Starting phenix.real_space_refine on Thu Aug 6 15:29:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11wo_76137/08_2026/11wo_76137.cif Found real_map, /net/cci-nas-00/data/ceres_data/11wo_76137/08_2026/11wo_76137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11wo_76137/08_2026/11wo_76137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11wo_76137/08_2026/11wo_76137.map" model { file = "/net/cci-nas-00/data/ceres_data/11wo_76137/08_2026/11wo_76137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11wo_76137/08_2026/11wo_76137.cif" } resolution = 3.3 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 75 5.16 5 C 9828 2.51 5 N 2652 2.21 5 O 2850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15414 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5107 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 613} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'APC': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C Time building chain proxies: 4.74, per 1000 atoms: 0.31 Number of scatterers: 15414 At special positions: 0 Unit cell: (85.14, 135.88, 142.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 9 15.00 O 2850 8.00 N 2652 7.00 C 9828 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: 1.00 Conformation dependent library (CDL) restraints added in 517.9 milliseconds 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3630 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 24 sheets defined 39.6% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.594A pdb=" N PHE A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.818A pdb=" N MET A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.873A pdb=" N ILE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.539A pdb=" N VAL A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 removed outlier: 3.576A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 287 through 302 Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.643A pdb=" N LEU A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 359 Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 378 through 381 removed outlier: 3.740A pdb=" N VAL A 381 " --> pdb=" O ASN A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 399 through 409 Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 538 through 547 removed outlier: 3.526A pdb=" N ILE A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 597 Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 645 through 660 removed outlier: 4.274A pdb=" N HIS A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 660 " --> pdb=" O TYR A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 31 through 45 Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.593A pdb=" N PHE B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.818A pdb=" N MET B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.873A pdb=" N ILE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 removed outlier: 3.539A pdb=" N VAL B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 removed outlier: 3.576A pdb=" N VAL B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 287 through 302 Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.643A pdb=" N LEU B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 378 through 381 removed outlier: 3.740A pdb=" N VAL B 381 " --> pdb=" O ASN B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 399 through 409 Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 491 through 499 Processing helix chain 'B' and resid 538 through 547 removed outlier: 3.526A pdb=" N ILE B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 597 Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 645 through 660 removed outlier: 4.275A pdb=" N HIS B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 660 " --> pdb=" O TYR B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.593A pdb=" N PHE C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 120 through 137 removed outlier: 3.818A pdb=" N MET C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 166 removed outlier: 3.872A pdb=" N ILE C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.540A pdb=" N VAL C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.575A pdb=" N VAL C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 326 through 333 removed outlier: 3.643A pdb=" N LEU C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 378 through 381 removed outlier: 3.740A pdb=" N VAL C 381 " --> pdb=" O ASN C 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 381' Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 491 through 499 Processing helix chain 'C' and resid 538 through 547 removed outlier: 3.525A pdb=" N ILE C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 597 Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 645 through 660 removed outlier: 4.274A pdb=" N HIS C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 660 " --> pdb=" O TYR C 656 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 68 through 71 removed outlier: 3.624A pdb=" N ASP A 76 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.889A pdb=" N ARG A 116 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE A 106 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 118 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 104 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 338 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 106 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.492A pdb=" N VAL A 225 