 0.001 PHE C 259 TYR 0.012 0.001 TYR D 344 ARG 0.012 0.000 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.7944 (m-80) cc_final: 0.7447 (m-80) REVERT: A 416 MET cc_start: 0.9123 (mmm) cc_final: 0.8763 (mmm) REVERT: B 235 MET cc_start: 0.4239 (mmt) cc_final: 0.3919 (mmm) REVERT: B 270 MET cc_start: 0.8701 (mmm) cc_final: 0.8484 (mmm) REVERT: B 348 MET cc_start: 0.9207 (tpt) cc_final: 0.8957 (tpt) REVERT: C 126 VAL cc_start: 0.9684 (t) cc_final: 0.9450 (p) REVERT: C 172 ARG cc_start: 0.8889 (tmt170) cc_final: 0.8638 (ttt180) REVERT: C 371 LEU cc_start: 0.9580 (tp) cc_final: 0.9354 (tp) REVERT: C 416 MET cc_start: 0.8991 (mmp) cc_final: 0.8692 (tpp) REVERT: D 235 MET cc_start: 0.8250 (mmt) cc_final: 0.7515 (mmm) REVERT: D 240 PHE cc_start: 0.9196 (t80) cc_final: 0.8857 (t80) REVERT: D 263 MET cc_start: 0.9267 (mtp) cc_final: 0.8908 (mpp) REVERT: D 348 MET cc_start: 0.9257 (tpt) cc_final: 0.8967 (tpt) REVERT: D 357 ARG cc_start: 0.9378 (tpt170) cc_final: 0.9128 (tpt170) REVERT: D 376 ASN cc_start: 0.9444 (t0) cc_final: 0.9212 (m-40) REVERT: D 416 MET cc_start: 0.8759 (mmm) cc_final: 0.8462 (mmm) REVERT: E 142 ILE cc_start: 0.9284 (mm) cc_final: 0.8995 (mm) REVERT: E 301 MET cc_start: 0.9440 (ptp) cc_final: 0.9216 (ptp) REVERT: E 315 SER cc_start: 0.8914 (m) cc_final: 0.8684 (p) REVERT: E 416 MET cc_start: 0.8468 (mmm) cc_final: 0.8059 (mmm) REVERT: E 417 PHE cc_start: 0.8218 (m-80) cc_final: 0.7879 (m-80) REVERT: F 42 MET cc_start: 0.8379 (ttp) cc_final: 0.8001 (tmm) REVERT: F 105 TYR cc_start: 0.9348 (t80) cc_final: 0.9110 (t80) REVERT: F 235 MET cc_start: 0.7671 (tpt) cc_final: 0.6739 (mtp) REVERT: F 242 MET cc_start: 0.9390 (ptm) cc_final: 0.9020 (ppp) REVERT: F 263 MET cc_start: 0.8414 (mtt) cc_final: 0.8058 (mmm) REVERT: F 270 MET cc_start: 0.9313 (ttt) cc_final: 0.8625 (tpp) REVERT: F 348 MET cc_start: 0.9515 (mpp) cc_final: 0.9280 (mpp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3567 time to fit residues: 132.8302 Evaluate side-chains 177 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 264 optimal weight: 40.0000 chunk 242 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21423 Z= 0.213 Angle : 0.559 10.665 29035 Z= 0.294 Chirality : 0.039 0.157 3290 Planarity : 0.004 0.051 3812 Dihedral : 6.766 128.918 3150 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2649 helix: 1.90 (0.14), residues: 1453 sheet: -0.43 (0.30), residues: 339 loop : -0.32 (0.23), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 457 HIS 0.003 0.001 HIS E 29 PHE 0.021 0.002 PHE F 259 TYR 0.016 0.002 TYR E 311 ARG 0.011 0.001 ARG E 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.607 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 60 PHE cc_start: 0.8082 (m-80) cc_final: 0.7474 (m-80) REVERT: A 263 MET cc_start: 0.6803 (mpp) cc_final: 0.6307 (mpp) REVERT: A 416 MET cc_start: 0.9144 (mmm) cc_final: 0.8806 (mmm) REVERT: B 235 MET cc_start: 0.4380 (mmt) cc_final: 0.3846 (mmm) REVERT: B 348 MET cc_start: 0.9215 (tpt) cc_final: 0.8935 (tpt) REVERT: C 371 LEU cc_start: 0.9591 (tp) cc_final: 0.9322 (tp) REVERT: D 105 TYR cc_start: 0.8962 (t80) cc_final: 0.8743 (t80) REVERT: D 235 MET cc_start: 0.8298 (mmt) cc_final: 0.7576 (mmm) REVERT: D 240 PHE cc_start: 0.9262 (t80) cc_final: 0.8921 (t80) REVERT: D 263 MET cc_start: 0.9348 (mtp) cc_final: 0.8962 (mtm) REVERT: D 348 MET cc_start: 0.9301 (tpt) cc_final: 0.8950 (tpt) REVERT: D 357 ARG cc_start: 0.9358 (tpt170) cc_final: 0.9129 (tpt170) REVERT: D 376 ASN cc_start: 0.9490 (t0) cc_final: 0.9279 (m-40) REVERT: D 416 MET cc_start: 0.8900 (mmm) cc_final: 0.8479 (mmm) REVERT: E 301 MET cc_start: 0.9438 (ptp) cc_final: 0.9234 (ptp) REVERT: E 315 SER cc_start: 0.8983 (m) cc_final: 0.8743 (p) REVERT: E 339 LEU cc_start: 0.9281 (tp) cc_final: 0.9042 (tp) REVERT: E 414 LEU cc_start: 0.8677 (mt) cc_final: 0.8336 (mt) REVERT: F 42 MET cc_start: 0.8424 (ttp) cc_final: 0.8012 (tmm) REVERT: F 105 TYR cc_start: 0.9388 (t80) cc_final: 0.9134 (t80) REVERT: F 235 MET cc_start: 0.7854 (tpt) cc_final: 0.7399 (mmm) REVERT: F 242 MET cc_start: 0.9373 (ptm) cc_final: 0.9015 (ppp) REVERT: F 263 MET cc_start: 0.8464 (mtt) cc_final: 0.8115 (mmm) REVERT: F 348 MET cc_start: 0.9525 (mpp) cc_final: 0.9318 (mpp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3458 time to fit residues: 119.7560 Evaluate side-chains 170 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 88 optimal weight: 0.4980 chunk 216 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.059513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.046429 restraints weight = 245188.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.047416 restraints weight = 135798.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.047886 restraints weight = 89747.880| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21423 Z= 0.204 Angle : 0.556 15.059 29035 Z= 0.292 Chirality : 0.040 0.155 3290 Planarity : 0.004 0.056 3812 Dihedral : 6.850 128.899 3150 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 0.04 % Allowed : 0.27 % Favored : 99.69 % 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: 1.26 (0.17), residues: 2649 helix: 1.84 (0.14), residues: 1451 sheet: -0.42 (0.30), residues: 334 loop : -0.28 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 48 HIS 0.003 0.001 HIS E 67 PHE 0.024 0.002 PHE C 259 TYR 0.014 0.001 TYR E 311 ARG 0.014 0.001 ARG E 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3923.56 seconds wall clock time: 72 minutes 51.31 seconds (4371.31 seconds total)