Starting phenix.real_space_refine on Sat Mar 16 02:29:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/03_2024/7ysr_34081_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/03_2024/7ysr_34081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/03_2024/7ysr_34081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/03_2024/7ysr_34081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/03_2024/7ysr_34081_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/03_2024/7ysr_34081_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 98 5.16 5 C 8462 2.51 5 N 2298 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13456 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3314 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "C" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3314 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.41, per 1000 atoms: 0.62 Number of scatterers: 13456 At special positions: 0 Unit cell: (112.32, 109.08, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 12 15.00 O 2586 8.00 N 2298 7.00 C 8462 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: 5.23 Conformation dependent library (CDL) restraints added in 2.6 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 12 sheets defined 46.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 82 through 85 removed outlier: 3.967A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 127 removed outlier: 5.842A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.421A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.698A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.743A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 4.026A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.668A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.664A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.850A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 111 through 128 removed outlier: 4.853A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.043A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 224 through 243 removed outlier: 4.467A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.928A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.821A pdb=" N LEU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 415 through 434 Processing helix chain 'C' and resid 10 through 27 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 111 through 127 removed outlier: 5.711A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.360A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.696A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.935A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 383 through 398 removed outlier: 3.547A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 3.793A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 removed outlier: 3.684A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 80 removed outlier: 3.577A pdb=" N ASP D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 111 through 128 removed outlier: 4.931A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 4.537A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 214 Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.504A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.881A pdb=" N LEU D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 415 through 434 Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.539A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 167 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N PHE A 202 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 53 through 56 removed outlier: 4.039A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= D, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.039A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.846A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 201 through 203 removed outlier: 7.195A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 