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 193 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 192 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 196 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS A 169 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR A 272 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 171 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 269 " --> pdb=" O HIS A 285 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 285 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 486 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 198 through 201 Processing sheet with id=5, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.712A pdb=" N ILE A 365 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 391 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 454 through 457 removed outlier: 7.097A pdb=" N VAL A 470 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA A 512 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY A 472 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASP A 510 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU A 474 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 508 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=8, first strand: chain 'A' and resid 552 through 561 removed outlier: 6.153A pdb=" N LEU A 574 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A 555 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE A 572 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 557 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN A 570 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY A 559 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA A 568 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.625A pdb=" N ASP B 76 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.889A pdb=" N ARG B 116 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE B 106 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 118 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 104 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 338 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 106 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.492A pdb=" N VAL B 225 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 193 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 192 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 196 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS B 169 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR B 272 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 171 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE B 269 " --> pdb=" O HIS B 285 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS B 285 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 486 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 198 through 201 Processing sheet with id=13, first strand: chain 'B' and resid 362 through 365 removed outlier: 3.711A pdb=" N ILE B 365 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 391 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 454 through 457 removed outlier: 7.096A pdb=" N VAL B 470 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA B 512 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLY B 472 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASP B 510 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU B 474 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 508 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=16, first strand: chain 'B' and resid 552 through 561 removed outlier: 6.154A pdb=" N LEU B 574 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER B 555 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE B 572 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 557 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN B 570 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY B 559 " --> pdb=" O ALA B 568 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA B 568 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 68 through 71 removed outlier: 3.623A pdb=" N ASP C 76 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.890A pdb=" N ARG C 116 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE C 106 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 118 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 104 " --> pdb=" O THR C 336 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL C 338 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 106 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 243 through 245 removed outlier: 6.492A pdb=" N VAL C 225 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 193 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 192 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 196 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS C 169 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR C 272 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL C 171 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE C 269 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS C 285 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR C 486 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 198 through 201 Processing sheet with id=21, first strand: chain 'C' and resid 362 through 365 removed outlier: 3.711A pdb=" N ILE C 365 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU C 391 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 454 