Starting phenix.real_space_refine on Fri Feb 16 04:43:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/02_2024/8g4d_29717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/02_2024/8g4d_29717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/02_2024/8g4d_29717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/02_2024/8g4d_29717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/02_2024/8g4d_29717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4d_29717/02_2024/8g4d_29717_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.014 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 6 5.49 5 S 64 5.16 5 C 9315 2.51 5 N 2390 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "E GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14402 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1932 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "C" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1932 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.91, per 1000 atoms: 0.55 Number of scatterers: 14402 At special positions: 0 Unit cell: (102.896, 124.696, 178.76, 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 64 16.00 P 6 15.00 O 2627 8.00 N 2390 7.00 C 9315 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: 5.52 Conformation dependent library (CDL) restraints added in 2.7 seconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 14 sheets defined 55.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 20 through 39 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.150A pdb=" N THR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.733A pdb=" N GLU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 150 through 176 removed outlier: 4.044A pdb=" N ILE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 224 removed outlier: 3.537A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.505A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 291 through 315 Processing helix chain 'A' and resid 318 through 324 Processing helix chain 'A' and resid 334 through 343 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 448 through 451 No H-bonds generated for 'chain 'A' and resid 448 through 451' Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 513 through 555 removed outlier: 4.544A pdb=" N ALA A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 562 No H-bonds generated for 'chain 'A' and resid 559 through 562' Processing helix chain 'A' and resid 572 through 602 Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 614 through 643 removed outlier: 4.397A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 102 through 110 Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.656A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 204 through 207 No H-bonds generated for 'chain 'B' and resid 204 through 207' Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 102 through 110 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 134 through 138 removed outlier: 4.682A pdb=" N ASP C 138 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.621A pdb=" N PHE C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 4.050A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 4.208A pdb=" N TYR C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 11 through 29 Processing helix chain 'D' and resid 36 through 72 removed outlier: 4.047A pdb=" N ILE D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 85 through 137 Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 144 through 170 removed outlier: 4.453A pdb=" N SER D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 218 through 235 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 269 through 272 removed outlier: 4.167A pdb=" N PHE D 272 " --> pdb=" O PRO D 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 282 through 285 No H-bonds generated for 'chain 'D' and resid 282 through 285' Processing helix chain 'D' and resid 290 through 302 Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 10 through 29 removed outlier: 3.733A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 39 through 60 Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 87 through 137 removed outlier: 3.540A pdb=" N GLU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 144 through 174 removed outlier: 3.897A pdb=" N PHE E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU E 173 