65 through 68 removed outlier: 8.662A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C 134 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE C 7 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 136 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL C 9 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE C 138 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 167 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHE C 202 " --> pdb=" O ALA C 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.979A pdb=" N LYS C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.688A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 65 through 68 removed outlier: 8.012A pdb=" N VAL D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= L, first strand: chain 'D' and resid 201 through 203 removed outlier: 7.102A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1638 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: 4.03 Time building geometry restraints manager: 5.79 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: 4452 1.34 - 1.46: 3244 1.46 - 1.58: 5894 1.58 - 1.70: 22 1.70 - 1.82: 152 Bond restraints: 13764 Sorted by residual: bond pdb=" C ARG A 320 " pdb=" N GLY A 321 " ideal model delta sigma weight residual 1.334 1.322 0.012 1.12e-02 7.97e+03 1.20e+00 bond pdb=" CB LYS D 124 " pdb=" CG LYS D 124 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.64e-01 bond pdb=" C VAL D 62 " pdb=" O VAL D 62 " ideal model delta sigma weight residual 1.232 1.241 -0.008 8.90e-03 1.26e+04 8.62e-01 bond pdb=" CA ILE C 171 " pdb=" CB ILE C 171 " ideal model delta sigma weight residual 1.527 1.538 -0.012 1.31e-02 5.83e+03 7.94e-01 bond pdb=" C SER B 324 " pdb=" N MET B 325 " ideal model delta sigma weight residual 1.333 1.320 0.013 1.56e-02 4.11e+03 7.24e-01 ... (remaining 13759 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.90: 351 105.90 - 112.94: 7263 112.94 - 119.98: 4900 119.98 - 127.03: 6020 127.03 - 134.07: 160 Bond angle restraints: 18694 Sorted by residual: angle pdb=" CA MET B 325 " pdb=" C MET B 325 " pdb=" N LYS B 326 " ideal model delta sigma weight residual 118.59 123.67 -5.08 1.63e+00 3.76e-01 9.72e+00 angle pdb=" C ARG C 214 " pdb=" N ARG C 215 " pdb=" CA ARG C 215 " ideal model delta sigma weight residual 122.60 117.90 4.70 1.56e+00 4.11e-01 9.06e+00 angle pdb=" CA MET A 317 " pdb=" CB MET A 317 " pdb=" CG MET A 317 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.92e+00 angle pdb=" CB MET A 317 " pdb=" CG MET A 317 " pdb=" SD MET A 317 " ideal model delta sigma weight residual 112.70 120.75 -8.05 3.00e+00 1.11e-01 7.21e+00 angle pdb=" CB MET D 332 " pdb=" CG MET D 332 " pdb=" SD MET D 332 " ideal model delta sigma weight residual 112.70 120.58 -7.88 3.00e+00 1.11e-01 6.90e+00 ... (remaining 18689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 8019 35.37 - 70.74: 142 70.74 - 106.12: 11 106.12 - 141.49: 3 141.49 - 176.86: 1 Dihedral angle restraints: 8176 sinusoidal: 3280 harmonic: 4896 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -113.87 -176.86 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -157.88 -132.85 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -11.36 115.95 1 2.00e+01 2.50e-03 3.45e+01 ... (remaining 8173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1346 0.036 - 0.072: 474 0.072 - 0.109: 175 0.109 - 0.145: 43 0.145 - 0.181: 4 Chirality restraints: 2042 Sorted by residual: chirality pdb=" CB ILE D 318 " pdb=" CA ILE D 318 " pdb=" CG1 ILE D 318 " pdb=" CG2 ILE D 318 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB THR D 221 " pdb=" CA THR D 221 " pdb=" OG1 THR D 221 " pdb=" CG2 THR D 221 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB THR B 221 " pdb=" CA THR B 221 " pdb=" OG1 THR B 221 " pdb=" CG2 THR B 221 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 2039 not shown) Planarity restraints: 2426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 