Starting phenix.real_space_refine on Sat Aug 23 11:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggd_40003/08_2025/8ggd_40003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggd_40003/08_2025/8ggd_40003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ggd_40003/08_2025/8ggd_40003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggd_40003/08_2025/8ggd_40003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ggd_40003/08_2025/8ggd_40003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggd_40003/08_2025/8ggd_40003.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7432 2.51 5 N 2060 2.21 5 O 2164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11724 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 299} Chain: "C" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 299} Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 299} Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2164 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 1 Time building chain proxies: 2.94, per 1000 atoms: 0.25 Number of scatterers: 11724 At special positions: 0 Unit cell: (103.2, 107.5, 133.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2164 8.00 N 2060 7.00 C 7432 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 - 3.00 Amino acid : True - 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: 0.91 Conformation dependent library (CDL) restraints added in 604.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 51.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.515A pdb=" N GLN D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.537A pdb=" N VAL D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 95 through 115 removed outlier: 3.547A pdb=" N PHE D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 157 through 171 removed outlier: 4.008A pdb=" N ALA D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 removed outlier: 4.104A pdb=" N ILE D 197 " --> pdb=" O TYR D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 203 through 225 removed outlier: 3.535A pdb=" N GLN D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 251 removed outlier: 3.505A pdb=" N ALA D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 322 removed outlier: 3.607A pdb=" N LYS D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA D 319 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.509A pdb=" N LEU B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 95 through 116 removed outlier: 4.372A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 157 through 171 Processing helix chain 'B' and resid 204 through 225 removed outlier: 5.572A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 removed outlier: 3.503A pdb=" N GLU B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 320 removed outlier: 3.669A pdb=" N MET B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'C' and resid 13 through 23 removed outlier: 3.615A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 47 Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 99 through 116 removed outlier: 4.359A pdb=" N GLY C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix removed outlier: 3.585A pdb=" N ILE C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 169 removed outlier: 4.170A pdb=" N GLY C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.328A pdb=" N ILE C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 234 through 252 Processing helix chain 'C' and resid 299 through 322 removed outlier: 5.383A pdb=" N VAL C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 322 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 23 removed outlier: 3.616A pdb=" N ARG A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.623A pdb=" N ASP A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 95 through 116 removed outlier: 4.173A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 145 removed outlier: 3.858A pdb=" N ILE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 4.126A pdb=" N LEU A 152 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 4.192A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.205A pdb=" N GLU A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.712A pdb=" N VAL A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.716A pdb=" N GLU A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.515A pdb=" N MET A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 344 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 362 through 373 removed outlier: 4.051A pdb=" N LEU E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN E 371 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 387 removed outlier: 3.744A pdb=" N LEU E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 406 removed outlier: 4.079A pdb=" N THR E 401 " --> pdb=" O ARG E 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 404 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 405 " --> pdb=" O THR E 401 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 423 Processing helix chain 'E' and resid 427 through 438 removed outlier: 3.711A pdb=" N ALA E 434 " --> pdb=" O HIS E 430 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 456 removed outlier: 4.061A pdb=" N GLN E 448 " --> pdb=" O GLY E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 