Starting phenix.real_space_refine on Tue Jul 29 22:21:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggd_40003/07_2025/8ggd_40003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggd_40003/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggd_40003/07_2025/8ggd_40003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggd_40003/07_2025/8ggd_40003.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggd_40003/07_2025/8ggd_40003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggd_40003/07_2025/8ggd_40003.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.75, per 1000 atoms: 0.66 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: 2.72 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.18 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: 3.78 Time building geometry restraints manager: 3.27 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: 2.330 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.790 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.027 0.002 TRP E 548 HIS 0.003 0.001 HIS D 172 PHE 0.017 0.001 PHE E 350 TYR 0.033 0.001 TYR E 595 ARG 0.003 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.20478 ( 509) hydrogen bonds : angle 6.48606 ( 1488) covalent geometry : bond 0.00392 (11936) covalent geometry : angle 0.74137 (16245) *********************** 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 : 1.461 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: 0.2506 time to fit residues: 61.5724 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 : 1.343 ------------------------------------------------------------------------------- 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 130 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN E 374 ASN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084742 restraints weight = 24526.284| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.22 r_work: 0.3066 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 11936 Z= 0.162 Angle : 0.655 11.703 16245 Z= 0.333 Chirality : 0.045 0.211 1944 Planarity : 0.007 0.121 2110 Dihedral : 5.968 59.449 1700 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.16 % Favored : 89.26 % Rotamer: Outliers : 1.42 % Allowed : 7.97 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.25 (0.22), residues: 1555 helix: 0.72 (0.20), residues: 743 sheet: -1.70 (0.38), residues: 202 loop : -2.51 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 548 HIS 0.005 0.001 HIS E 437 PHE 0.022 0.002 PHE C 100 TYR 0.014 0.002 TYR A 259 ARG 0.005 0.000 ARG E 625 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 509) hydrogen bonds : angle 4.57493 ( 1488) covalent geometry : bond 0.00400 (11936) covalent geometry : angle 0.65453 (16245) *********************** 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 135 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7089 (tmm) cc_final: 0.6411 (tmm) REVERT: B 194 TYR cc_start: 0.8513 (m-10) cc_final: 0.8309 (m-80) REVERT: E 425 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7900 (tptt) REVERT: E 436 SER cc_start: 0.8959 (m) cc_final: 0.8574 (t) REVERT: E 559 ASN cc_start: 0.7754 (p0) cc_final: 0.7344 (t0) REVERT: E 591 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7459 (p0) REVERT: E 592 MET cc_start: 0.8402 (tpp) cc_final: 0.7545 (ppp) REVERT: E 594 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6587 (mp10) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 0.2543 time to fit residues: 48.7539 Evaluate side-chains 122 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 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 121 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN ** E 442 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 = 0.3625 r_free = 0.3625 target = 0.112146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084906 restraints weight = 24621.339| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.22 r_work: 0.3069 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1624 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= 0.135 Angle : 0.592 8.252 16245 Z= 0.302 Chirality : 0.043 0.213 1944 Planarity : 0.007 0.124 2110 Dihedral : 5.467 59.947 1694 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.71 % Favored : 89.71 % Rotamer: Outliers : 1.66 % Allowed : 12.47 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % 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: -0.94 (0.22), residues: 1555 helix: 1.00 (0.20), residues: 746 sheet: -1.58 (0.37), residues: 212 loop : -2.41 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 548 HIS 0.004 0.001 HIS A 172 PHE 0.014 0.001 PHE C 100 TYR 0.013 0.001 TYR A 259 ARG 0.004 0.000 ARG E 625 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 509) hydrogen bonds : angle 4.18834 ( 1488) covalent geometry : bond 0.00342 (11936) covalent geometry : angle 0.59244 (16245) *********************** 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 136 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: E 425 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7885 (tptt) REVERT: E 436 SER cc_start: 0.8984 (m) cc_final: 0.8616 (t) REVERT: E 559 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7325 (t0) REVERT: E 591 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7591 (p0) REVERT: E 592 MET cc_start: 0.8380 (tpp) cc_final: 0.7829 (ppp) REVERT: E 594 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7270 (mp10) outliers start: 21 outliers final: 10 residues