Starting phenix.real_space_refine on Sun Dec 10 16:27:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/12_2023/8tah_41135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/12_2023/8tah_41135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/12_2023/8tah_41135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/12_2023/8tah_41135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/12_2023/8tah_41135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/12_2023/8tah_41135_updated.pdb" } resolution = 2.89 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 71 5.16 5 C 9529 2.51 5 N 2566 2.21 5 O 2804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14978 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3225 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2723 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2701 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2301 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "E" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1415 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "F" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1371 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain: "G" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1091 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "H" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.51, per 1000 atoms: 0.57 Number of scatterers: 14978 At special positions: 0 Unit cell: (100.8, 137.76, 140.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 6 15.00 Mg 2 11.99 O 2804 8.00 N 2566 7.00 C 9529 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: 5.74 Conformation dependent library (CDL) restraints added in 3.0 seconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3534 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 17 sheets defined 35.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.827A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 220 through 231 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.731A pdb=" N PHE A 276 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 277 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY A 278 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.627A pdb=" N PHE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 273 through 282' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.935A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.625A pdb=" N CYS A 408 " --> pdb=" O PRO A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.525A pdb=" N VAL B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.548A pdb=" N LEU B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 256 through 264 removed outlier: 3.681A pdb=" N PHE B 259 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 260 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA B 261 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Proline residue: B 262 - end of helix No H-bonds generated for 'chain 'B' and resid 256 through 264' Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 353 through 364 Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 384 through 387 No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'C' and resid 357 through 363 removed outlier: 3.656A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.966A pdb=" N HIS D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 116 through 133 removed outlier: 4.705A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 237 through 280 removed outlier: 4.432A pdb=" N THR D 246 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 54 removed outlier: 4.755A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 81 removed outlier: 3.571A pdb=" N LYS E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 99 Processing helix chain 'E' and resid 123 through 148 removed outlier: 3.905A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'F' and resid 6 through 19 Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 166 removed outlier: 4.388A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 51 through 58 Processing helix chain 'G' and resid 69 through 84 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 100 through 115 removed outlier: 4.385A pdb=" N GLU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 136 removed outlier: 4.277A pdb=" N GLN G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 Processing sheet with id= A, first strand: chain 'A' and resid 139 through 143 removed outlier: 6.582A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS A 8 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR A 113 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL A 10 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 60 through 62 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.356A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 254 through 259 Processing sheet with id= E, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.000A pdb=" N LYS B 19 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS B 106 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N CYS B 11 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 108 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B 13 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 110 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY B 135 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 109 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR B 137 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLU B 111 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 139 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 301 through 304 removed outlier: 6.373A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 242 through 245 Processing sheet with id= H, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.693A