389 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C LYS B 389 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS B 389 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 390 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 89 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 123 " 0.130 9.50e-02 1.11e+02 5.83e-02 2.14e+00 pdb=" NE ARG A 123 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 123 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 123 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 123 " 0.006 2.00e-02 2.50e+03 ... (remaining 2423 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 365 2.69 - 3.25: 14560 3.25 - 3.80: 23368 3.80 - 4.35: 29159 4.35 - 4.90: 47868 Nonbonded interactions: 115320 Sorted by model distance: nonbonded pdb=" OH TYR B 185 " pdb=" O MET B 398 " model vdw 2.142 2.440 nonbonded pdb=" OH TYR D 185 " pdb=" O MET D 398 " model vdw 2.158 2.440 nonbonded pdb=" OH TYR C 185 " pdb=" O MET C 398 " model vdw 2.161 2.440 nonbonded pdb=" OH TYR A 185 " pdb=" O MET A 398 " model vdw 2.166 2.440 nonbonded pdb=" NH1 ARG C 215 " pdb=" OD1 ASN C 216 " model vdw 2.173 2.520 ... (remaining 115315 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 34.020 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 40.490 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.003 0.028 13764 Z= 0.197 Angle : 0.590 8.053 18694 Z= 0.308 Chirality : 0.043 0.181 2042 Planarity : 0.004 0.058 2426 Dihedral : 14.906 176.861 5040 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.51 (0.21), residues: 1684 helix: 1.05 (0.19), residues: 746 sheet: 0.30 (0.32), residues: 280 loop : -0.36 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 21 HIS 0.005 0.001 HIS A 197 PHE 0.013 0.001 PHE B 377 TYR 0.021 0.001 TYR C 224 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.8338 (ptt) cc_final: 0.7980 (ptt) REVERT: D 124 LYS cc_start: 0.9584 (tmtt) cc_final: 0.9361 (tptp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2629 time to fit residues: 50.3737 Evaluate side-chains 95 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13764 Z= 0.258 Angle : 0.542 7.379 18694 Z= 0.274 Chirality : 0.042 0.144 2042 Planarity : 0.004 0.064 2426 Dihedral : 8.549 178.968 1902 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.14 % Allowed : 5.96 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.72 (0.21), residues: 1684 helix: 1.30 (0.19), residues: 756 sheet: 0.43 (0.33), residues: 264 loop : -0.39 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 21 HIS 0.005 0.001 HIS C 8 PHE 0.012 0.001 PHE C 149 TYR 0.012 0.001 TYR D 61 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8097 (mpp) cc_final: 0.7860 (mpp) REVERT: B 124 LYS cc_start: 0.9470 (tmtt) cc_final: 0.9229 (tptp) REVERT: D 75 MET cc_start: 0.7955 (mtp) cc_final: 0.7740 (mtp) REVERT: D 124 LYS cc_start: 0.9585 (tmtt) cc_final: 0.9332 (tptp) REVERT: D 235 MET cc_start: 0.8554 (mtm) cc_final: 0.8190 (mtm) REVERT: D 301 MET cc_start: 0.8550 (mmm) cc_final: 0.8175 (mmp) REVERT: D 302 MET cc_start: 0.8414 (mtm) cc_final: 0.8194 (mtm) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.2560 time to fit residues: 47.4913 Evaluate side-chains 91 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 193 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13764 Z= 0.237 Angle : 0.546 7.425 18694 Z= 0.275 Chirality : 0.043 0.169 2042 Planarity : 0.004 0.066 2426 Dihedral : 8.570 179.365 1902 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.80 (0.21), residues: 1684 helix: 1.50 (0.19), residues: 734 sheet: 0.30 (0.32), residues: 272 loop : -0.37 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.007 0.001 HIS C 192 PHE 0.015 0.001 PHE C 138 TYR 0.024 0.001 TYR A 224 ARG 0.005 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8086 (mpp) cc_final: 0.7747 (mpp) REVERT: A 377 MET cc_start: 0.8302 (ppp) cc_final: 0.7905 (ppp) REVERT: B 124 LYS