processed: 130 average time/residue: 0.2410 time to fit residues: 46.3388 Evaluate side-chains 118 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 C residue 66 VAL Chi-restraints excluded: chain A residue 88 VAL 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 153 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 34 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.113625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.086269 restraints weight = 24456.463| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.24 r_work: 0.3094 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11936 Z= 0.114 Angle : 0.572 8.211 16245 Z= 0.289 Chirality : 0.043 0.212 1944 Planarity : 0.007 0.125 2110 Dihedral : 5.045 56.790 1690 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.94 % Favored : 90.48 % Rotamer: Outliers : 1.58 % Allowed : 15.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1555 helix: 1.15 (0.20), residues: 761 sheet: -1.66 (0.41), residues: 172 loop : -2.24 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 548 HIS 0.002 0.001 HIS A 172 PHE 0.027 0.001 PHE C 100 TYR 0.009 0.001 TYR A 259 ARG 0.007 0.000 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 509) hydrogen bonds : angle 3.87604 ( 1488) covalent geometry : bond 0.00289 (11936) covalent geometry : angle 0.57193 (16245) *********************** 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 135 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.367 Fit side-chains REVERT: D 157 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8622 (tt) REVERT: B 1 MET cc_start: 0.7051 (tmm) cc_final: 0.6493 (tmm) REVERT: B 194 TYR cc_start: 0.8460 (m-80) cc_final: 0.8132 (m-80) REVERT: E 350 PHE cc_start: 0.7675 (m-80) cc_final: 0.7330 (m-80) REVERT: E 425 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7846 (tptt) REVERT: E 436 SER cc_start: 0.8949 (m) cc_final: 0.8612 (t) REVERT: E 559 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7313 (t0) REVERT: E 592 MET cc_start: 0.8363 (tpp) cc_final: 0.7887 (ppp) REVERT: E 613 THR cc_start: 0.7108 (p) cc_final: 0.6769 (p) outliers start: 20 outliers final: 11 residues processed: 130 average time/residue: 0.2366 time to fit residues: 45.3061 Evaluate side-chains 119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 D residue 251 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 83 VAL 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 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 97 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084706 restraints weight = 24356.053| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.21 r_work: 0.3067 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1914 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= 0.136 Angle : 0.590 7.841 16245 Z= 0.299 Chirality : 0.043 0.212 1944 Planarity : 0.007 0.125 2110 Dihedral : 4.765 53.836 1684 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.32 % Favored : 90.10 % Rotamer: Outliers : 2.21 % Allowed : 16.10 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % 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: -0.69 (0.23), residues: 1555 helix: 1.21 (0.20), residues: 761 sheet: -1.66 (0.39), residues: 182 loop : -2.27 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 548 HIS 0.004 0.001 HIS A 172 PHE 0.019 0.001 PHE C 100 TYR 0.015 0.001 TYR D 147 ARG 0.003 0.000 ARG E 625 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 509) hydrogen bonds : angle 3.91482 ( 1488) covalent geometry : bond 0.00348 (11936) covalent geometry : angle 0.58977 (16245) *********************** 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 135 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: D 157 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8717 (tt) REVERT: B 1 MET cc_start: 0.7105 (tmm) cc_final: 0.6493 (tmm) REVERT: E 425 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7847 (tptt) REVERT: E 436 SER cc_start: 0.8966 (m) cc_final: 0.8651 (t) outliers start: 28 outliers final: 15 residues processed: 129 average time/residue: 0.2307 time to fit residues: 43.9606 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 : 1.312 ------------------------------------------------------------------------------- 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 B residue 190 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 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 69 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085486 restraints weight = 24627.305| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.24 r_work: 0.3078 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2000 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 : 0.597 12.762 16245 Z= 0.296 Chirality : 0.043 0.210 1944 Planarity : 0.006 0.125 2110 Dihedral : 4.675 49.394 1684 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.62 % Favored : 90.80 % Rotamer: Outliers : 1.89 % Allowed : 17.13 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % 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: -0.59 (0.23), residues: 1555 helix: 1.29 (0.20), residues: 761 sheet: -1.58 (0.40), residues: 182 loop : -2.25 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 548 HIS 0.003 0.001 HIS A 172 PHE 0.018 0.001 PHE C 100 TYR 0.014 0.001 TYR D 147 ARG 0.003 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 509) hydrogen bonds : angle 3.80957 ( 1488) covalent geometry : bond 0.00308 (11936) covalent geometry : angle 