Starting phenix.real_space_refine on Sun Dec 10 05:00:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/12_2023/7ysr_34081_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/12_2023/7ysr_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_34081/12_2023/7ysr_34081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/12_2023/7ysr_34081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/12_2023/7ysr_34081_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/12_2023/7ysr_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-1.21rc1-5172/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: 7.28, per 1000 atoms: 0.54 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: 5.96 Conformation dependent library (CDL) restraints added in 2.7 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: 3.15 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: 4.17 Time building geometry restraints manager: 6.36 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: 9.470 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: 35.540 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 40.200 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.450 ------------------------------------------------------------------------------- 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 : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2750 time to fit residues: 52.8075 Evaluate side-chains 95 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1549 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.0654 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= 0.259 Angle : 0.543 7.389 18694 Z= 0.274 Chirality : 0.042 0.144 2042 Planarity : 0.004 0.064 2426 Dihedral : 8.557 179.115 1902 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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: 1.31 (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 0.017 0.001 TRP C 21 HIS 0.005 0.001 HIS C 8 PHE 0.013 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 : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.2737 time to fit residues: 50.4701 Evaluate side-chains 90 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0749 ------------------------------------------------------------------------------- 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: 7.9990 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.8298 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13764 Z= 0.273 Angle : 0.569 8.185 18694 Z= 0.287 Chirality : 0.043 0.162 2042 Planarity : 0.004 0.068 2426 Dihedral : 8.633 179.733 1902 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % 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 (0.21), residues: 1684 helix: 1.48 (0.19), residues: 732 sheet: 0.21 (0.31), residues: 272 loop : -0.42 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 21 HIS 0.007 0.001 HIS C 192 PHE 0.015 0.001 PHE C 138 TYR 0.027 0.002 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 122 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2170 time to fit residues: 39.5213 Evaluate side-chains 91 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9478 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 228 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 293 GLN ** 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 C 283 HIS D 331 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13764 Z= 0.437 Angle : 0.696 8.204 18694 Z= 0.357 Chirality : 0.046 0.165 2042 Planarity : 0.005 0.082 2426 Dihedral : 8.947 177.239 1902 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: 0.21 (0.20), residues: 1684 helix: 1.00 (0.19), residues: 728 sheet: -0.11 (0.32), residues: 256 loop : -0.58 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 21 HIS 0.009 0.002 HIS C 192 PHE 0.022 0.002 PHE B 214 TYR 0.019 0.002 TYR A 224 ARG 0.010 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 124 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.2995 time to fit residues: 53.8982 Evaluate side-chains 88 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1714 time to fit residues: 2.4843 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 256 GLN B 293 GLN ** 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 ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13764 Z= 0.339 Angle : 0.636 8.054 18694 Z= 0.325 Chirality : 0.045 0.163 2042 Planarity : 0.005 0.081 2426 Dihedral : 8.914 179.252 1902 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: 0.16 (0.20), residues: 1684 helix: 0.95 (0.19), residues: 738 sheet: -0.01 (0.32), residues: 246 loop : -0.68 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 21 HIS 0.008 0.001 HIS C 8 PHE 0.018 0.002 PHE C 138 TYR 0.020 0.002 TYR C 108 ARG 0.007 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 126 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2839 time to fit residues: 52.1687 Evaluate side-chains 88 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1453 ------------------------------------------------------------------------------- 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: 0.3980 chunk 146 optimal weight: 8.9990 chunk 32 optimal weight: 0.0270 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN D 433 GLN D 436 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13764 Z= 0.160 Angle : 0.563 7.453 18694 Z= 0.281 Chirality : 0.043 0.155 2042 Planarity : 0.004 0.075 2426 Dihedral : 8.632 177.937 1902 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 2.08 % Favored : 97.85 % 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: 0.50 (0.20), residues: 1684 helix: 1.25 (0.19), residues: 726 sheet: 0.06 (0.31), residues: 272 loop : -0.45 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 21 HIS 0.005 0.001 HIS C 8 PHE 0.019 0.001 PHE D 214 TYR 0.016 0.001 TYR C 224 ARG 0.006 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 135 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.3156 time to fit residues: 61.6743 Evaluate side-chains 88 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9120 ------------------------------------------------------------------------------- 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: 7.