through 457 removed outlier: 7.097A pdb=" N VAL C 470 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA C 512 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLY C 472 " --> pdb=" O ASP C 510 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASP C 510 " --> pdb=" O GLY C 472 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU C 474 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 508 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'C' and resid 531 through 532 Processing sheet with id=24, first strand: chain 'C' and resid 552 through 561 removed outlier: 6.153A pdb=" N LEU C 574 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER C 555 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE C 572 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 557 " --> pdb=" O ASN C 570 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN C 570 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY C 559 " --> pdb=" O ALA C 568 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA C 568 " --> pdb=" O GLY C 559 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1566 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: 3.00 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5013 1.34 - 1.46: 3648 1.46 - 1.58: 7029 1.58 - 1.70: 6 1.70 - 1.82: 129 Bond restraints: 15825 Sorted by residual: bond pdb=" N ILE C 619 " pdb=" CA ILE C 619 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.80e+00 bond pdb=" N ILE B 619 " pdb=" CA ILE B 619 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.68e+00 bond pdb=" N ILE A 619 " pdb=" CA ILE A 619 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.32e+00 bond pdb=" N LYS C 618 " pdb=" CA LYS C 618 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.62e+00 bond pdb=" N LYS B 618 " pdb=" CA LYS B 618 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.58e+00 ... (remaining 15820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 21081 1.82 - 3.64: 441 3.64 - 5.46: 48 5.46 - 7.29: 9 7.29 - 9.11: 6 Bond angle restraints: 21585 Sorted by residual: angle pdb=" CA LYS C 618 " pdb=" C LYS C 618 " pdb=" O LYS C 618 " ideal model delta sigma weight residual 122.01 118.27 3.74 1.05e+00 9.07e-01 1.27e+01 angle pdb=" CA LYS A 618 " pdb=" C LYS A 618 " pdb=" O LYS A 618 " ideal model delta sigma weight residual 122.01 118.27 3.74 1.05e+00 9.07e-01 1.27e+01 angle pdb=" CA LYS B 618 " pdb=" C LYS B 618 " pdb=" O LYS B 618 " ideal model delta sigma weight residual 122.01 118.28 3.73 1.05e+00 9.07e-01 1.26e+01 angle pdb=" N ARG A 615 " pdb=" CA ARG A 615 " pdb=" C ARG A 615 " ideal model delta sigma weight residual 112.34 107.81 4.53 1.30e+00 5.92e-01 1.21e+01 angle pdb=" N ARG B 615 " pdb=" CA ARG B 615 " pdb=" C ARG B 615 " ideal model delta sigma weight residual 112.34 107.82 4.52 1.30e+00 5.92e-01 1.21e+01 ... (remaining 21580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 8283 16.62 - 33.25: 888 33.25 - 49.87: 210 49.87 - 66.49: 51 66.49 - 83.12: 15 Dihedral angle restraints: 9447 sinusoidal: 3768 harmonic: 5679 Sorted by residual: dihedral pdb=" CA ASP B 562 " pdb=" CB ASP B 562 " pdb=" CG ASP B 562 " pdb=" OD1 ASP B 562 " ideal model delta sinusoidal sigma weight residual -30.00 -88.15 58.15 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP C 562 " pdb=" CB ASP C 562 " pdb=" CG ASP C 562 " pdb=" OD1 ASP C 562 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 562 " pdb=" CB ASP A 562 " pdb=" CG ASP A 562 " pdb=" OD1 ASP A 562 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 9444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1645 0.041 - 0.083: 544 0.083 - 0.124: 187 0.124 - 0.165: 18 0.165 - 0.206: 6 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CA MET C 620 " pdb=" N MET C 620 " pdb=" C MET C 620 " pdb=" CB MET C 620 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA MET A 620 " pdb=" N MET A 620 " pdb=" C MET A 620 " pdb=" CB MET A 620 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA MET B 620 " pdb=" N MET B 620 " pdb=" C MET B 620 " pdb=" CB MET B 620 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2397 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 263 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 264 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 263 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO C 264 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 264 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 264 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 263 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A 264 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " -0.025 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5253 2.85 - 3.36: 14347 3.36 - 3.87: 25428 3.87 - 4.39: 28449 4.39 - 4.90: 48850 Nonbonded interactions: 122327 Sorted by model distance: nonbonded pdb=" CD1 ILE B 97 " pdb=" OE1 GLN C 69 " model vdw 2.336 3.460 nonbonded pdb=" CD1 ILE A 97 " pdb=" OE1 GLN B 69 " model vdw 2.336 3.460 nonbonded pdb=" OE1 GLN A 69 " pdb=" CD1 ILE C 97 " model vdw 2.337 3.460 nonbonded pdb=" C THR C 640 " pdb=" OG1 THR C 640 " model vdw 2.541 2.616 nonbonded pdb=" C THR A 640 " pdb=" OG1 THR A 640 " model vdw 2.542 2.616 ... (remaining 122322 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.350 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.770 Find NCS groups from input model: 0.140 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: 0.020 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 