0.59739 (16245) *********************** 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 133 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.576 Fit side-chains REVERT: D 157 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8692 (tt) REVERT: B 1 MET cc_start: 0.7089 (tmm) cc_final: 0.6460 (tmm) REVERT: E 350 PHE cc_start: 0.7612 (m-80) cc_final: 0.7195 (m-80) REVERT: E 359 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6756 (t70) REVERT: E 425 LYS cc_start: 0.8320 (ttmm) cc_final: 0.7871 (tptt) REVERT: E 436 SER cc_start: 0.8973 (m) cc_final: 0.8690 (t) REVERT: E 538 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8438 (m) REVERT: E 592 MET cc_start: 0.8718 (tpp) cc_final: 0.8369 (tpp) REVERT: E 613 THR cc_start: 0.7155 (p) cc_final: 0.6831 (p) outliers start: 24 outliers final: 17 residues processed: 128 average time/residue: 0.3046 time to fit residues: 57.7289 Evaluate side-chains 126 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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 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 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 589 TYR 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 127 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 83 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 137 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.113998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086718 restraints weight = 24524.067| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.23 r_work: 0.3103 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2082 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= 0.110 Angle : 0.600 13.534 16245 Z= 0.294 Chirality : 0.042 0.208 1944 Planarity : 0.006 0.124 2110 Dihedral : 4.528 43.329 1684 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.55 % Favored : 90.87 % Rotamer: Outliers : 2.21 % Allowed : 16.97 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -0.45 (0.23), residues: 1555 helix: 1.41 (0.20), residues: 761 sheet: -1.53 (0.41), residues: 172 loop : -2.17 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 548 HIS 0.002 0.000 HIS A 172 PHE 0.017 0.001 PHE C 100 TYR 0.008 0.001 TYR A 259 ARG 0.006 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 509) hydrogen bonds : angle 3.67650 ( 1488) covalent geometry : bond 0.00281 (11936) covalent geometry : angle 0.60021 (16245) *********************** 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 138 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.724 Fit side-chains REVERT: D 157 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8665 (tt) REVERT: B 1 MET cc_start: 0.7126 (tmm) cc_final: 0.6463 (tmm) REVERT: E 350 PHE cc_start: 0.7592 (m-80) cc_final: 0.7174 (m-80) REVERT: E 359 HIS cc_start: 0.7036 (OUTLIER) cc_final: 0.6812 (t70) REVERT: E 361 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7321 (ptpt) REVERT: E 425 LYS cc_start: 0.8301 (ttmm) cc_final: 0.7855 (tptt) REVERT: E 436 SER cc_start: 0.8952 (m) cc_final: 0.8717 (t) REVERT: E 538 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8436 (m) REVERT: E 559 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7130 (t0) outliers start: 28 outliers final: 13 residues processed: 134 average time/residue: 0.3039 time to fit residues: 61.0391 Evaluate side-chains 121 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 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 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 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 7 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 0.3980 chunk 117 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.113442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.086149 restraints weight = 24525.726| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.24 r_work: 0.3088 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2153 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= 0.119 Angle : 0.614 11.245 16245 Z= 0.302 Chirality : 0.043 0.208 1944 Planarity : 0.006 0.124 2110 Dihedral : 4.493 38.487 1684 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.42 % Favored : 91.00 % Rotamer: Outliers : 1.66 % Allowed : 17.36 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1555 helix: 1.48 (0.20), residues: 761 sheet: -1.52 (0.42), residues: 161 loop : -2.14 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 548 HIS 0.003 0.001 HIS A 172 PHE 0.015 0.001 PHE C 100 TYR 0.011 0.001 TYR D 147 ARG 0.006 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 509) hydrogen bonds : angle 3.68625 ( 1488) covalent geometry : bond 0.00305 (11936) covalent geometry : angle 0.61394 (16245) *********************** 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 130 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.410 Fit side-chains REVERT: E 350 PHE cc_start: 0.7566 (m-80) cc_final: 0.7161 (m-80) REVERT: E 361 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7826 (ptpt) REVERT: E 425 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7842 (tptt) REVERT: E 436 SER cc_start: 0.8953 (m) cc_final: 0.8714 (t) REVERT: E 538 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8429 (m) REVERT: E 592 MET cc_start: 0.8759 (tpp) cc_final: 0.8406 (tpp) REVERT: E 613 THR cc_start: 0.7183 (p) cc_final: 0.6858 (p) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 0.2407 time to fit residues: 44.9427 Evaluate side-chains 121 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 