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 196 through 201 Processing helix chain 'E' and resid 219 through 235 Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 282 through 285 Processing helix chain 'E' and resid 290 through 299 Processing helix chain 'E' and resid 330 through 333 No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing sheet with id= A, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.308A pdb=" N ILE A 484 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 356 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 485 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 354 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.919A pdb=" N THR B 63 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 221 through 226 removed outlier: 3.804A pdb=" N PHE B 215 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN B 224 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 213 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE B 197 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B 38 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET B 199 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 167 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 200 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.506A pdb=" N ILE B 26 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS B 11 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS B 24 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.567A pdb=" N THR C 63 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 36 through 39 removed outlier: 6.415A pdb=" N ARG C 212 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET C 39 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 214 " --> pdb=" O MET C 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 88 through 90 removed outlier: 5.697A pdb=" N THR C 196 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA C 167 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 198 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 11 through 15 removed outlier: 6.914A pdb=" N TYR C 13 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU C 21 " --> pdb=" O TYR C 13 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN C 15 " --> pdb=" O LYS C 19 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.560A pdb=" N GLU D 179 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 216 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 181 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 214 " --> pdb=" O ILE D 181 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 206 through 208 Processing sheet with id= K, first strand: chain 'D' and resid 252 through 257 removed outlier: 3.504A pdb=" N VAL D 256 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 311 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 317 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 180 through 182 Processing sheet with id= M, first strand: chain 'E' and resid 205 through 209 removed outlier: 6.124A pdb=" N ILE E 241 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN E 208 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 243 " --> pdb=" O GLN E 208 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 305 through 311 removed outlier: 3.802A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4573 1.35 - 1.50: 3825 1.50 - 1.65: 6165 1.65 - 1.80: 62 1.80 - 1.95: 54 Bond restraints: 14679 Sorted by residual: bond pdb=" N VAL C 2 " pdb=" CA VAL C 2 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" C LYS A 558 " pdb=" N PRO A 559 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL B 2 " pdb=" CA VAL B 2 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.78e+00 bond pdb=" N ILE C 3 " pdb=" CA ILE C 3 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.38e-02 5.25e+03 7.51e+00 bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.22e-02 6.72e+03 7.11e+00 ... (remaining 14674 not shown) Histogram of bond angle deviations from ideal: 95.72 - 103.44: 121 103.44 - 111.16: 5719 111.16 - 118.88: 6277 118.88 - 126.60: 7524 126.60 - 134.31: 149 Bond angle restraints: 19790 Sorted by residual: angle pdb=" N TYR A 561 " pdb=" CA TYR A 561 " pdb=" C TYR A 561 " ideal model delta sigma weight residual 113.88 106.09 7.79 1.23e+00 6.61e-01 4.01e+01 angle pdb=" N GLU E 83 " pdb=" CA GLU E 83 " pdb=" C GLU E 83 " ideal model delta