502 removed outlier: 3.849A pdb=" N ALA E 502 " --> pdb=" O THR E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 523 removed outlier: 3.781A pdb=" N LEU E 517 " --> pdb=" O LEU E 513 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY E 518 " --> pdb=" O HIS E 514 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 519 " --> pdb=" O ALA E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 541 removed outlier: 4.001A pdb=" N ALA E 531 " --> pdb=" O PHE E 527 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS E 532 " --> pdb=" O ASP E 528 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E 539 " --> pdb=" O ARG E 535 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E 541 " --> pdb=" O ALA E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 557 removed outlier: 4.017A pdb=" N TRP E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 575 removed outlier: 3.536A pdb=" N LEU E 572 " --> pdb=" O TYR E 568 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 573 " --> pdb=" O ASN E 569 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN E 575 " --> pdb=" O ALA E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 592 removed outlier: 3.564A pdb=" N MET E 582 " --> pdb=" O TYR E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 610 removed outlier: 5.302A pdb=" N ARG E 604 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 610 " --> pdb=" O ILE E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 618 Processing helix chain 'E' and resid 624 through 638 removed outlier: 3.555A pdb=" N TRP E 628 " --> pdb=" O THR E 624 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 57 through 58 removed outlier: 6.872A pdb=" N VAL D 4 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N TYR D 34 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 6 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE D 82 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'D' and resid 257 through 263 removed outlier: 4.032A pdb=" N ALA D 260 " --> pdb=" O MET D 275 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET D 275 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL D 278 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 35 removed outlier: 3.911A pdb=" N ASP B 35 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'B' and resid 257 through 262 removed outlier: 3.915A pdb=" N ALA B 260 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 275 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 273 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 283 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 54 through 60 removed outlier: 3.689A pdb=" N THR C 55 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 35 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'C' and resid 257 through 259 removed outlier: 3.856A pdb=" N ARG C 286 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 56 through 59 removed outlier: 6.278A pdb=" N LEU A 31 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ALA A 59 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 33 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 4 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 6 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AB4, first strand: chain 'A' and resid 257 through 258 removed outlier: 3.861A pdb=" N ARG A 286 " --> pdb=" O VAL A 278 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1488 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: 1.77 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3004 1.33 - 1.45: 1854 1.45 - 1.57: 6961 1.57 - 1.70: 1 1.70 - 1.82: 116 Bond restraints: 11936 Sorted by residual: bond pdb=" C LEU C 63 " pdb=" N PRO C 64 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.09e+00 bond pdb=" N TYR E 595 " pdb=" CA TYR E 595 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.13e-02 7.83e+03 7.47e+00 bond pdb=" N THR A 317 " pdb=" CA THR A 317 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.00e-02 1.00e+04 7.46e+00 bond pdb=" CA ARG D 171 " pdb=" C ARG D 171 " ideal model delta sigma weight residual 1.523 1.487 0.037 1.34e-02 5.57e+03 7.45e+00 bond pdb=" N ILE A 144 " pdb=" CA ILE A 144 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.32e+00 ... (remaining 11931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 15935 2.43 - 4.85: 271 4.85 - 7.28: 28 7.28 - 9.70: 7 9.70 - 12.13: 4 Bond angle restraints: 16245 Sorted by residual: angle pdb=" N ASN A 131 " pdb=" CA ASN A 131 " pdb=" C ASN A 131 " ideal model delta sigma weight residual 113.41 103.68 9.73 1.22e+00 6.72e-01 6.36e+01 angle pdb=" C HIS D 172 " pdb=" N PRO D 173 " pdb=" CA PRO D 173 " ideal model delta sigma weight residual 119.56 113.91 5.65 1.01e+00 9.80e-01 3.12e+01 angle pdb=" N CYS E 410 " pdb=" CA CYS E 410 " pdb=" C CYS E 410 " ideal model delta sigma weight residual 114.62 108.72 5.90 1.14e+00 7.69e-01 2.68e+01 angle pdb=" N ILE A 13 " pdb=" CA ILE A 13 " pdb=" C ILE A 13 " ideal model delta sigma weight residual 112.29 107.43 4.86 9.40e-01 1.13e+00 2.67e+01 angle pdb=" N GLY C 61 " pdb=" CA GLY C 61 " pdb=" C GLY C 61 " ideal model delta sigma weight residual 113.18 125.31 -12.13 2.37e+00 1.78e-01 2.62e+01 ... (remaining 