cc_start: 0.9501 (tmtt) cc_final: 0.9242 (tptp) REVERT: B 325 MET cc_start: 0.8463 (ptt) cc_final: 0.8184 (ptt) REVERT: D 124 LYS cc_start: 0.9540 (tmtt) cc_final: 0.9303 (tptp) REVERT: D 235 MET cc_start: 0.8553 (mtm) cc_final: 0.8188 (mtm) REVERT: D 301 MET cc_start: 0.8445 (mmm) cc_final: 0.8013 (mmp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2298 time to fit residues: 42.3469 Evaluate side-chains 94 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13764 Z= 0.310 Angle : 0.592 7.647 18694 Z= 0.302 Chirality : 0.044 0.161 2042 Planarity : 0.004 0.071 2426 Dihedral : 8.683 179.460 1902 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.58 (0.20), residues: 1684 helix: 1.33 (0.19), residues: 728 sheet: 0.16 (0.31), residues: 272 loop : -0.47 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 21 HIS 0.008 0.001 HIS C 192 PHE 0.019 0.002 PHE B 214 TYR 0.013 0.002 TYR A 224 ARG 0.006 0.001 ARG D 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.8183 (ppp) cc_final: 0.7777 (ppp) REVERT: B 124 LYS cc_start: 0.9564 (tmtt) cc_final: 0.9253 (tptp) REVERT: B 156 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8777 (mmmm) REVERT: B 325 MET cc_start: 0.8589 (ptt) cc_final: 0.8118 (ptp) REVERT: C 302 MET cc_start: 0.8542 (mtm) cc_final: 0.8292 (mtm) REVERT: C 377 MET cc_start: 0.8446 (ppp) cc_final: 0.8127 (ppp) REVERT: D 124 LYS cc_start: 0.9541 (tmtt) cc_final: 0.9297 (tptp) REVERT: D 235 MET cc_start: 0.8542 (mtm) cc_final: 0.8178 (mtm) REVERT: D 295 MET cc_start: 0.8399 (tpt) cc_final: 0.8158 (tpp) REVERT: D 302 MET cc_start: 0.8468 (mtm) cc_final: 0.8142 (mtm) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2823 time to fit residues: 51.8672 Evaluate side-chains 93 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 247 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13764 Z= 0.306 Angle : 0.599 7.714 18694 Z= 0.304 Chirality : 0.044 0.166 2042 Planarity : 0.004 0.074 2426 Dihedral : 8.749 179.651 1902 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.14 % Allowed : 3.40 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.46 (0.20), residues: 1684 helix: 1.19 (0.19), residues: 740 sheet: 0.26 (0.32), residues: 258 loop : -0.57 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.007 0.001 HIS C 8 PHE 0.016 0.002 PHE C 138 TYR 0.018 0.002 TYR D 432 ARG 0.008 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8297 (t80) cc_final: 0.7696 (t80) REVERT: A 313 MET cc_start: 0.8108 (mpp) cc_final: 0.7810 (mpp) REVERT: B 124 LYS cc_start: 0.9477 (tmtt) cc_final: 0.9204 (tptp) REVERT: B 156 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8745 (mmmm) REVERT: C 377 MET cc_start: 0.8361 (ppp) cc_final: 0.7466 (ppp) REVERT: D 124 LYS cc_start: 0.9548 (tmtt) cc_final: 0.9303 (tptp) REVERT: D 235 MET cc_start: 0.8560 (mtm) cc_final: 0.8180 (mtm) REVERT: D 295 MET cc_start: 0.8405 (tpt) cc_final: 0.8042 (tpp) REVERT: D 301 MET cc_start: 0.8629 (mmm) cc_final: 0.8261 (mmp) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.2650 time to fit residues: 49.1633 Evaluate side-chains 94 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN B 293 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN C 128 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 436 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13764 Z= 0.198 Angle : 0.558 7.511 18694 Z= 0.282 Chirality : 0.043 0.159 2042 Planarity : 0.004 0.072 2426 Dihedral : 8.627 178.718 1902 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.07 % Allowed : 2.15 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.56 (0.20), residues: 1684 helix: 1.25 (0.19), residues: 742 sheet: 0.36 (0.32), residues: 258 loop : -0.52 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.006 0.001 HIS C 8 PHE 0.012 0.001 PHE B 388 TYR 0.010 0.001 TYR C 83 ARG 0.005 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8244 (t80) cc_final: 0.7654 (t80) REVERT: A 313 MET cc_start: 