pdb=" N ALA C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 347 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.355A pdb=" N LYS C 36 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS C 44 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 87 through 91 removed outlier: 4.241A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 131 through 137 Processing sheet with id= L, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.805A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 243 removed outlier: 3.947A pdb=" N THR C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 209 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 249 through 254 removed outlier: 7.022A pdb=" N ALA C 263 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL C 252 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 261 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE C 254 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER C 259 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 284 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN C 273 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE C 282 " --> pdb=" O ASN C 273 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 32 through 36 Processing sheet with id= P, first strand: chain 'D' and resid 142 through 144 Processing sheet with id= Q, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.620A pdb=" N LYS F 60 " --> pdb=" O ALA F 75 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1626 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: 4.52 Time building geometry restraints manager: 6.22 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: 4776 1.34 - 1.46: 2876 1.46 - 1.58: 7540 1.58 - 1.69: 8 1.69 - 1.81: 110 Bond restraints: 15310 Sorted by residual: bond pdb=" N ALA D 284 " pdb=" CA ALA D 284 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.33e-02 5.65e+03 4.16e+00 bond pdb=" N VAL G 151 " pdb=" CA VAL G 151 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.61e+00 bond pdb=" C LEU B 313 " pdb=" N PRO B 314 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.97e+00 bond pdb=" C ARG F 6 " pdb=" N PRO F 7 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.40e+00 bond pdb=" N GLY E 175 " pdb=" CA GLY E 175 " ideal model delta sigma weight residual 1.451 1.476 -0.025 1.60e-02 3.91e+03 2.36e+00 ... (remaining 15305 not shown) Histogram of bond angle deviations from ideal: 98.77 - 106.99: 489 106.99 - 115.20: 9241 115.20 - 123.41: 10407 123.41 - 131.62: 565 131.62 - 139.84: 34 Bond angle restraints: 20736 Sorted by residual: angle pdb=" N VAL A 55 " pdb=" CA VAL A 55 " pdb=" C VAL A 55 " ideal model delta sigma weight residual 112.29 108.25 4.04 9.40e-01 1.13e+00 1.85e+01 angle pdb=" C VAL C 335 " pdb=" N ASP C 336 " pdb=" CA ASP C 336 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C SER C 236 " pdb=" N VAL C 237 " pdb=" CA VAL C 237 " ideal model delta sigma weight residual 121.97 127.82 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" CA LYS C 139 " pdb=" C LYS C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 118.44 123.47 -5.03 1.59e+00 3.96e-01 1.00e+01 angle pdb=" C ASN E 153 " pdb=" N ASP E 154 " pdb=" CA ASP E 154 " ideal model delta sigma weight residual 122.40 126.87 -4.47 1.45e+00 4.76e-01 9.50e+00 ... (remaining 20731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8532 17.89 - 35.78: 534 35.78 - 53.67: 139 53.67 - 71.56: 28 71.56 - 89.45: 6 Dihedral angle restraints: 9239 sinusoidal: 3765 harmonic: 5474 Sorted by residual: dihedral pdb=" CA ASN F 100 " pdb=" C ASN F 100 " pdb=" N PHE F 101 " pdb=" CA PHE F 101 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN E 152 " pdb=" C GLN E 152 " pdb=" N ASN E 153 " pdb=" CA ASN E 153 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASP C 336 " pdb=" C ASP C 336 " pdb=" N LYS C 337 " pdb=" CA LYS C 337 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1516 0.042 - 0.084: 523 0.084 - 0.127: 201 0.127 - 0.169: 37 0.169 - 0.211: 10 Chirality restraints: 2287 Sorted by residual: chirality pdb=" CB VAL A 311 " pdb=" CA VAL A 311 " pdb=" CG1 VAL A 311 " pdb=" CG2 VAL A 311 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 55 " pdb=" CA VAL A 55 " pdb=" CG1 VAL A 55 " pdb=" CG2 VAL A 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA LYS C 139 " pdb=" N LYS C 139 " pdb=" C LYS C 139 " pdb=" CB LYS C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 2284 not shown) Planarity restraints: 2666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 228 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO D 229 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 151 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO C 152 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 313 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A 314 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 314 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 314 " -0.035 5.00e-02 4.00e+02 ... (remaining 2663 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 113 2.61 - 3.19: 11447 3.19 - 3.76: 22454 3.76 - 4.33: 32418 4.33 - 4.90: 53786 Nonbonded interactions: 120218 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O2B ATP A 502 " model vdw 2.043 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP A 502 " model vdw 2.073 2.170 nonbonded pdb="MG MG B 501 " pdb=" O2G ATP B 502 " model vdw 2.282 2.170 nonbonded pdb=" O VAL G 142 " pdb=" OG1 THR G 146 " model vdw 2.326 2.440 nonbonded pdb=" O SER E 157 " pdb=" OG1 THR E 161 " model vdw 2.333 2.440 ... (remaining 120213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.220 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 43.170 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.005 0.054 15310 Z= 0.295 Angle : 0.656 