16240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6573 17.99 - 35.98: 575 35.98 - 53.97: 124 53.97 - 71.96: 23 71.96 - 89.95: 8 Dihedral angle restraints: 7303 sinusoidal: 2837 harmonic: 4466 Sorted by residual: dihedral pdb=" CA HIS A 172 " pdb=" C HIS A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta harmonic sigma weight residual 180.00 151.06 28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU C 301 " pdb=" C LEU C 301 " pdb=" N GLU C 302 " pdb=" CA GLU C 302 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA HIS E 359 " pdb=" C HIS E 359 " pdb=" N ASP E 360 " pdb=" CA ASP E 360 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 7300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1491 0.050 - 0.100: 332 0.100 - 0.149: 108 0.149 - 0.199: 9 0.199 - 0.249: 4 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA HIS D 172 " pdb=" N HIS D 172 " pdb=" C HIS D 172 " pdb=" CB HIS D 172 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO E 615 " pdb=" N PRO E 615 " pdb=" C PRO E 615 " pdb=" CB PRO E 615 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LEU E 597 " pdb=" N LEU E 597 " pdb=" C LEU E 597 " pdb=" CB LEU E 597 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1941 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 614 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO E 615 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO E 615 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 615 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 63 " 0.071 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO C 64 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 128 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 129 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.057 5.00e-02 4.00e+02 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1897 2.76 - 3.30: 11495 3.30 - 3.83: 18182 3.83 - 4.37: 20174 4.37 - 4.90: 35976 Nonbonded interactions: 87724 Sorted by model distance: nonbonded pdb=" O ALA E 335 " pdb=" NE2 GLN E 338 " model vdw 2.228 3.120 nonbonded pdb=" O GLU E 618 " pdb=" NH1 ARG E 621 " model vdw 2.230 3.120 nonbonded pdb=" OH TYR B 147 " pdb=" OD2 ASP B 263 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR E 568 " pdb=" OD1 ASN E 584 " model vdw 2.233 3.040 nonbonded pdb=" OXT LEU A 323 " pdb=" ND2 ASN E 439 " model vdw 2.246 3.120 ... (remaining 87719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.810 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.570 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 11936 Z= 0.245 Angle : 0.741 12.131 16245 Z= 0.435 Chirality : 0.048 0.249 1944 Planarity : 0.006 0.119 2110 Dihedral : 14.509 89.953 4433 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 1.35 % Allowed : 11.00 % Favored : 87.65 % Rotamer: Outliers : 2.76 % Allowed : 0.87 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.22), residues: 1555 helix: 0.44 (0.21), residues: 727 sheet: -1.96 (0.41), residues: 172 loop : -2.29 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.033 0.001 TYR E 595 PHE 0.017 0.001 PHE E 350 TRP 0.027 0.002 TRP E 548 HIS 0.003 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00392 (11936) covalent geometry : angle 0.74137 (16245) hydrogen bonds : bond 0.20478 ( 509) hydrogen bonds : angle 6.48606 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 PRO cc_start: 0.8860 (Cg_exo) cc_final: 0.8476 (Cg_endo) REVERT: A 235 MET cc_start: 0.7992 (ttm) cc_final: 0.7575 (tpp) REVERT: E 425 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7920 (tptt) REVERT: E 501 TYR cc_start: 0.7075 (m-10) cc_final: 0.6623 (m-80) REVERT: E 591 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7089 (p0) outliers start: 35 outliers final: 8 residues processed: 171 average time/residue: 0.1032 time to fit residues: 25.1624 Evaluate side-chains 113 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 591 ASN Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 634 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN E 442 ASN E 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.112798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085598 restraints weight = 24533.039| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.24 r_work: 0.3081 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 11936 Z= 0.150 Angle : 0.643 11.428 16245 Z= 0.328 Chirality : 0.044 0.211 1944 Planarity : 0.007 0.120 2110 Dihedral : 5.934 59.516 1700 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.77 % Favored : 89.65 % Rotamer: Outliers : 1.50 % Allowed : 7.66 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.22), residues: 1555 helix: 0.78 (0.20), residues: 743 sheet: -1.65 (0.38), residues: 202 loop : -2.48 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 625 TYR 0.015 0.001 TYR E 595 PHE 0.022 0.001 PHE C 100 TRP 0.010 0.001 TRP E 548 HIS 0.004 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00364 (11936) covalent geometry : angle 0.64277 (16245) hydrogen bonds : bond 0.04480 ( 509) hydrogen bonds : angle 4.56756 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7103 (tmm) cc_final: 0.6500 (tmm) REVERT: E 425 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7906 (tptt) REVERT: E 436 SER cc_start: 0.8979 (m) cc_final: 0.8579 (t) REVERT: E 559 ASN cc_start: 0.7686 (p0) cc_final: 0.7356 (t0) REVERT: E 591 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7412 (p0) REVERT: E 592 MET cc_start: 0.8349 (tpp) cc_final: 0.7518 (ppp) REVERT: E 594 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6563 (mp10) outliers start: 19 outliers final: 14 residues processed: 133 average time/residue: 0.1061 time to fit residues: 20.3115 Evaluate side-chains 123 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 591 ASN Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 82 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 149 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.113456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.086429 restraints weight = 24589.216| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.23 r_work: 0.3098 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11936 Z= 0.120 Angle : 0.579 8.325 16245 Z= 0.294 Chirality : 0.043 0.212 1944 Planarity : 0.007 0.124 2110 Dihedral : 5.385 59.416 1694 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.52 % Favored : 89.90 % Rotamer: Outliers : 1.58 % Allowed : 12.00 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.23), residues: 1555 helix: 1.06 (0.20), residues: 756 sheet: -1.64 (0.41), residues: 172 loop : -2.28 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 625 TYR 0.014 0.001 TYR D 147 PHE 0.015 0.001 PHE C 100 TRP 0.004 0.001 TRP E 548 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00302 (11936) covalent geometry : angle 0.57948 (16245) hydrogen bonds : bond 0.03678 ( 509) hydrogen bonds : angle 4.09470 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7103 (tmm) cc_final: 0.6451 (tmm) REVERT: B 194 TYR cc_start: 0.8335 (m-80) cc_final: 0.8119 (m-80) REVERT: E 425 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7832 (tptt) REVERT: E 436 SER cc_start: 0.8944 (m) cc_final: 0.8602 (t) REVERT: E 495 ASP cc_start: 0.8138 (m-30) cc_final: 0.7889 (p0) REVERT: E 559 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7380 (t0) REVERT: E 591 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7492 (p0) REVERT: E 592 MET cc_start: 0.8353 (tpp) cc_final: 0.7734 (ppp) REVERT: E 594 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7118 (mp10) outliers start: 20 outliers final: 11 residues processed: 135 average time/residue: 0.1016 time to fit residues: 20.3185 Evaluate side-chains 126 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 591 ASN Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 141 optimal weight: 0.0980 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS ** E 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.084578 restraints weight = 24684.759| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.23 r_work: 0.3065 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 11936 Z= 0.138 Angle : 0.592 8.257 16245 Z= 0.300 Chirality : 0.043 0.213 1944 Planarity : 0.007 0.125 2110 Dihedral : 5.107 56.805 1689 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.58 % Favored : 89.84 % Rotamer: Outliers : 1.74 % Allowed : 15.23 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.23), residues: 1555 helix: 1.13 (0.20), residues: 761 sheet: -1.64 (0.40), residues: 182 loop : -2.32 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.015 0.001 TYR A 259 PHE 0.027 0.001 PHE C 100 TRP 0.003 0.001 TRP E 548 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00352 (11936) covalent geometry : angle 0.59220 (16245) hydrogen bonds : bond 0.03973 ( 509) hydrogen bonds : angle 4.00593 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.713 Fit side-chains REVERT: D 157 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 194 TYR cc_start: 0.8433 (m-80) cc_final: 0.8117 (m-80) REVERT: E 425 LYS cc_start: 0.8316 (ttmm) cc_final: 0.7822 (tptt) REVERT: E 436 SER cc_start: 0.8960 (m) cc_final: 0.8662 (t) REVERT: E 495 ASP cc_start: 0.8161 (m-30) cc_final: 0.7912 (p0) REVERT: E 559 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7355 (t0) REVERT: E 592 MET cc_start: 0.8454 (tpp) cc_final: 0.7892 (ppp) REVERT: E 613 THR cc_start: 0.7183 (p) cc_final: 0.6858 (p) outliers start: 22 outliers final: 15 residues processed: 126 average time/residue: 0.1085 time to fit residues: 20.0970 Evaluate side-chains 117 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 591 ASN Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 101 optimal weight: 0.0970 chunk 28 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS ** E 616 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.111071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084927 restraints weight = 24647.604| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.07 r_work: 0.3089 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 11936 Z= 0.152 Angle : 0.598 7.917 16245 Z= 0.303 Chirality : 0.044 0.213 1944 Planarity : 0.007 0.126 2110 Dihedral : 4.849 53.211 1684 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.13 % Favored : 90.29 % Rotamer: Outliers : 2.53 % Allowed : 15.94 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.22), residues: 1555 helix: 1.19 (0.20), residues: 747 sheet: -1.68 (0.39), residues: 182 loop : -2.33 