0.035 15825 Z= 0.197 Angle : 0.631 9.106 21585 Z= 0.353 Chirality : 0.046 0.206 2400 Planarity : 0.004 0.053 2754 Dihedral : 14.837 83.116 5817 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.04 % Allowed : 11.44 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.21 (0.20), residues: 1965 helix: 1.10 (0.21), residues: 645 sheet: -0.90 (0.33), residues: 240 loop : -0.70 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 523 TYR 0.013 0.001 TYR A 656 PHE 0.009 0.001 PHE B 572 TRP 0.009 0.001 TRP B 405 HIS 0.006 0.001 HIS C 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (15825) covalent geometry : angle 0.63063 / 0.35 (21585) hydrogen bonds : bond 0.17868 / 12.48 ( 546) hydrogen bonds : angle 7.11006 / 5.12 ( 1566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 ASP cc_start: 0.7948 (m-30) cc_final: 0.7657 (m-30) outliers start: 17 outliers final: 4 residues processed: 108 average time/residue: 0.1336 time to fit residues: 22.0535 Evaluate side-chains 74 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 GLN B 305 HIS C 374 GLN C 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.157814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097856 restraints weight = 44116.941| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.37 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 15825 Z= 0.341 Angle : 0.701 10.047 21585 Z= 0.356 Chirality : 0.049 0.174 2400 Planarity : 0.005 0.045 2754 Dihedral : 7.410 83.936 2268 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.71 % Allowed : 12.78 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.42 (0.20), residues: 1965 helix: 0.87 (0.20), residues: 657 sheet: -1.81 (0.31), residues: 258 loop : -0.55 (0.21), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 371 TYR 0.019 0.002 TYR C 107 PHE 0.016 0.002 PHE B 403 TRP 0.018 0.002 TRP A 246 HIS 0.008 0.002 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.34 (15825) covalent geometry : angle 0.70122 / 0.36 (21585) hydrogen bonds : bond 0.04991 / 3.50 ( 546) hydrogen bonds : angle 5.39182 / 3.93 ( 1566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8430 (m) REVERT: A 573 ILE cc_start: 0.5918 (OUTLIER) cc_final: 0.5621 (mt) REVERT: A 635 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5920 (tt) REVERT: B 151 MET cc_start: 0.8175 (mmm) cc_final: 0.7903 (mmm) REVERT: C 310 MET cc_start: 0.8554 (tpp) cc_final: 0.8289 (tpp) outliers start: 28 outliers final: 14 residues processed: 94 average time/residue: 0.1028 time to fit residues: 15.9472 Evaluate side-chains 84 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 104 optimal weight: 0.2980 chunk 179 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.158911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099629 restraints weight = 43608.993| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.65 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15825 Z= 0.166 Angle : 0.572 9.729 21585 Z= 0.289 Chirality : 0.045 0.159 2400 Planarity : 0.004 0.051 2754 Dihedral : 7.234 83.399 2266 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.96 % Allowed : 13.58 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.20), residues: 1965 helix: 0.97 (0.20), residues: 657 sheet: -1.38 (0.29), residues: 294 loop : -0.54 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 359 TYR 0.011 0.001 TYR A 256 PHE 0.027 0.001 PHE B 403 TRP 0.012 0.001 TRP B 246 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15825) covalent geometry : angle 0.57217 / 0.29 (21585) hydrogen bonds : bond 0.03847 / 2.69 ( 546) hydrogen bonds : angle 5.00565 / 3.62 ( 1566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.5679 (OUTLIER) cc_final: 0.5398 (mt) REVERT: A 635 ILE cc_start: 0.6250 (OUTLIER) cc_final: 0.5890 (tt) REVERT: B 151 MET cc_start: 0.8427 (mmm) cc_final: 0.8114 (mmm) REVERT: C 310 MET cc_start: 0.8829 (tpp) cc_final: 0.8498 (tpp) REVERT: C 469 ASP cc_start: 0.8899 (m-30) cc_final: 0.8653 (m-30) outliers start: 32 outliers final: 19 residues processed: 92 average time/residue: 0.1032 time to fit residues: 15.6340 Evaluate side-chains 85 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 148 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 171 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.160015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100911 restraints weight = 43252.031| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.66 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15825 Z= 0.111 Angle : 0.522 8.934 21585 Z= 0.264 Chirality : 0.044 0.161 2400 Planarity : 0.004 0.046 2754 Dihedral : 6.996 82.907 2265 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.83 % Allowed : 14.68 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.06 (0.20), residues: 1965 helix: 1.08 (0.20), residues: 660 sheet: -0.77 (0.32), residues: 264 loop : -0.51 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.009 0.001 TYR A 256 PHE 0.013 0.001 PHE B 403 TRP 0.009 0.001 TRP A 246 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (15825) covalent geometry : angle 0.52242 / 0.26 (21585) hydrogen bonds : bond 0.02970 / 2.05 ( 546) hydrogen bonds : angle 4.65335 / 3.34 ( 1566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 HIS cc_start: 0.9197 (OUTLIER) cc_final: 0.8404 (m90) REVERT: A 573 ILE cc_start: 0.5340 (OUTLIER) cc_final: 0.5002 (mt) REVERT: A 635 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5734 (tt) REVERT: B 151 MET cc_start: 0.8468 (mmm) cc_final: 0.8165 (mmm) REVERT: C 310 MET cc_start: 0.8852 (tpp) cc_final: 0.8477 (tpp) REVERT: C 469 ASP cc_start: 0.8853 (m-30) cc_final: 0.8520 (m-30) REVERT: C 631 GLU cc_start: -0.2859 (OUTLIER) cc_final: -0.3318 (tt0) outliers start: 30 outliers final: 16 residues processed: 95 average time/residue: 0.0999 time to fit residues: 15.7469 Evaluate side-chains 85 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 78 optimal weight: 0.3980 chunk 68 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.161783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090274 restraints weight = 37272.087| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 5.42 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15825 Z= 0.184 Angle : 0.559 8.360 21585 Z= 0.281 Chirality : 0.045 0.156 2400 Planarity : 0.004 0.040 2754 Dihedral : 6.948 83.479 2264 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.96 % Allowed : 14.98 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.02 (0.20), residues: 1965 helix: 1.04 (0.20), residues: 663 sheet: -0.75 (0.32), residues: 264 loop : -0.44 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 414 TYR 0.014 0.001 TYR C 256 PHE 0.014 0.001 PHE B 403 TRP 0.012 0.001 TRP B 246 HIS 0.005 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (15825) covalent geometry : angle 0.55941 / 0.28 (21585) hydrogen bonds : bond 0.03676 / 2.58 ( 546) hydrogen bonds : angle 4.69133 / 3.40 ( 1566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.8857 (m90) REVERT: A 573 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5842 (mt) REVERT: A 635 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.5537 (tt) REVERT: B 404 MET cc_start: 0.8771 (mmp) cc_final: 0.8557 (mmm) REVERT: C 310 MET cc_start: 0.7945 (tpp) cc_final: 0.7655 (tpp) REVERT: C 631 GLU cc_start: -0.2134 (OUTLIER) cc_final: -0.2564 (tt0) outliers start: 32 outliers final: 22 residues processed: 93 average time/residue: 0.1044 time to fit residues: 16.2593 Evaluate side-chains 88 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 176 optimal weight: 8.9990 chunk 73 optimal weight: 0.0770 chunk 34 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 overall best weight: 1.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.162193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090704 restraints weight = 37138.564| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 5.64 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15825 Z= 0.151 Angle : 0.532 8.465 21585 Z= 0.267 Chirality : 0.045 0.153 2400 Planarity : 0.004 0.040 2754 Dihedral : 6.911 83.206 2264 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.77 % Allowed : 15.11 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.04 (0.20), residues: 1965 helix: 1.16 (0.21), residues: 660 sheet: -0.76 (0.32), residues: 264 loop : -0.44 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 414 TYR 0.010 0.001 TYR C 256 PHE 0.013 0.001 PHE B 49 TRP 0.011 0.001 TRP A 246 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (15825) covalent geometry : angle 0.53160 / 0.27 (21585) hydrogen bonds : bond 0.03234 / 2.25 ( 546) hydrogen bonds : angle 4.55749 / 3.29 ( 1566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 HIS cc_start: 0.9298 (OUTLIER) cc_final: 0.8743 (m90) REVERT: A 573 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5851 (mt) REVERT: C 310 MET cc_start: 0.7892 (tpp) cc_final: 0.7605 (tpp) outliers start: 29 outliers final: 21 residues processed: 90 average time/residue: 0.1027 time to fit residues: 15.7006 Evaluate side-chains 84 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 95 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 153 optimal weight: 0.0020 chunk 86 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 179 optimal weight: 0.0570 chunk 184 optimal weight: 50.0000 chunk 168 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 ASN C 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.163579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.091867 restraints weight = 36395.817| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 5.87 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15825 Z= 0.098 Angle : 0.511 8.333 21585 Z= 0.255 Chirality : 0.044 0.152 2400 Planarity : 0.003 0.039 2754 Dihedral : 6.808 82.850 2264 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.83 % Allowed : 15.41 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.11 (0.20), residues: 1965 helix: 1.18 (0.21), residues: 663 sheet: -0.73 (0.32), residues: 264 loop : -0.36 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 414 TYR 0.008 0.001 TYR A 256 PHE 0.014 0.001 PHE B 49 TRP 0.008 0.001 TRP A 246 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (15825) covalent geometry : angle 0.51065 / 0.25 (21585) hydrogen bonds : bond 0.02719 / 1.87 ( 546) hydrogen bonds : angle 4.41088 / 3.17 ( 1566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 HIS cc_start: 0.9162 (OUTLIER) cc_final: 0.8241 (m90) REVERT: A 573 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5857 (mt) REVERT: C 214 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9213 (ptpp) REVERT: C 310 MET cc_start: 0.7841 (tpp) cc_final: 0.7564 (tpp) outliers start: 30 outliers final: 22 residues processed: 90 average time/residue: 0.1045 time to fit residues: 15.9099 Evaluate side-chains 86 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 163 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 ASN C 