sigma weight residual 114.56 108.76 5.80 1.27e+00 6.20e-01 2.08e+01 angle pdb=" C GLN D 162 " pdb=" N GLN D 163 " pdb=" CA GLN D 163 " ideal model delta sigma weight residual 122.06 114.59 7.47 1.86e+00 2.89e-01 1.61e+01 angle pdb=" C ILE D 225 " pdb=" N ARG D 226 " pdb=" CA ARG D 226 " ideal model delta sigma weight residual 121.58 114.03 7.55 1.95e+00 2.63e-01 1.50e+01 angle pdb=" N THR D 69 " pdb=" CA THR D 69 " pdb=" C THR D 69 " ideal model delta sigma weight residual 111.36 107.31 4.05 1.09e+00 8.42e-01 1.38e+01 ... (remaining 19785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 8510 30.70 - 61.40: 300 61.40 - 92.09: 29 92.09 - 122.79: 0 122.79 - 153.49: 1 Dihedral angle restraints: 8840 sinusoidal: 3616 harmonic: 5224 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual 292.27 138.78 153.49 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA GLY A 604 " pdb=" C GLY A 604 " pdb=" N TRP A 605 " pdb=" CA TRP A 605 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA MET E 140 " pdb=" C MET E 140 " pdb=" N GLU E 141 " pdb=" CA GLU E 141 " ideal model delta harmonic sigma weight residual -180.00 -160.63 -19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 8837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1661 0.042 - 0.085: 443 0.085 - 0.127: 143 0.127 - 0.169: 12 0.169 - 0.212: 3 Chirality restraints: 2262 Sorted by residual: chirality pdb=" CB ILE E 243 " pdb=" CA ILE E 243 " pdb=" CG1 ILE E 243 " pdb=" CG2 ILE E 243 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLN D 163 " pdb=" N GLN D 163 " pdb=" C GLN D 163 " pdb=" CB GLN D 163 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CB ILE C 3 " pdb=" CA ILE C 3 " pdb=" CG1 ILE C 3 " pdb=" CG2 ILE C 3 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 2259 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 122 " -0.011 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP E 122 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 122 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP E 122 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP E 122 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP E 122 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 122 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 122 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 122 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 122 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 605 " 0.021 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 605 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 605 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 605 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 605 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 605 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " -0.022 2.00e-02 2.50e+03 1.43e-02 5.14e+00 pdb=" CG TRP E 153 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " -0.003 2.00e-02 2.50e+03 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2306 2.76 - 3.30: 14605 3.30 - 3.83: 23473 3.83 - 4.37: 25986 4.37 - 4.90: 44551 Nonbonded interactions: 110921 Sorted by model distance: nonbonded pdb=" OE1 GLN E 247 " pdb=" OG1 THR E 252 " model vdw 2.228 2.440 nonbonded pdb=" O THR D 128 " pdb=" OG1 THR D 131 " model vdw 2.236 2.440 nonbonded pdb=" OD1 ASN C 95 " pdb=" NH2 ARG C 156 " model vdw 2.248 2.520 nonbonded pdb=" NH2 ARG A 9 " pdb=" O THR C 99 " model vdw 2.249 2.520 nonbonded pdb=" O ARG E 226 " pdb=" OG1 THR E 230 " model vdw 2.251 2.440 ... (remaining 110916 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 5.590 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: 10.270 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 38.040 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 0.061 14679 Z= 0.203 Angle : 0.679 11.346 19790 Z= 0.383 Chirality : 0.043 0.212 2262 Planarity : 0.004 0.067 2467 Dihedral : 15.325 153.488 5458 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.64 % Allowed : 0.45 % Favored : 98.92 % 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: 0.05 (0.21), residues: 1783 helix: 1.43 (0.17), residues: 1017 sheet: -2.67 (0.45), residues: 116 loop : -1.72 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP E 122 HIS 0.013 0.001 HIS E 157 PHE 0.021 0.001 PHE A 501 TYR 0.021 0.001 TYR A 638 ARG 0.016 0.001 ARG E 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8205 (t0) cc_final: 0.7860 (t0) REVERT: C 95 ASN cc_start: 0.7965 (p0) cc_final: 0.7749 (p0) REVERT: C 117 LYS cc_start: 0.6903 (mmmt) cc_final: 0.6569 (tppt) REVERT: D 23 MET cc_start: 0.7397 (ptm) cc_final: 0.6957 (ptt) REVERT: D 169 ILE cc_start: 0.7642 (pt) cc_final: 0.7326 (tp) REVERT: E 112 LEU cc_start: 0.7911 (tp) cc_final: 0.7695 (tt) REVERT: E 120 MET cc_start: 0.8340 (tpt) cc_final: 0.7997 (tpp) REVERT: E 157 HIS cc_start: 0.8354 (p90) cc_final: 0.8079 (p90) outliers start: 10 outliers final: 0 residues processed: 223 average time/residue: 0.2424 time to fit residues: 82.0810 Evaluate side-chains 159 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.0070 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14679 Z= 0.173 Angle : 0.589 9.334 19790 Z= 0.305 Chirality : 0.041 0.188 2262 Planarity : 0.003 0.053 2467 Dihedral : 7.479 151.902 1943 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.02 % Allowed : 7.91 % Favored : 91.07 % 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: 0.29 (0.21), residues: 1783 helix: 1.61 (0.17), residues: 1012 sheet: -2.66 (0.42), residues: 128 loop : -1.52 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 153 HIS 0.010 0.001 HIS E 134 PHE 0.024 0.001 PHE A 223 TYR 0.017 0.001 TYR A 623 ARG 0.007 0.000 ARG E 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 MET cc_start: 0.7757 (tpt) cc_final: 0.7326 (tpt) REVERT: A 369 MET cc_start: 0.4515 (mmm) cc_final: 0.3402 (mmp) REVERT: A 487 ASN cc_start: 0.8285 (t0) cc_final: 0.8034 (t0) REVERT: B 199 MET cc_start: 0.7594 (ptt) cc_final: 0.7243 (ptt) REVERT: C 117 LYS cc_start: 0.6933 (mmmt) cc_final: 0.6568 (tppt) REVERT: E 157 HIS cc_start: 0.8348 (p90) cc_final: 0.8141 (p90) outliers start: 16 outliers final: 10 residues processed: 178 average time/residue: 0.2603 time to fit residues: 70.5056 Evaluate side-chains 168 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 109 optimal weight: 0.0270 chunk 44 optimal weight: 30.0000 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14679 Z= 0.270 Angle : 0.626 10.590 19790 Z= 0.324 Chirality : 0.042 0.163 2262 Planarity : 0.003 0.050 2467 Dihedral : 7.476 149.158 1943 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.66 % Allowed : 11.30 % Favored : 87.05 % 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: 0.15 (0.21), residues: 1783 helix: 1.46 (0.17), residues: 1016 sheet: -2.70 (0.42), residues: 126 loop : -1.55 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 605 HIS 0.007 0.001 HIS C 86 PHE 0.030 0.002 PHE A 223 TYR 0.024 0.002 TYR A 314 ARG 0.012 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.6961 (mmt) cc_final: 0.6412 (mmt) REVERT: A 369 MET cc_start: 0.4410 (mmm) cc_final: 0.3572 (mmp) REVERT: A 487 ASN cc_start: 0.8358 (t0) cc_final: 0.8135 (t0) REVERT: B 199 MET cc_start: 0.7893 (ptt) cc_final: 0.7573 (ptt) REVERT: C 71 MET cc_start: 0.7812 (mmp) cc_final: 0.6234 (tmm) REVERT: C 95 ASN cc_start: 0.8224 (p0) cc_final: 0.7873 (p0) REVERT: D 67 LEU cc_start: 0.4282 (OUTLIER) cc_final: 0.3297 (tt) REVERT: E 157 HIS cc_start: 0.8413 (p90) cc_final: 0.8209 (p90) outliers start: 26 outliers final: 18 residues processed: 174 average time/residue: 0.2780 time to fit residues: 74.5784 Evaluate side-chains 164 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 384 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14679 Z= 0.244 Angle : 0.599 9.918 19790 Z= 0.311 Chirality : 0.042 0.311 2262 Planarity : 0.003 0.049 2467 Dihedral : 7.461 148.980 1943 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.11 % Allowed : 14.23 % Favored : 83.66 % 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: 0.15 (0.21), residues: 1783 helix: 1.43 (0.17), residues: 1021 sheet: -2.87 (0.48), residues: 96 loop : -1.57 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 220 HIS 0.011 0.001 HIS D 108 PHE 0.029 0.001 PHE A 223 TYR 0.020 0.001 TYR A 314 ARG 0.016 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.4341 (mmm) cc_final: 0.3702 (mmp) REVERT: B 199 MET cc_start: 0.7906 (ptt) cc_final: 0.7545 (ptt) REVERT: C 95 ASN cc_start: 0.8198 (p0) cc_final: 0.7866 (p0) REVERT: E 157 HIS cc_start: 0.8405 (p-80) cc_final: 0.8198 (p-80) outliers start: 33 outliers final: 26 residues processed: 172 average time/residue: 0.2589 time to fit residues: 67.8797 Evaluate side-chains 172 