7.888 20736 Z= 0.380 Chirality : 0.050 0.211 2287 Planarity : 0.007 0.083 2666 Dihedral : 13.050 89.449 5705 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.46 % Allowed : 8.62 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.17), residues: 1862 helix: -2.37 (0.14), residues: 692 sheet: 0.21 (0.27), residues: 365 loop : -1.27 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 221 HIS 0.006 0.001 HIS C 224 PHE 0.023 0.002 PHE C 111 TYR 0.016 0.001 TYR D 250 ARG 0.003 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 470 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 23 residues processed: 517 average time/residue: 1.5036 time to fit residues: 840.9804 Evaluate side-chains 464 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 441 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 4 average time/residue: 0.2020 time to fit residues: 3.8283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 255 GLN A 318 ASN B 76 ASN C 30 HIS D 254 HIS ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN F 125 GLN F 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15310 Z= 0.423 Angle : 0.560 7.724 20736 Z= 0.299 Chirality : 0.047 0.157 2287 Planarity : 0.005 0.064 2666 Dihedral : 6.704 81.480 2107 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 4.71 % Allowed : 14.57 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 1862 helix: -0.19 (0.19), residues: 683 sheet: 0.21 (0.27), residues: 366 loop : -0.97 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 378 HIS 0.007 0.001 HIS F 137 PHE 0.026 0.002 PHE F 101 TYR 0.024 0.002 TYR D 43 ARG 0.006 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 452 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 43 residues processed: 488 average time/residue: 1.5295 time to fit residues: 806.4984 Evaluate side-chains 489 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 446 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 23 residues processed: 21 average time/residue: 0.4793 time to fit residues: 15.0110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 219 GLN A 255 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN F 100 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15310 Z= 0.182 Angle : 0.466 6.043 20736 Z= 0.250 Chirality : 0.043 0.149 2287 Planarity : 0.004 0.053 2666 Dihedral : 6.066 71.921 2107 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 4.46 % Allowed : 17.11 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1862 helix: 0.68 (0.20), residues: 689 sheet: 0.26 (0.27), residues: 368 loop : -0.77 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.014 0.001 PHE C 111 TYR 0.014 0.001 TYR D 250 ARG 0.005 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 478 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 46 residues processed: 513 average time/residue: 1.5301 time to fit residues: 848.2615 Evaluate side-chains 489 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 443 time to evaluate : 1.513 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 24 residues processed: 22 average time/residue: 0.8733 time to fit residues: 24.2804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 0.0060 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN A 318 ASN B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15310 Z= 0.203 Angle : 0.473 6.918 20736 Z= 0.251 Chirality : 0.043 0.149 2287 Planarity : 0.004 0.048 2666 Dihedral : 5.827 69.939 2107 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 3.41 % Allowed : 18.78 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1862 helix: 1.19 (0.21), residues: 684 sheet: 0.23 (0.26), residues: 375 loop : -0.67 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 378 HIS 0.004 0.001 HIS F 137 PHE 0.017 0.001 PHE A 276 TYR 0.014 0.001 TYR D 43 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 453 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 41 residues processed: 484 average time/residue: 1.6099 time to fit residues: 839.8361 Evaluate side-chains 487 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 446 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 27 residues processed: 15 average time/residue: 0.7583 time to fit residues: 15.6708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN A 318 ASN B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 15310 Z= 0.514 Angle : 0.589 8.748 20736 Z= 0.312 Chirality : 0.049 0.166 2287 Planarity : 0.004 0.057 2666 Dihedral : 6.624 78.621 2107 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 4.65 % Allowed : 18.16 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 1862 helix: 1.10 (0.20), residues: 681 sheet: 0.19 (0.26), residues: 380 loop : -0.75 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 104 HIS 0.007 0.002 HIS C 54 PHE 0.027 0.002 PHE F 101 TYR 0.027 0.002 TYR D 43 ARG 0.009 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 444 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 53 residues processed: 484 average time/residue: 1.5857 time to fit residues: 828.2238 Evaluate side-chains 491 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 438 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 30 residues processed: 24 average time/residue: 0.7346 time to fit residues: 22.9314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN A 318 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN F 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15310 Z= 0.237 Angle : 0.502 7.534 20736 Z= 0.266 Chirality : 0.044 0.154 2287 Planarity : 0.004 0.052 2666 Dihedral : 6.213 74.900 2107 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 3.91 % Allowed : 20.09 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1862 helix: 1.32 (0.21), residues: 687 sheet: 0.20 (0.26), residues: 380 loop : -0.63 