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.016 0.001 TYR A 259 PHE 0.019 0.001 PHE C 100 TRP 0.025 0.002 TRP E 548 HIS 0.012 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00388 (11936) covalent geometry : angle 0.59756 (16245) hydrogen bonds : bond 0.04072 ( 509) hydrogen bonds : angle 4.04935 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: E 425 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7887 (tptt) REVERT: E 436 SER cc_start: 0.9073 (m) cc_final: 0.8686 (t) REVERT: E 495 ASP cc_start: 0.8191 (m-30) cc_final: 0.7934 (p0) REVERT: E 559 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7278 (t0) outliers start: 32 outliers final: 19 residues processed: 128 average time/residue: 0.1064 time to fit residues: 19.8785 Evaluate side-chains 117 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 591 ASN Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.085872 restraints weight = 24492.883| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.23 r_work: 0.3086 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 11936 Z= 0.115 Angle : 0.598 13.149 16245 Z= 0.294 Chirality : 0.043 0.211 1944 Planarity : 0.006 0.126 2110 Dihedral : 4.671 47.810 1684 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.81 % Favored : 90.61 % Rotamer: Outliers : 1.89 % Allowed : 16.97 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.23), residues: 1555 helix: 1.34 (0.20), residues: 752 sheet: -1.55 (0.40), residues: 182 loop : -2.28 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.010 0.001 TYR A 259 PHE 0.019 0.001 PHE C 100 TRP 0.018 0.001 TRP E 548 HIS 0.008 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00292 (11936) covalent geometry : angle 0.59785 (16245) hydrogen bonds : bond 0.03338 ( 509) hydrogen bonds : angle 3.84869 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.494 Fit side-chains REVERT: E 350 PHE cc_start: 0.7612 (m-80) cc_final: 0.7203 (m-80) REVERT: E 425 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7881 (tptt) REVERT: E 436 SER cc_start: 0.9084 (m) cc_final: 0.8736 (p) REVERT: E 437 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7326 (m-70) REVERT: E 495 ASP cc_start: 0.8167 (m-30) cc_final: 0.7911 (p0) REVERT: E 559 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7249 (t0) REVERT: E 592 MET cc_start: 0.8718 (tpp) cc_final: 0.8366 (tpp) outliers start: 24 outliers final: 15 residues processed: 131 average time/residue: 0.1150 time to fit residues: 22.0836 Evaluate side-chains 122 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 591 ASN Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 46 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.085949 restraints weight = 24243.772| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.21 r_work: 0.3088 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 11936 Z= 0.116 Angle : 0.608 12.734 16245 Z= 0.297 Chirality : 0.043 0.210 1944 Planarity : 0.006 0.125 2110 Dihedral : 4.589 44.031 1684 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.81 % Favored : 90.61 % Rotamer: Outliers : 2.05 % Allowed : 16.89 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.23), residues: 1555 helix: 1.40 (0.20), residues: 761 sheet: -1.50 (0.40), residues: 182 loop : -2.25 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.013 0.001 TYR D 147 PHE 0.016 0.001 PHE C 100 TRP 0.013 0.001 TRP E 548 HIS 0.006 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00297 (11936) covalent geometry : angle 0.60768 (16245) hydrogen bonds : bond 0.03260 ( 509) hydrogen bonds : angle 3.79743 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: E 350 PHE cc_start: 0.7614 (m-80) cc_final: 0.7178 (m-80) REVERT: E 359 HIS cc_start: 0.7083 (OUTLIER) cc_final: 0.6819 (t70) REVERT: E 425 LYS cc_start: 0.8323 (ttmm) cc_final: 0.7847 (tptt) REVERT: E 436 SER cc_start: 0.9104 (m) cc_final: 0.8778 (p) REVERT: E 495 ASP cc_start: 0.8154 (m-30) cc_final: 0.7907 (p0) REVERT: E 538 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8383 (m) REVERT: E 592 MET cc_start: 0.8725 (tpp) cc_final: 0.8395 (tpp) outliers start: 26 outliers final: 16 residues processed: 128 average time/residue: 0.1146 time to fit residues: 21.4939 Evaluate side-chains 121 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 589 TYR Chi-restraints excluded: chain E residue 591 ASN Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.084268 restraints weight = 24772.162| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.08 r_work: 0.3081 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 11936 Z= 0.158 Angle : 0.653 10.817 16245 Z= 0.324 Chirality : 0.044 0.212 1944 Planarity : 0.007 0.125 2110 Dihedral : 4.752 40.561 1684 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.45 % Favored : 89.97 % Rotamer: Outliers : 1.97 % Allowed : 17.36 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.22), residues: 1555 helix: 1.36 (0.20), residues: 752 sheet: -1.65 (0.39), residues: 182 loop : -2.34 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.017 0.001 TYR A 259 PHE 0.014 0.001 PHE C 100 TRP 0.015 0.001 TRP E 548 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00404 (11936) covalent geometry : angle 0.65276 (16245) hydrogen bonds : bond 0.04123 ( 509) hydrogen