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 7.9990 chunk 97 optimal weight: 0.0010 chunk 2 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14679 Z= 0.193 Angle : 0.586 10.871 19790 Z= 0.299 Chirality : 0.041 0.286 2262 Planarity : 0.003 0.073 2467 Dihedral : 7.376 148.991 1943 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.36 % Allowed : 15.95 % Favored : 81.68 % 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: 0.31 (0.21), residues: 1783 helix: 1.56 (0.17), residues: 1021 sheet: -2.76 (0.49), residues: 96 loop : -1.51 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 122 HIS 0.007 0.001 HIS D 165 PHE 0.029 0.001 PHE A 223 TYR 0.016 0.001 TYR A 623 ARG 0.013 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 152 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: A 369 MET cc_start: 0.4304 (mmm) cc_final: 0.3755 (mmp) REVERT: B 199 MET cc_start: 0.7837 (ptt) cc_final: 0.7458 (ptt) REVERT: C 95 ASN cc_start: 0.8137 (p0) cc_final: 0.7854 (p0) REVERT: E 19 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.5408 (mt0) outliers start: 37 outliers final: 28 residues processed: 178 average time/residue: 0.2480 time to fit residues: 66.8883 Evaluate side-chains 175 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 142 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 89 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: A 155 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14679 Z= 0.215 Angle : 0.598 16.088 19790 Z= 0.306 Chirality : 0.041 0.210 2262 Planarity : 0.004 0.103 2467 Dihedral : 7.368 148.459 1943 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.23 % Allowed : 16.78 % Favored : 80.98 % 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: 0.29 (0.21), residues: 1783 helix: 1.54 (0.17), residues: 1015 sheet: -2.69 (0.48), residues: 106 loop : -1.48 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 122 HIS 0.014 0.001 HIS E 157 PHE 0.031 0.001 PHE A 223 TYR 0.016 0.001 TYR A 623 ARG 0.016 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: A 369 MET cc_start: 0.4080 (mmm) cc_final: 0.3767 (mmp) REVERT: B 199 MET cc_start: 0.7852 (ptt) cc_final: 0.7457 (ptt) REVERT: C 71 MET cc_start: 0.7692 (mmp) cc_final: 0.6228 (tmm) REVERT: C 95 ASN cc_start: 0.8126 (p0) cc_final: 0.7861 (p0) outliers start: 35 outliers final: 29 residues processed: 170 average time/residue: 0.2348 time to fit residues: 62.1114 Evaluate side-chains 173 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 40.0000 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 125 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 170 optimal weight: 0.0040 chunk 106 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN D 80 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14679 Z= 0.152 Angle : 0.577 12.116 19790 Z= 0.292 Chirality : 0.040 0.222 2262 Planarity : 0.003 0.050 2467 Dihedral : 7.229 149.701 1943 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.04 % Allowed : 17.68 % Favored : 80.28 % 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 (0.21), residues: 1783 helix: 1.73 (0.17), residues: 1010 sheet: -2.33 (0.45), residues: 126 loop : -1.47 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 122 HIS 0.012 0.001 HIS E 157 PHE 0.031 0.001 PHE A 501 TYR 0.017 0.001 TYR E 293 ARG 0.011 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: A 369 MET cc_start: 0.3987 (mmm) cc_final: 0.3721 (mmp) REVERT: B 9 ILE cc_start: 0.8166 (mm) cc_final: 0.7823 (mm) REVERT: B 199 MET cc_start: 0.7650 (ptt) cc_final: 0.7217 (ptt) REVERT: C 71 MET cc_start: 0.7684 (mmp) cc_final: 0.6121 (tmm) REVERT: C 95 ASN cc_start: 0.8160 (p0) cc_final: 0.7810 (p0) outliers start: 32 outliers final: 21 residues processed: 171 average time/residue: 0.2411 time to fit residues: 63.5510 Evaluate side-chains 172 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14679 Z= 0.194 Angle : 0.594 12.891 19790 Z= 0.301 Chirality : 0.041 0.214 2262 Planarity : 0.003 0.067 2467 Dihedral : 7.220 148.462 1943 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.17 % Allowed : 17.93 % Favored : 79.90 % 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: 0.43 (0.21), residues: 1783 helix: 1.69 (0.17), residues: 1014 sheet: -2.62 (0.46), residues: 115 loop : -1.44 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 122 HIS 0.011 0.001 HIS E 157 PHE 0.031 0.001 PHE A 223 