0.8119 (mpp) cc_final: 0.7757 (mpp) REVERT: A 377 MET cc_start: 0.8275 (ppp) cc_final: 0.7808 (ppp) REVERT: B 124 LYS cc_start: 0.9463 (tmtt) cc_final: 0.9185 (tptp) REVERT: B 156 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8748 (mmmm) REVERT: B 329 ASP cc_start: 0.9336 (m-30) cc_final: 0.9134 (m-30) REVERT: C 124 LYS cc_start: 0.8858 (pttm) cc_final: 0.8567 (pttp) REVERT: C 302 MET cc_start: 0.8502 (mtm) cc_final: 0.8203 (mtm) REVERT: C 377 MET cc_start: 0.8475 (ppp) cc_final: 0.7751 (ppp) REVERT: D 124 LYS cc_start: 0.9530 (tmtt) cc_final: 0.9288 (tptp) REVERT: D 182 VAL cc_start: 0.9384 (m) cc_final: 0.9102 (p) REVERT: D 301 MET cc_start: 0.8556 (mmm) cc_final: 0.8208 (mmp) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.2643 time to fit residues: 50.1658 Evaluate side-chains 95 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 334 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13764 Z= 0.232 Angle : 0.575 7.508 18694 Z= 0.290 Chirality : 0.043 0.171 2042 Planarity : 0.004 0.070 2426 Dihedral : 8.621 178.766 1902 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.52 (0.20), residues: 1684 helix: 1.20 (0.19), residues: 744 sheet: 0.34 (0.32), residues: 258 loop : -0.53 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.007 0.001 HIS C 8 PHE 0.016 0.001 PHE C 138 TYR 0.022 0.001 TYR D 432 ARG 0.005 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8215 (t80) cc_final: 0.7656 (t80) REVERT: A 313 MET cc_start: 0.8142 (mpp) cc_final: 0.7764 (mpp) REVERT: A 377 MET cc_start: 0.8296 (ppp) cc_final: 0.7891 (ppp) REVERT: B 124 LYS cc_start: 0.9460 (tmtt) cc_final: 0.9193 (tptp) REVERT: B 156 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8784 (mmmm) REVERT: C 302 MET cc_start: 0.8414 (mtm) cc_final: 0.8177 (mtm) REVERT: C 377 MET cc_start: 0.8399 (ppp) cc_final: 0.7278 (ppp) REVERT: D 75 MET cc_start: 0.7730 (mtp) cc_final: 0.7459 (mtp) REVERT: D 124 LYS cc_start: 0.9526 (tmtt) cc_final: 0.9282 (tptp) REVERT: D 182 VAL cc_start: 0.9386 (m) cc_final: 0.9105 (p) REVERT: D 301 MET cc_start: 0.8540 (mmm) cc_final: 0.8125 (mmp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2779 time to fit residues: 52.5086 Evaluate side-chains 98 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 110 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 334 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 247 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13764 Z= 0.154 Angle : 0.557 7.256 18694 Z= 0.277 Chirality : 0.043 0.166 2042 Planarity : 0.004 0.067 2426 Dihedral : 8.482 177.223 1902 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.20), residues: 1684 helix: 1.38 (0.19), residues: 732 sheet: 0.29 (0.31), residues: 272 loop : -0.43 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 21 HIS 0.006 0.001 HIS A 88 PHE 0.011 0.001 PHE D 377 TYR 0.029 0.001 TYR A 224 ARG 0.005 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8172 (t80) cc_final: 0.7572 (t80) REVERT: A 313 MET cc_start: 0.8067 (mpp) cc_final: 0.7859 (mpp) REVERT: A 377 MET cc_start: 0.8291 (ppp) cc_final: 0.7819 (ppp) REVERT: B 124 LYS cc_start: 0.9460 (tmtt) cc_final: 0.9213 (tptp) REVERT: B 156 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8764 (mmmm) REVERT: B 301 MET cc_start: 0.8340 (mmp) cc_final: 0.8080 (mmp) REVERT: C 302 MET cc_start: 0.8423 (mtm) cc_final: 0.8210 (mtm) REVERT: C 377 MET cc_start: 0.8615 (ppp) cc_final: 0.7745 (ppp) REVERT: D 75 MET cc_start: 0.7729 (mtp) cc_final: 0.7499 (mtp) REVERT: D 124 LYS cc_start: 0.9516 (tmtt) cc_final: 0.9290 (tptp) REVERT: D 182 VAL cc_start: 0.9328 (m) cc_final: 0.9047 (p) REVERT: D 301 MET cc_start: 0.8511 (mmm) cc_final: 0.8091 (mmp) REVERT: D 302 MET cc_start: 0.8515 (mtm) cc_final: 0.8205 (mtm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3029 time to fit residues: 58.2690 Evaluate side-chains 98 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13764 Z= 0.179 Angle : 