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 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 8 HIS B 293 GLN ** 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 ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13764 Z= 0.344 Angle : 0.629 7.917 18694 Z= 0.321 Chirality : 0.045 0.198 2042 Planarity : 0.005 0.076 2426 Dihedral : 8.752 179.332 1902 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 0.38 (0.20), residues: 1684 helix: 1.16 (0.19), residues: 728 sheet: -0.06 (0.31), residues: 272 loop : -0.50 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.008 0.001 HIS C 8 PHE 0.019 0.002 PHE C 138 TYR 0.031 0.002 TYR A 224 ARG 0.013 0.001 ARG D 284 *********************** 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 121 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2683 time to fit residues: 47.9268 Evaluate side-chains 87 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13764 Z= 0.157 Angle : 0.578 8.675 18694 Z= 0.289 Chirality : 0.043 0.173 2042 Planarity : 0.004 0.070 2426 Dihedral : 8.563 178.187 1902 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 0.57 (0.20), residues: 1684 helix: 1.26 (0.19), residues: 732 sheet: 0.23 (0.33), residues: 254 loop : -0.44 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 21 HIS 0.009 0.001 HIS A 88 PHE 0.010 0.001 PHE C 149 TYR 0.021 0.001 TYR A 224 ARG 0.012 0.001 ARG C 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 123 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2792 time to fit residues: 50.6901 Evaluate side-chains 89 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9841 ------------------------------------------------------------------------------- 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: 6.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 0.8240 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13764 Z= 0.150 Angle : 0.562 7.552 18694 Z= 0.280 Chirality : 0.043 0.210 2042 Planarity : 0.004 0.063 2426 Dihedral : 8.449 177.234 1902 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 0.64 (0.20), residues: 1684 helix: 1.32 (0.19), residues: 732 sheet: 0.32 (0.32), residues: 254 loop : -0.43 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS C 8 PHE 0.013 0.001 PHE C 138 TYR 0.020 0.001 TYR A 224 ARG 0.007 0.000 ARG C 123 *********************** 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 : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2840 time to fit residues: 54.2971 Evaluate side-chains 96 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2147 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN B 293 GLN B 331 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** 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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13764 Z= 0.149 Angle : 0.564 8.670 18694 Z= 0.278 Chirality : 0.043 0.212 2042 Planarity : 0.004 0.059 2426 Dihedral : 8.371 176.745 1902 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.74 (0.21), residues: 1684 helix: 1.35 (0.19), residues: 734 sheet: 0.46 (0.31), residues: 272 loop : -0.37 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 346 HIS 0.005 0.001 HIS B 406 PHE 0.008 0.001 PHE D 377 TYR 0.018 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 131 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2725 time to fit residues: 52.5885 Evaluate side-chains 97 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1593 ------------------------------------------------------------------------------- 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: 5.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** 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 336 GLN ** 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 = 0.3246 r_free = 0.3246 target = 0.053277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046222 restraints weight = 76055.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.047551 restraints weight = 45305.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.048509 restraints weight = 31099.927| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13764 Z= 0.152 Angle : 0.562 7.926 18694 Z= 0.278 Chirality : 0.043 0.213 2042 Planarity : 0.004 0.059 2426 Dihedral : 8.354 176.758 1902 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.82 (0.21), residues: 1684 helix: 1.41 (0.19), residues: 736 sheet: 0.52 (0.31), residues: 272 loop : -0.34 (0.24), residues: 676 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 0.018 0.001 TYR A 224 ARG 0.004 0.000 ARG A 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.76 seconds wall clock time: 51 minutes 38.77 seconds (3098.77 seconds total)