TYR 0.016 0.001 TYR A 314 ARG 0.013 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: A 369 MET cc_start: 0.4038 (mmm) cc_final: 0.3632 (mmp) REVERT: B 199 MET cc_start: 0.7791 (ptt) cc_final: 0.7375 (ptt) REVERT: C 71 MET cc_start: 0.7765 (mmp) cc_final: 0.6157 (tmm) REVERT: C 95 ASN cc_start: 0.8160 (p0) cc_final: 0.7843 (p0) REVERT: E 19 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.4327 (mt0) outliers start: 34 outliers final: 28 residues processed: 172 average time/residue: 0.2385 time to fit residues: 63.3064 Evaluate side-chains 177 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 19 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 20.0000 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14679 Z= 0.292 Angle : 0.659 13.743 19790 Z= 0.335 Chirality : 0.043 0.232 2262 Planarity : 0.004 0.054 2467 Dihedral : 7.360 146.480 1943 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 2.17 % Allowed : 18.25 % Favored : 79.58 % 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 (0.21), residues: 1783 helix: 1.37 (0.16), residues: 1027 sheet: -2.80 (0.46), residues: 115 loop : -1.41 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 122 HIS 0.010 0.001 HIS E 157 PHE 0.035 0.002 PHE A 501 TYR 0.027 0.002 TYR A 314 ARG 0.012 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: A 369 MET cc_start: 0.4158 (mmm) cc_final: 0.3781 (mmp) REVERT: A 487 ASN cc_start: 0.8393 (t0) cc_final: 0.8168 (t0) REVERT: B 199 MET cc_start: 0.7997 (ptt) cc_final: 0.7624 (ptt) REVERT: C 71 MET cc_start: 0.7795 (mmp) cc_final: 0.6148 (tmm) REVERT: C 95 ASN cc_start: 0.8197 (p0) cc_final: 0.7922 (p0) REVERT: D 67 LEU cc_start: 0.4062 (OUTLIER) cc_final: 0.3088 (tt) REVERT: E 19 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.5018 (mt0) outliers start: 34 outliers final: 28 residues processed: 175 average time/residue: 0.2382 time to fit residues: 64.3266 Evaluate side-chains 175 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 19 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14679 Z= 0.239 Angle : 0.630 13.390 19790 Z= 0.320 Chirality : 0.042 0.230 2262 Planarity : 0.003 0.050 2467 Dihedral : 7.301 147.115 1943 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.11 % Favored : 93.83 % Rotamer: Outliers : 1.98 % Allowed : 18.63 % Favored : 79.39 % 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: 0.19 (0.21), residues: 1783 helix: 1.50 (0.17), residues: 1010 sheet: -2.81 (0.43), residues: 129 loop : -1.46 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP D 220 HIS 0.011 0.001 HIS E 157 PHE 0.036 0.001 PHE A 501 TYR 0.019 0.002 TYR A 314 ARG 0.011 0.001 ARG C 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: A 487 ASN cc_start: 0.8373 (t0) cc_final: 0.8154 (t0) REVERT: B 199 MET cc_start: 0.7939 (ptt) cc_final: 0.7549 (ptt) REVERT: C 71 MET cc_start: 0.7816 (mmp) cc_final: 0.5964 (tmm) REVERT: C 95 ASN cc_start: 0.8184 (p0) cc_final: 0.7903 (p0) REVERT: D 67 LEU cc_start: 0.3976 (OUTLIER) cc_final: 0.3009 (tt) REVERT: E 19 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.5027 (mt0) outliers start: 31 outliers final: 27 residues processed: 169 average time/residue: 0.2538 time to fit residues: 65.2282 Evaluate side-chains 175 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 19 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.186245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.142867 restraints weight = 25730.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137711 restraints weight = 27536.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139730 restraints weight = 24606.113| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14679 Z= 0.166 Angle : 0.597 13.427 19790 Z= 0.301 Chirality : 0.041 0.220 2262 Planarity : 0.003 0.050 2467 Dihedral : 7.190 148.897 1943 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 1.47 % Allowed : 19.27 % Favored : 79.26 % 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: 0.44 (0.21), residues: 1783 helix: 1.71 (0.17), residues: 1008 sheet: -2.55 (0.46), residues: 115 loop : -1.44 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP D 220 HIS 0.016 0.001 HIS E 157 PHE 0.033 0.001 PHE A 501 TYR 0.015 0.001 TYR A 623 ARG 0.012 0.000 ARG C 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2679.89 seconds wall clock time: 49 minutes 49.63 seconds (2989.63 seconds total)