0.555 7.210 18694 Z= 0.278 Chirality : 0.043 0.200 2042 Planarity : 0.004 0.064 2426 Dihedral : 8.456 177.342 1902 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.70 (0.20), residues: 1684 helix: 1.37 (0.19), residues: 734 sheet: 0.34 (0.32), residues: 272 loop : -0.42 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 21 HIS 0.006 0.001 HIS C 8 PHE 0.016 0.001 PHE C 138 TYR 0.025 0.001 TYR A 224 ARG 0.005 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8152 (t80) cc_final: 0.7553 (t80) REVERT: A 377 MET cc_start: 0.8294 (ppp) cc_final: 0.7749 (ppp) REVERT: B 124 LYS cc_start: 0.9464 (tmtt) cc_final: 0.9201 (tptp) REVERT: B 156 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8770 (mmmm) REVERT: B 301 MET cc_start: 0.8375 (mmp) cc_final: 0.8106 (mmp) REVERT: B 329 ASP cc_start: 0.9355 (m-30) cc_final: 0.9150 (m-30) REVERT: C 302 MET cc_start: 0.8395 (mtm) cc_final: 0.8129 (mtm) REVERT: C 377 MET cc_start: 0.8609 (ppp) cc_final: 0.7761 (ppp) REVERT: D 75 MET cc_start: 0.7729 (mtp) cc_final: 0.7491 (mtp) REVERT: D 124 LYS cc_start: 0.9520 (tmtt) cc_final: 0.9294 (tptp) REVERT: D 182 VAL cc_start: 0.9328 (m) cc_final: 0.9058 (p) REVERT: D 301 MET cc_start: 0.8537 (mmm) cc_final: 0.8133 (mmp) REVERT: D 302 MET cc_start: 0.8495 (mtm) cc_final: 0.8224 (mtm) REVERT: D 329 ASP cc_start: 0.9335 (m-30) cc_final: 0.9095 (m-30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2809 time to fit residues: 53.0125 Evaluate side-chains 100 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 154 optimal weight: 0.1980 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13764 Z= 0.175 Angle : 0.559 7.154 18694 Z= 0.278 Chirality : 0.043 0.188 2042 Planarity : 0.004 0.063 2426 Dihedral : 8.433 177.258 1902 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.73 (0.20), residues: 1684 helix: 1.41 (0.19), residues: 732 sheet: 0.50 (0.31), residues: 278 loop : -0.48 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 21 HIS 0.005 0.001 HIS C 8 PHE 0.010 0.001 PHE D 377 TYR 0.023 0.001 TYR A 224 ARG 0.005 0.000 ARG C 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8156 (t80) cc_final: 0.7555 (t80) REVERT: A 377 MET cc_start: 0.8332 (ppp) cc_final: 0.7755 (ppp) REVERT: B 124 LYS cc_start: 0.9467 (tmtt) cc_final: 0.9195 (tptp) REVERT: B 156 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8774 (mmmm) REVERT: B 301 MET cc_start: 0.8381 (mmp) cc_final: 0.8120 (mmp) REVERT: C 302 MET cc_start: 0.8363 (mtm) cc_final: 0.8095 (mtm) REVERT: C 377 MET cc_start: 0.8670 (ppp) cc_final: 0.7793 (ppp) REVERT: D 75 MET cc_start: 0.7721 (mtp) cc_final: 0.7495 (mtp) REVERT: D 124 LYS cc_start: 0.9515 (tmtt) cc_final: 0.9281 (tptp) REVERT: D 182 VAL cc_start: 0.9316 (m) cc_final: 0.9065 (p) REVERT: D 235 MET cc_start: 0.8502 (mtm) cc_final: 0.8156 (mtm) REVERT: D 301 MET cc_start: 0.8593 (mmm) cc_final: 0.8171 (mmp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2494 time to fit residues: 48.3150 Evaluate side-chains 99 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.052862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.045853 restraints weight = 75850.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.047179 restraints weight = 44889.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048096 restraints weight = 30803.377| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13764 Z= 0.158 Angle : 0.553 8.560 18694 Z= 0.274 Chirality : 0.043 0.184 2042 Planarity : 0.004 0.061 2426 Dihedral : 8.389 176.839 1902 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.77 (0.20), residues: 1684 helix: 1.45 (0.19), residues: 732 sheet: 0.47 (0.31), residues: 280 loop : -0.46 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.005 0.001 HIS C 8 PHE 0.014 0.001 PHE C 138 TYR 0.021 0.001 TYR A 224 ARG 0.005 0.000 ARG C 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.57 seconds wall clock time: 49 minutes 27.25 seconds (2967.25 seconds total)