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.164189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095705 restraints weight = 36375.771| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 6.43 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15825 Z= 0.092 Angle : 0.499 10.771 21585 Z= 0.248 Chirality : 0.044 0.151 2400 Planarity : 0.003 0.038 2754 Dihedral : 6.687 82.650 2264 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.65 % Allowed : 16.02 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.19 (0.20), residues: 1965 helix: 1.29 (0.21), residues: 663 sheet: -0.62 (0.35), residues: 234 loop : -0.39 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 414 TYR 0.010 0.001 TYR A 256 PHE 0.013 0.001 PHE B 49 TRP 0.007 0.001 TRP B 246 HIS 0.002 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (15825) covalent geometry : angle 0.49878 / 0.25 (21585) hydrogen bonds : bond 0.02558 / 1.75 ( 546) hydrogen bonds : angle 4.30730 / 3.10 ( 1566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.5827 (OUTLIER) cc_final: 0.5533 (mt) REVERT: B 440 MET cc_start: 0.5594 (tpp) cc_final: 0.5242 (tmm) REVERT: C 310 MET cc_start: 0.8144 (tpp) cc_final: 0.7800 (tpp) outliers start: 27 outliers final: 22 residues processed: 87 average time/residue: 0.1037 time to fit residues: 15.4028 Evaluate side-chains 86 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 47 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 HIS A 570 ASN C 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.162484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.090790 restraints weight = 36158.473| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 7.21 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15825 Z= 0.161 Angle : 0.537 11.417 21585 Z= 0.266 Chirality : 0.045 0.167 2400 Planarity : 0.004 0.042 2754 Dihedral : 6.761 83.125 2264 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.59 % Allowed : 16.09 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.22 (0.20), residues: 1965 helix: 1.31 (0.21), residues: 660 sheet: -0.64 (0.32), residues: 264 loop : -0.33 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 414 TYR 0.013 0.001 TYR A 256 PHE 0.011 0.001 PHE B 49 TRP 0.011 0.001 TRP B 246 HIS 0.005 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (15825) covalent geometry : angle 0.53674 / 0.27 (21585) hydrogen bonds : bond 0.03252 / 2.28 ( 546) hydrogen bonds : angle 4.39560 / 3.17 ( 1566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6063 (mt) REVERT: C 7 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.6928 (t0) REVERT: C 310 MET cc_start: 0.7660 (tpp) cc_final: 0.7427 (tpp) outliers start: 26 outliers final: 22 residues processed: 87 average time/residue: 0.0853 time to fit residues: 12.8191 Evaluate side-chains 86 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 169 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 182 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.163331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091811 restraints weight = 36740.796| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 7.41 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15825 Z= 0.108 Angle : 0.510 9.926 21585 Z= 0.254 Chirality : 0.044 0.174 2400 Planarity : 0.003 0.039 2754 Dihedral : 6.712 82.760 2264 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.47 % Allowed : 16.27 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1965 helix: 1.28 (0.21), residues: 663 sheet: -0.58 (0.32), residues: 264 loop : -0.26 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 414 TYR 0.009 0.001 TYR A 494 PHE 0.015 0.001 PHE B 49 TRP 0.008 0.001 TRP B 246 HIS 0.003 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15825) covalent geometry : angle 0.51012 / 0.25 (21585) hydrogen bonds : bond 0.02763 / 1.91 ( 546) hydrogen bonds : angle 4.33908 / 3.12 ( 1566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.6201 (OUTLIER) cc_final: 0.5940 (mt) REVERT: C 151 MET cc_start: 0.8661 (mmm) cc_final: 0.8425 (mmt) REVERT: C 310 MET cc_start: 0.7806 (tpp) cc_final: 0.7521 (tpp) outliers start: 24 outliers final: 22 residues processed: 85 average time/residue: 0.1054 time to fit residues: 15.3059 Evaluate side-chains 84 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 119 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 70 optimal weight: 0.2980 chunk 102 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.161851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092117 restraints weight = 36304.443| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 7.57 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15825 Z= 0.176 Angle : 0.550 12.346 21585 Z= 0.274 Chirality : 0.045 0.195 2400 Planarity : 0.004 0.040 2754 Dihedral : 6.773 83.200 2264 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.71 % Allowed : 15.90 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1965 helix: 1.26 (0.21), residues: 660 sheet: -0.61 (0.32), residues: 264 loop : -0.28 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 414 TYR 0.013 0.001 TYR A 256 PHE 0.007 0.001 PHE A 269 TRP 0.011 0.001 TRP B 246 HIS 0.005 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (15825) covalent geometry : angle 0.55046 / 0.27 (21585) hydrogen bonds : bond 0.03399 / 2.38 ( 546) hydrogen bonds : angle 4.46518 / 3.22 ( 1566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3758.16 seconds wall clock time: 65 minutes 19.78 seconds (3919.78 seconds total)