bonds : angle 4.01615 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: C 308 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7260 (p) REVERT: E 359 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6824 (t70) REVERT: E 425 LYS cc_start: 0.8316 (ttmm) cc_final: 0.7895 (tptt) REVERT: E 436 SER cc_start: 0.9095 (m) cc_final: 0.8700 (t) REVERT: E 538 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8464 (m) outliers start: 25 outliers final: 18 residues processed: 119 average time/residue: 0.1200 time to fit residues: 20.8778 Evaluate side-chains 117 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 589 TYR Chi-restraints excluded: chain E residue 591 ASN Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 22 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 54 optimal weight: 0.0030 chunk 26 optimal weight: 0.6980 chunk 103 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086451 restraints weight = 24236.834| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.23 r_work: 0.3095 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11936 Z= 0.114 Angle : 0.622 11.598 16245 Z= 0.304 Chirality : 0.043 0.209 1944 Planarity : 0.006 0.124 2110 Dihedral : 4.522 34.267 1684 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.42 % Favored : 90.93 % Rotamer: Outliers : 1.74 % Allowed : 18.07 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.23), residues: 1555 helix: 1.48 (0.20), residues: 761 sheet: -1.53 (0.40), residues: 176 loop : -2.26 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.008 0.001 TYR A 259 PHE 0.016 0.001 PHE C 100 TRP 0.010 0.001 TRP E 548 HIS 0.003 0.000 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00292 (11936) covalent geometry : angle 0.62159 (16245) hydrogen bonds : bond 0.02996 ( 509) hydrogen bonds : angle 3.77358 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: E 425 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7885 (tptt) REVERT: E 436 SER cc_start: 0.9041 (m) cc_final: 0.8633 (t) REVERT: E 538 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8425 (m) REVERT: E 592 MET cc_start: 0.8753 (tpp) cc_final: 0.8449 (tpp) outliers start: 22 outliers final: 15 residues processed: 126 average time/residue: 0.1151 time to fit residues: 21.3401 Evaluate side-chains 118 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 589 TYR Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 GLN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086285 restraints weight = 24434.117| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.23 r_work: 0.3095 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11936 Z= 0.118 Angle : 0.632 11.450 16245 Z= 0.310 Chirality : 0.043 0.208 1944 Planarity : 0.006 0.124 2110 Dihedral : 4.386 32.234 1682 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.62 % Favored : 90.74 % Rotamer: Outliers : 1.26 % Allowed : 18.47 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.23), residues: 1555 helix: 1.53 (0.20), residues: 761 sheet: -1.43 (0.40), residues: 182 loop : -2.19 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 90 TYR 0.008 0.001 TYR A 259 PHE 0.015 0.001 PHE C 100 TRP 0.010 0.001 TRP E 548 HIS 0.005 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00299 (11936) covalent geometry : angle 0.63171 (16245) hydrogen bonds : bond 0.03053 ( 509) hydrogen bonds : angle 3.71884 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.509 Fit side-chains REVERT: C 308 VAL cc_start: 0.7243 (OUTLIER) cc_final: 0.7006 (p) REVERT: E 361 LYS cc_start: 0.8599 (tmtt) cc_final: 0.8365 (ptpt) REVERT: E 425 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7870 (tptt) REVERT: E 436 SER cc_start: 0.9056 (m) cc_final: 0.8582 (t) REVERT: E 538 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8437 (m) REVERT: E 592 MET cc_start: 0.8837 (tpp) cc_final: 0.8445 (tpp) outliers start: 16 outliers final: 12 residues processed: 117 average time/residue: 0.1157 time to fit residues: 20.0389 Evaluate side-chains 114 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 589 TYR Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 630 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.113712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086360 restraints weight = 24331.343| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.23 r_work: 0.3093 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11936 Z= 0.120 Angle : 0.634 11.214 16245 Z= 0.310 Chirality : 0.043 0.207 1944 Planarity : 0.006 0.123 2110 Dihedral : 4.353 31.814 1682 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.23 % Favored : 91.13 % Rotamer: Outliers : 1.50 % Allowed : 18.15 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.23), residues: 1555 helix: 1.58 (0.20), residues: 760 sheet: -1.37 (0.41), residues: 172 loop : -2.12 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.010 0.001 TYR D 147 PHE 0.014 0.001 PHE C 100 TRP 0.011 0.001 TRP E 548 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00305 (11936) covalent geometry : angle 0.63398 (16245) hydrogen bonds : bond 0.03063 ( 509) hydrogen bonds : angle 3.70129 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.65 seconds wall clock time: 43 minutes 53.43 seconds (2633.43 seconds total)