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.017 0.001 PHE F 101 TYR 0.016 0.001 TYR D 43 ARG 0.009 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 448 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 44 residues processed: 478 average time/residue: 1.5763 time to fit residues: 814.1019 Evaluate side-chains 475 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 431 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 28 residues processed: 17 average time/residue: 0.6162 time to fit residues: 14.8971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN A 318 ASN B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN E 57 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15310 Z= 0.284 Angle : 0.513 7.927 20736 Z= 0.271 Chirality : 0.045 0.172 2287 Planarity : 0.004 0.052 2666 Dihedral : 6.178 75.556 2107 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 3.66 % Allowed : 21.08 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1862 helix: 1.40 (0.21), residues: 686 sheet: 0.24 (0.26), residues: 380 loop : -0.57 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 PHE 0.020 0.001 PHE F 101 TYR 0.019 0.001 TYR D 43 ARG 0.008 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 443 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 41 residues processed: 477 average time/residue: 1.5848 time to fit residues: 815.8140 Evaluate side-chains 479 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 438 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 13 average time/residue: 0.4158 time to fit residues: 9.4559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 0.0970 chunk 162 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 243 ASN A 255 GLN A 318 ASN B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN D 219 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15310 Z= 0.196 Angle : 0.486 8.193 20736 Z= 0.257 Chirality : 0.043 0.181 2287 Planarity : 0.004 0.050 2666 Dihedral : 5.858 71.562 2107 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 3.47 % Allowed : 21.02 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1862 helix: 1.49 (0.21), residues: 689 sheet: 0.31 (0.26), residues: 378 loop : -0.43 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.016 0.001 PHE C 111 TYR 0.013 0.001 TYR D 250 ARG 0.009 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 438 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 43 residues processed: 471 average time/residue: 1.6061 time to fit residues: 818.7977 Evaluate side-chains 474 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 431 time to evaluate : 1.963 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 30 residues processed: 14 average time/residue: 1.0447 time to fit residues: 19.4958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN A 318 ASN B 226 ASN B 352 HIS C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15310 Z= 0.277 Angle : 0.522 8.204 20736 Z= 0.274 Chirality : 0.045 0.196 2287 Planarity : 0.004 0.053 2666 Dihedral : 5.993 74.205 2107 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 3.16 % Allowed : 21.45 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1862 helix: 1.52 (0.21), residues: 682 sheet: 0.31 (0.26), residues: 378 loop : -0.46 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.020 0.001 PHE F 101 TYR 0.018 0.001 TYR D 43 ARG 0.009 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 432 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 43 residues processed: 459 average time/residue: 1.6161 time to fit residues: 800.1992 Evaluate side-chains 466 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 423 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 27 residues processed: 16 average time/residue: 0.5185 time to fit residues: 12.4338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN A 318 ASN A 373 GLN B 226 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15310 Z= 0.275 Angle : 0.518 8.273 20736 Z= 0.274 Chirality : 0.045 0.195 2287 Planarity : 0.004 0.053 2666 Dihedral : 6.014 75.335 2107 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 2.36 % Allowed : 22.69 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1862 helix: 1.51 (0.21), residues: 683 sheet: 0.31 (0.26), residues: 378 loop : -0.46 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 PHE 0.019 0.001 PHE F 101 TYR 0.017 0.001 TYR D 43 ARG 0.009 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 419 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 33 residues processed: 449 average time/residue: 1.5848 time to fit residues: 767.2697 Evaluate side-chains 456 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 423 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 27 residues processed: 6 average time/residue: 0.8583 time to fit residues: 8.3760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 129 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN A 318 ASN B 226 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN F 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106066 restraints weight = 20949.449| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.00 r_work: 0.3162 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15310 Z= 0.200 Angle : 0.493 8.368 20736 Z= 0.259 Chirality : 0.043 0.190 2287 Planarity : 0.004 0.051 2666 Dihedral : 5.692 71.417 2107 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 2.48 % Allowed : 22.57 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1862 helix: 1.63 (0.21), residues: 683 sheet: 0.33 (0.27), residues: 361 loop : -0.39 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.018 0.001 PHE A 276 TYR 0.013 0.001 TYR D 43 ARG 0.009 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10700.27 seconds wall clock time: 187 minutes 38.20 seconds (11258.20 seconds total)