410 CYS 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 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 85 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 148 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085364 restraints weight = 24432.559| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.22 r_work: 0.3072 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2203 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= 0.130 Angle : 0.631 11.156 16245 Z= 0.309 Chirality : 0.043 0.208 1944 Planarity : 0.006 0.124 2110 Dihedral : 4.547 34.855 1684 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.87 % Favored : 90.55 % Rotamer: Outliers : 1.42 % Allowed : 17.60 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.90 % 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: -0.39 (0.23), residues: 1555 helix: 1.49 (0.20), residues: 761 sheet: -1.55 (0.40), residues: 182 loop : -2.18 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 548 HIS 0.003 0.001 HIS A 172 PHE 0.014 0.001 PHE C 100 TYR 0.013 0.001 TYR D 147 ARG 0.007 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 509) hydrogen bonds : angle 3.76520 ( 1488) covalent geometry : bond 0.00333 (11936) covalent geometry : angle 0.63113 (16245) *********************** 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 121 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.582 Fit side-chains REVERT: E 425 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7851 (tptt) REVERT: E 436 SER cc_start: 0.8949 (m) cc_final: 0.8738 (t) REVERT: E 538 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8430 (m) outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 0.2405 time to fit residues: 41.6896 Evaluate side-chains 115 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 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 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 45 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 150 optimal weight: 7.9990 chunk 110 optimal weight: 0.0050 chunk 15 optimal weight: 0.3980 chunk 105 optimal weight: 0.0030 chunk 153 optimal weight: 6.9990 overall best weight: 0.3004 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.115034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.087903 restraints weight = 24165.787| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.22 r_work: 0.3121 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11936 Z= 0.111 Angle : 0.621 11.701 16245 Z= 0.302 Chirality : 0.043 0.207 1944 Planarity : 0.006 0.123 2110 Dihedral : 4.302 31.905 1682 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.62 % Favored : 90.80 % Rotamer: Outliers : 1.26 % Allowed : 18.00 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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 (0.23), residues: 1555 helix: 1.58 (0.20), residues: 761 sheet: -1.01 (0.49), residues: 121 loop : -2.08 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.002 0.000 HIS E 437 PHE 0.015 0.001 PHE C 100 TYR 0.010 0.001 TYR B 194 ARG 0.006 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.02708 ( 509) hydrogen bonds : angle 3.55536 ( 1488) covalent geometry : bond 0.00282 (11936) covalent geometry : angle 0.62104 (16245) ********************** 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 127 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: C 308 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7094 (p) REVERT: E 421 MET cc_start: 0.8722 (tmm) cc_final: 0.8398 (tmm) REVERT: E 425 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7826 (tptt) REVERT: E 436 SER cc_start: 0.8954 (m) cc_final: 0.8708 (t) REVERT: E 437 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.7123 (m-70) REVERT: E 538 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8413 (m) REVERT: E 592 MET cc_start: 0.8818 (tpp) cc_final: 0.8432 (tpp) outliers start: 16 outliers final: 12 residues processed: 123 average time/residue: 0.2895 time to fit residues: 53.7844 Evaluate side-chains 116 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 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 437 HIS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 585 MET 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 120 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 overall best weight: 0.2102 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.115916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088712 restraints weight = 24087.918| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.24 r_work: 0.3132 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11936 Z= 0.112 Angle : 0.625 11.699 16245 Z= 0.304 Chirality : 0.043 0.229 1944 Planarity : 0.006 0.123 2110 Dihedral : 4.246 32.711 1682 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.06 % Rotamer: Outliers : 1.34 % Allowed : 18.00 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -0.13 (0.23), residues: 1555 helix: 1.59 (0.20), residues: 763 sheet: -0.82 (0.52), residues: 111 loop : -2.02 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.012 0.000 HIS E 437 PHE 0.015 0.001 PHE C 100 TYR 0.012 0.001 TYR B 194 ARG 0.006 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.02631 ( 509) hydrogen bonds : angle 3.50835 ( 1488) covalent geometry : bond 0.00281 (11936) covalent geometry : angle 0.62467 (16245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5523.99 seconds wall clock time: 101 minutes 15.65 seconds (6075.65 seconds total)